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Reference attributes:Secondary Summary Id - Naming attributes:Accession Code,Assembly Serial,Model Serial,Chain Code,Library |
C:SECONDARY_SUMMARY_ID, S:10, A:0.0 | The database identifier of the Secondary Summary |
Entry Id   C:ENTRY_ID, S:10, A:0.0 | The database identifier of the Entry |
C:ACCESSION_CODE, S:8, A:0.0 | The PDB accession code of the entry |
Assembly Id C:ASSEMBLY_ID, S:10, A:0.0 | The database identifier of the Assembly |
C:ASSEMBLY_SERIAL, S:10, A:0.0 | The serial identifier of the assembly in the entry |
Model Id C:MODEL_ID, S:10, A:0.0 | The database identifier of the Model |
C:MODEL_SERIAL, S:10, A:0.0 | The serial identifier of the model in the entry |
Chain Id C:CHAIN_ID, S:10, A:0.0 | The database identifier of the Chain. If this is null then this record keeps information for the complete assembly and not for a chain only. |
C:CHAIN_CODE, S:24, A:0.0 | The standard code of the chain that uniquely identifies it in the assembly. It is an extension of the PDB chain Id.
If this is null then this record keeps information for the complete assembly and not for a chain only. |
Valid In Assymetric Unit   C:NON_ASSEMBLY_VALID, S:1, A:0.0 | This item is to be used not only in an assembly context, but also to represent the original asymmetric unit |
Number of Residues C:NUM_RESIDUE_DATA, S:10, A:0.0 | The number of residue secondary information available |
Strands C:STRANDS, S:10, A:0.0 | The number of strands in the chain/assembly |
Sheets C:SHEETS, S:10, A:0.0 | The number of sheets in the assembly. For chains it is the number of sheets that the chain participates in |
Helices C:HELICES, S:10, A:0.0 | The number of helices in the chain/assembly |
Alpha Helices C:ALPHA_HELICES, S:10, A:0.0 | The number of alpha helices in the chain/assembly |
Helices 3-10 C:HELICES_3_10, S:10, A:0.0 | The number of 3-10 helices in the chain/assembly |
Turns C:TURNS, S:10, A:0.0 | The number of turns in the chain/assembly |
Beta Turns C:BETA_TURNS, S:10, A:0.0 | The number of beta turns in the chain/assembly |
Gamma Turns C:GAMMA_TURNS, S:10, A:0.0 | The number of gamma turns in the chain/assembly |
Bulges C:BULGES, S:10, A:0.0 | The number of bulges in the chain/assembly |
Hairpins C:HAIRPINS, S:10, A:0.0 | The number of hairpins in the chain/assembly |
Beta Alpha Beta C:BETA_ALPHA_BETA, S:10, A:0.0 | The number of beta-alpha-beta motifs in the chain/assembly |
Psi Loops C:PSI_LOOPS, S:10, A:0.0 | The number of psi-loop motifs in the chain/assembly |
Percent Strand  C:PERCENT_STRAND, S:0, A:0.0 | The percentage of chain/assembly residues that are part of a strand |
Percent Alpha Helix C:PERCENT_ALPHA_HELIX, S:0, A:0.0 | The percentage of chain/assembly residues that are part of an alpha helix |
Percent 3-10 Helix C:PERCENT_3_10_HELIX, S:0, A:0.0 | The percentage of chain/assembly residues that are part of an 3-10 helix |
C:LIBRARY, S:255, A:0.0 | The library (method or program) that determined the structure |
of     | |
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Reference attributes:Helix Id - Naming attributes:Accession Code,Assembly Serial,Chain Code,Helix Serial |
C:HELIX_ID, S:10, A:5.0 | The database identifier of the Helix |
C:ACCESSION_CODE, S:255, A:4.0 | The PDB accession code of the entry |
C:ASSEMBLY_SERIAL, S:0, A:2.0 | The serial identifier of the assembly in the entry |
C:CHAIN_CODE, S:8, A:2.0 | The standard code of the chain that uniquely identifies it in the assembly. It is an extension of the PDB chain Id.
In cases where symmetry operations have been applied to a chain, these chains are named with a numeric suffix, ie. A,A1,A2,A3 ...
The chain id specified in the PDB file is also ignored for waters and bound molecules, and their codes are derived from the name of the chain that they are bound to.
Finally there are no "null" chain codes and in cases where no id was specified in the PDB file, then arbitrary chain codes are assigned (i.e. A,B) |
C:HELIX_SERIAL, S:10, A:3.0 | The serial identifier of the helix |
Assembly Id C:ASSEMBLY_ID, S:10, A:4.0 | The database identifier of the Assembly |
Beg Chain Code C:BEG_CHAIN_CODE, S:8, A:2.0 | The standard code of the Beg Chain |
Beggining Chain PDB Code C:BEG_CHAIN_PDB_CODE, S:2, A:1.0 | PDB code of the chain of the begining residue |
Begin ligand code C:BEG_CHEM_COMP_CODE, S:12, A:7.0 | The aminoacid (ligand) molecule code of the first residue of the helix |
Begin Insert Code C:BEG_PDB_INSERT_CODE, S:2, A:1.0 | The insertion code of the first residue of the helix |
Beg Residue Data Id C:BEG_RESIDUE_DATA_ID, S:10, A:5.0 | The database identifier of the Beg Residue Data |
Helix Type Details C:HELIX_TYPE_DETAILS, S:4000, A:1.0 | (obsolete) |
Beg Residue Id C:BEG_RESIDUE_ID, S:10, A:0.0 | The database identifier of the Beg Residue |
Helid Pdb Code C:HELID_PDB_CODE, S:765, A:1.0 | (obsolete) |
Beg Residue PDB Code C:BEG_RESIDUE_PDB_CODE, S:10, A:3.0 | |
Helix Details C:HELIX_DETAILS, S:4000, A:1.0 | (obsolete) |
Beg Residue PDB Seq C:BEG_RESIDUE_PDB_SEQ, S:38, A:3.0 | |
Helix Cif Conf Id C:HELIX_CIF_CONF_ID, S:60, A:1.0 | (obsolete) |
Chain Id C:CHAIN_ID, S:10, A:5.0 | The database identifier of the Chain |
Helix Classification C:HELIX_CLASSIFICATION, S:90, A:1.0 | (obsolete) |
Class PDB C:CLASS_PDB, S:10, A:2.0 | |
End Chain Code C:END_CHAIN_CODE, S:8, A:2.0 | The standard code of the End Chain |
Ending Chain PDB Code C:END_CHAIN_PDB_CODE, S:2, A:1.0 | PDB code of the chain of the ending residue |
End ligand code C:END_CHEM_COMP_CODE, S:12, A:7.0 | The aminoacid (ligand) molecule code of the last residue of the helix |
End Insert Code C:END_PDB_INSERT_CODE, S:2, A:1.0 | The insertion code of the last residue of the helix |
End Residue Data Id C:END_RESIDUE_DATA_ID, S:10, A:5.0 | The database identifier of the End Residue Data |
End Residue Id C:END_RESIDUE_ID, S:10, A:0.0 | The database identifier of the End Residue |
End Residue PDB Code C:END_RESIDUE_PDB_CODE, S:10, A:3.0 | |
End Residue PDB Seq C:END_RESIDUE_PDB_SEQ, S:38, A:3.0 | |
Entry Id C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
Begin Residue Serial C:BEG_RESIDUE_SERIAL, S:10, A:3.0 | The serial in the chain of the first residue of the helix |
Helix Type C:HELIX_TYPE, S:255, A:1.0 | The PDB classification for each type of helix. 1:Right-handed alpha (default), 2:Right-handed omega, 3:Right-handed pi, 4:Right-handed gamma, 5:Right-handed 310, 6:Left-handed alpha, 7:Left-handed omega, 8:Left-handed gamma, 9:27 ribbon/helix, 10:Polyproline |
Length in Angstrom C:LENGTH_ANGSTROM, S:0, A:9.0 | The length in Angstrom of the helix |
Library C:LIBRARY, S:255, A:4.0 | The library (method or program) that determined the structure |
Linearity C:LINEARITY, S:0, A:9.0 | A measure of the deviation of the helix geometry from an ideal helix (in degrees) |
Model Id C:MODEL_ID, S:10, A:4.0 | The database identifier of the Model |
Model Serial C:MODEL_SERIAL, S:10, A:2.0 | The serial identifier of the model in the entry |
Next Kinked Id C:NEXT_KINKED_ID, S:10, A:1.0 | The database identifier of the Next Kinked |
Number of Residues C:NUM_RESIDUES, S:10, A:2.0 | The number of residues in the helix |
Number of Residues Per Turn C:NUM_RESIDUES_PER_TURN, S:0, A:9.0 | The number of residues per turn (ideally 3.6 for alpha helices) |
End Residue Serial C:END_RESIDUE_SERIAL, S:10, A:3.0 | The serial in the chain of the last residue of the helix |
Pitch C:PITCH, S:0, A:9.0 | The helix pitch in Angstroms of the helix |
Prev Kinked Id C:PREV_KINKED_ID, S:10, A:1.0 | The database identifier of the Prev Kinked |
Unit Rise C:UNIT_RISE, S:0, A:9.0 | The unit rise in Ang of the helix |
Valid In Assymetric Unit C:NON_ASSEMBLY_VALID, S:1, A:1.0 | This item is to be used not only in an assembly context, but also to represent the original asymmetric unit |
helix    | |
has | |
has | |
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of | |
contacts | |
of | |
of | |
2nd helix in | |
1st helix in | |
kinked | |
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Reference attributes:Residue Data Id - Naming attributes:Accession Code,Assembly Serial,Chain Code |
C:RESIDUE_DATA_ID, S:10, A:5.0 | The database identifier of the Residue Data |
C:ACCESSION_CODE, S:255, A:4.0 | The PDB accession code of the entry |
C:ASSEMBLY_SERIAL, S:3, A:2.0 | The serial identifier of the assembly in the entry |
C:CHAIN_CODE, S:8, A:2.0 | The standard code of the chain that uniquely identifies it in the assembly. It is an extension of the PDB chain Id.
In cases where symmetry operations have been applied to a chain, these chains are named with a numeric suffix, ie. A,A1,A2,A3 ...
The chain id specified in the PDB file is also ignored for waters and bound molecules, and their codes are derived from the name of the chain that they are bound to.
Finally there are no "null" chain codes and in cases where no id was specified in the PDB file, then arbitrary chain codes are assigned (i.e. A,B) |
Alpha C:ALPHA, S:0, A:9.0 | The value in degrees of the backbone virtual torsion angle defined by the four C-Alpha atoms of residues i-1,i,i+1,i+2. used to define chirality ( - if less than 0.0 degrees or + if greater than or equal to 0.0 degrees) |
Assembly Id C:ASSEMBLY_ID, S:10, A:4.0 | The database identifier of the Assembly |
C Alpha Chiral Flag C:C_A_CHIRAL_FLAG, S:38, A:3.0 | A flag to indicate the correctness of the C-alpha atoms chirality. The value is 0 if acceptable and -1 if the condition below is met if (_struct_mon_prot.ebi_Calpha_chiral_value .lt.23.0D0 .or. _struct_mon_prot.ebi_Calpha_chiral_value .gt.45.0D0) |
C Alpha Chiral Value C:C_A_CHIRAL_VALUE, S:0, A:10.0 | The peptide C-alpha chirality value in degrees. |
C Alpha Chiral Sign C:C_ALPHA_CHIRAL_SIGN, S:1, A:1.0 | The chirality of the C-alpha atom from the the value in degrees of the backbone virtual torsion angle defined by the four C-Alpha atoms of residues i-1,i,i+1,i+2. used to define chirality is negative if less than 0.0 degrees or positive if greater than or equal to 0.0 degrees. |
Chain Break C:CHAIN_BREAK, S:1, A:1.0 | A symbol to indicate if there is a chain break at this residue. |
Chain Id C:CHAIN_ID, S:10, A:5.0 | The database identifier of the Chain |
Chain Msd Code C:CHAIN_MSD_CODE, S:8, A:5.0 | An internal longer code for a chain (defined by MSD) that includes the type of the chain (protein, bound molecule etc). It does not identify uniquely a chain in an assembly; the chain code has to be used instead |
Residue Serial C:RESIDUE_SERIAL, S:10, A:3.0 | Serial number of the residue in the chain.
Starts with 1 for the first residue (N-terminal or 5'-terminal) in the chain, and increases by 1 with each position along the chain uniquely identifying the residue in the chain. |
Chain PDB Code C:CHAIN_PDB_CODE, S:3, A:1.0 | The original code of the chain as found in the PDB. There are problems with the chain code since it is not used in a consistent way in the PDB.
Firstly in many cases this is null in cases where there is a single chain in the entry.
Additionally very often the same chain code is used both for a polymer chain and a bound molecule (that is bound to it).
So generally the PDB chain code is often not a distinct identified for a chain. For this reason the chain code was introduced which is consistent and uniform.
The purpose of the chain code is to uniquely identify a chain in an assembly. So in cases where chain A is used 4 times in an assembly, the generated chains will have chain codes A, A1, A2, A3.
Although for the chain that has been marked as non-symmetric valid (that should be used to extract the original asymmetric PDB data), then the original PDB code is used (if it is correct) i.e. A.
In these cases where a chain in the PDB did not have a chain code, then the first not used letter is reserved (i.e. A).
When 2 different chains (i.e. polymer chain and bound molecule chain) share the same PDB code, then the chain code of the bound molecule is consistently derived from the chain code of the polymer chain
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Ligand code C:CHEM_COMP_CODE, S:12, A:7.0 | The standard extended molecule code of the aminoacid or ligand. It is composed by the PDB 3 letter code with an optional topological indicator appended after an underscore |
Chi1 C:CHI1, S:0, A:9.0 | The value in degrees of the side chain torsion angle chi1, for those residues containing such an angle. |
Chi1 Details C:CHI1_DETAILS, S:30, A:3.0 | A derscriptor to indicate if there is a problem or unusal value for the _struct_mon_prot.chi1 torsion angle |
Chi1 Severity C:CHI1_SEVERITY, S:38, A:2.0 | A flag to indicate how far an observed _struct_mon_prot.chi1 value deviates from one of the expected values. The severity level given is residue dependent. |
Chi2 C:CHI2, S:0, A:7.0 | The value in degrees of the side chain torsion angle chi2, for those residues containing such an angle. |
Chi2 Severity C:CHI2_SEVERITY, S:38, A:2.0 | A flag to indicate how far an observed _struct_mon_prot.chi2 value deviates from one of the expected values. The severity level is set by taking the nearest expected target angle (60, -60 , 180 degrees) and the Delta = abs(Angle-Chi2_target) and assigning the _struct_mon_prot.ebi_chi2_severity_flag as 0:chi2 acceptable, 1:chi2 warning Delta > 30 degrees, 2:chi2 poor Delta > 40 degrees, 3:chi2 severe error Delta > 50 degrees |
Chi3 C:CHI3, S:0, A:1.0 | The value in degrees of the side chain torsion angle chi3, for those residues containing such an angle. |
Chi4 C:CHI4, S:0, A:1.0 | The value in degrees of the side chain torsion angle chi4, for those residues containing such an angle. |
Chi5 C:CHI5, S:0, A:1.0 | The value in degrees of the side chain torsion angle chi5, for those residues containing such an angle. |
Code 1 Letter C:CODE_1_LETTER, S:1, A:1.0 | One code letter for the ligand (aminoacid, nucleic acid) in order to construct sequences. |
3 Letter Code C:CODE_3_LETTER, S:3, A:3.0 | This attribute provides a code from the chem comp dictionary for standard residues.
This attribute must be the same for small molecules that represent our variations on topology/chemistry for a polymer component e.g. All ALA's should have a code_3_letter of ALA.
All adenosine nucleotides should have a 3 letter code of A, except for those that have a topology of 'free'.
This code is now obsolete and the Comp Code should be used instead in most cases |
Details C:DETAILS, S:1000, A:1.0 | |
Dssp Name C:DSSP_NAME, S:30, A:7.0 | |
DSSP Structure Descriptor C:DSSP_STRUCTURE, S:7, A:3.0 | The DSSP program string descriptor to describe secondary structure details, see Wolfgang Kabsch and Chris Sander, MPI MF, Heidelberg, 1983. Reference: Kabsch,W. and Sander,C. (1983) Biopolymers 22, 2577-2637. A 7-character string that is composed by characters: 1:3-turns/helix, 2:4-turns/helix, 3:5-turns/helix, 4:geometrical bend, 5:chirality, 6:beta bridge label, 7:beta bridge label |
DSSP Symbol C:DSSP_SYMBOL, S:1, A:1.0 | A symbol for the secondary structure as derived by DSSP B:bulge, C:coil, E:strand, G:3-10-helix, H:alpha-helix, S:bend, I:inverse-turn, T:beta-turn |
Entry Id C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
Helix Id C:HELIX_ID, S:10, A:3.0 | The database identifier of the Helix |
Helix Serial C:HELIX_SERIAL, S:10, A:2.0 | Serial identifier of the helix that the residue belongs |
Kappa C:KAPPA, S:0, A:9.0 | The value in degrees of the backbone virtual bond angle (bend angle) defined by the three C-alpha atoms of residues i-2,i,i+2. used to define bend |
Kinked Helix Id C:KINKED_HELIX_ID, S:10, A:1.0 | The database identifier of the Kinked Helix |
Kinked Helix Serial C:KINKED_HELIX_SERIAL, S:10, A:1.0 | Serial identifier of the kinked helix that the residue is also attached |
Library C:LIBRARY, S:255, A:4.0 | The library (method or program) that determined the structure |
Main chain dihedral flag C:MC_DHDRL_FLAG, S:38, A:2.0 | A flag value to indicate if there is a serious error in the main chain dihedrals for the current residue |
Mean B All C:MEAN_B_ALL, S:8, A:1.0 | The mean value of the isotropic temperature factor for all atoms in the monomer.
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Mean B Main C:MEAN_B_MAIN, S:8, A:1.0 | The mean value of the isotropic temperature factor for atoms in the main chain of the monomer.
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Mean B Side C:MEAN_B_SIDE, S:8, A:1.0 | The mean value of the isotropic temperature factor for atoms in the side chain of the monomer.
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Model Id C:MODEL_ID, S:10, A:4.0 | The database identifier of the Model |
Model Serial C:MODEL_SERIAL, S:38, A:2.0 | The serial identifier of the model in the entry |
Ncbi Tax Id C:NCBI_TAX_ID, S:10, A:1.0 | The NCBI taxonomy identifier (taxid) that points to a node of the taxonomy tree |
Nh Accept 1Chain Code C:NH_ACCEPT_1_CHAIN_CODE, S:8, A:2.0 | The standard code of the Nh Accept 1Chain |
H - Acceptor 1 Chain PDB Code C:NH_ACCEPT_1_CHAIN_PDB_CODE, S:2, A:1.0 | PDB code of the chain of the first hydrogen acceptor residue |
1st NH-Acceptor code C:NH_ACCEPT_1_CHEM_COMP_CODE, S:12, A:5.0 | Code of the 1st residue that has a C=O that makes the best energy hydrogen bond partner (N-H-->O) to the current residue`s NH group |
Nh Accept 1Energy C:NH_ACCEPT_1_ENERGY, S:0, A:7.0 | The value in kcal/mol of the electrostatic H-bond energy of the hydrogen bond (N-H-->O) identified between the current residue and the first acceptor residue |
Nh Accept 1PDB Insert Code C:NH_ACCEPT_1_PDB_INSERT_CODE, S:2, A:1.0 | |
Nh Accept 1Residue Id C:NH_ACCEPT_1_RESIDUE_ID, S:10, A:4.0 | The database identifier of the Nh Accept 1Residue |
Nh Accept 1 Residue PDB Code C:NH_ACCEPT_1_RESIDUE_PDB_CODE, S:10, A:3.0 | |
Nh Accept 1Residue PDB Seq C:NH_ACCEPT_1_RESIDUE_PDB_SEQ, S:38, A:2.0 | Sequence id of the residue that has a C=O that makes the best energy hydrogen bond partner (N-H-->O) to the current residue`s NH group |
Nh Accept 2Chain Code C:NH_ACCEPT_2_CHAIN_CODE, S:8, A:2.0 | The standard code of the Nh Accept 2Chain |
H - Acceptor 2 Chain PDB Code C:NH_ACCEPT_2_CHAIN_PDB_CODE, S:2, A:1.0 | PDB code of the chain of the second hydrogen acceptor residue |
2nd NH-Acceptor code C:NH_ACCEPT_2_CHEM_COMP_CODE, S:12, A:2.0 | Code of the 2nd residue that has a C=O that makes the best energy hydrogen bond partner (N-H-->O) to the current residue`s NH group |
1st Acceptor Serial C:NH_ACCEPT_1_RESIDUE_SERIAL, S:10, A:1.0 | |
Nh Accept 2Energy C:NH_ACCEPT_2_ENERGY, S:0, A:2.0 | |
Nh Accept 2PDB Insert Code C:NH_ACCEPT_2_PDB_INSERT_CODE, S:2, A:1.0 | |
Nh Accept 2Residue Id C:NH_ACCEPT_2_RESIDUE_ID, S:10, A:2.0 | The database identifier of the Nh Accept 2Residue |
Nh Accept 2Residue PDB Code C:NH_ACCEPT_2_RESIDUE_PDB_CODE, S:10, A:2.0 | |
Nh Accept 2Residue PDB Seq C:NH_ACCEPT_2_RESIDUE_PDB_SEQ, S:38, A:2.0 | |
Valid In Assymetric Unit C:NON_ASSEMBLY_VALID, S:1, A:1.0 | This item is to be used not only in an assembly context, but also to represent the original asymmetric unit |
O Donor 1Chain Code C:O_DONOR_1_CHAIN_CODE, S:8, A:2.0 | The standard code of the O Donor 1Chain |
Oxygen Donor 1 Chain PDB Code C:O_DONOR_1_CHAIN_PDB_CODE, S:2, A:1.0 | PDB code of the chain of the first oxygen donor residue |
1st O-Donor code C:O_DONOR_1_CHEM_COMP_CODE, S:12, A:4.0 | Code of the 1st residue that has a NH group that makes the best energy hydrogen bond partner (O-->H-N) to the current residue`s C=O group |
1st Donor Serial C:O_DONOR_1_RESIDUE_SERIAL, S:10, A:1.0 | |
O Donor 1Energy C:O_DONOR_1_ENERGY, S:0, A:7.0 | The value in kcal/mol of the electrostatic H-bond energy of the hydrogen bond (O-->H-N) identified between the current residue and the first donor |
O Donor 1PDB Insert Code C:O_DONOR_1_PDB_INSERT_CODE, S:2, A:1.0 | |
O Donor 1Residue Id C:O_DONOR_1_RESIDUE_ID, S:10, A:4.0 | The database identifier of the O Donor 1Residue |
O Donor 1Residue PDB Code C:O_DONOR_1_RESIDUE_PDB_CODE, S:10, A:3.0 | |
O Donor 1Residue PDB Seq C:O_DONOR_1_RESIDUE_PDB_SEQ, S:38, A:2.0 | Sequence id of the residue that has a NH group that makes the best energy hydrogen bond partner (O-->H-N) to the current residue`s C=O group |
O Donor 2Chain Code C:O_DONOR_2_CHAIN_CODE, S:8, A:2.0 | The standard code of the O Donor 2Chain |
Oxygen Donor 2 Chain PDB Code C:O_DONOR_2_CHAIN_PDB_CODE, S:2, A:1.0 | PDB code of the chain of the second oxygen donor residue |
2nd O-Donor code C:O_DONOR_2_CHEM_COMP_CODE, S:12, A:1.0 | Code of the 2nd residue that has a NH group that makes the best energy hydrogen bond partner (O-->H-N) to the current residue`s C=O group |
O Donor 2Energy C:O_DONOR_2_ENERGY, S:0, A:2.0 | |
2nd Acceptor Serial C:NH_ACCEPT_2_RESIDUE_SERIAL, S:10, A:1.0 | |
O Donor 2PDB Insert Code C:O_DONOR_2_PDB_INSERT_CODE, S:2, A:1.0 | |
O Donor 2Residue Id C:O_DONOR_2_RESIDUE_ID, S:10, A:2.0 | The database identifier of the O Donor 2Residue |
O Donor 2Residue PDB Code C:O_DONOR_2_RESIDUE_PDB_CODE, S:10, A:2.0 | |
O Donor 2Residue PDB Seq C:O_DONOR_2_RESIDUE_PDB_SEQ, S:38, A:2.0 | |
Omega C:OMEGA, S:0, A:10.0 | The value in degrees of the main chain torsion angle omega |
PDB Insert Code C:PDB_INSERT_CODE, S:2, A:1.0 | The insertion code of the residue, as was originally found in the PDB. |
Phi C:PHI, S:0, A:10.0 | The value in degrees of the main chain torsion angle phi (C'----N---Ca---C) |
Promotif Symbol C:PROMOTIF_SYMBOL, S:1, A:1.0 | A symbol derived by PROMOTIF Hutchinson, E. G. & Thornton, J. M. (1996) PROMOTIF - Protein Science 5, 212-220
In the standard DSSP algorithm, a residue is included in a secondary structure only if its NH and CO groups form the appropriate hydrogen bonds or alternatively, for beta sheets only, if the CO(i-1) and NH(i+1) groups are involved in the appropriate hydrogen bonds.
(IUPAC rule 6.2 (1970): to be involved in a particular secondary structure, a residue should have phi and psi values close to the ideal values)
The Promotif symbol conforms to IUPAC convention rule 6.3: a residue is considered part of a beta sheet or alpha helix if either its NH or CO groups are involved in the appropriate hydrogen bonds.
In practice this means that one extra residue is added to the ends of each strand and helix where possible which are classified using lower case letters for the secondary structure, instead of upper case
(E for beta strands, H for alpha helices and G for 3,10 helices).
The PROMOTIF output for several of the motifs described in this documentation contain reference to assigned regions of the Ramachandran plot.
These were originally assigned by Efimov (1991).
The major regions are alpha (alpha-helical region), beta E (beta sheet region), beta P (polyproline region), alpha L (left handed alpha helical region occupied mainly by glycine),
gamma L (adjacent to alpha L and again populated mainly by glycine) and epsilon, which is another small region in the bottom right hand corner of the Ramachandran plot, occupied mainly by glycine residues.
Region English letter
alpha A, a*
beta E B
beta P P
alpha L L
gamma L G
epsilon E
*"A" refers to the core regions of the Ramachandran plot occupied by alpha-helical residues in good quality high resolution structures. "a" refers to a region immediately surrounding the "A" region, which is
occupied by helical residues in less well defined structures.
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Psi C:PSI, S:0, A:10.0 | The value in degrees of the main chain torsion angle psi (N---Ca---C----N') |
Rel Asa In Complex C:REL_ASA_IN_COMPLEX, S:0, A:1.0 | Accessible surface area for residue in complex |
2nd Donor Serial C:O_DONOR_2_RESIDUE_SERIAL, S:10, A:1.0 | |
Rel Asa Isolated C:REL_ASA_ISOLATED, S:0, A:1.0 | Accessible surface area for residue in isolated chain |
Residue Id C:RESIDUE_ID, S:10, A:5.0 | The database identifier of the Residue |
Residue PDB Seq C:RESIDUE_PDB_SEQ, S:38, A:3.0 | The sequence of the residue, as was originally found in the PDB (has to be used together with insert code). |
RSCC All C:RSCC_ALL, S:8, A:1.0 | The real-space (linear) correlation coefficient RSCC, as described by Jones et al., evaluated over all atoms in the monomer.
sum|p~obs~ - | * sum|p~calc~ - |
RSCC = -------------------------------------------------
[ sum|p~obs~ - |^2^ * sum|p~calc~ - |^2^ ]^1/2^
p~obs~ = the density in an "experimental" map
p~calc~ = the density in a "calculated" map
sum is taken over the specified grid points
The details of how these maps were calculated should be described in _struct_mon_details.RSCC. < > indicates an average and the sums are taken over all map grid points near the relevant atoms. The radius for including grid points in the calculation should also be given in _struct_mon_details.RSCC.
Ref: Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119.
|
RSCC Main C:RSCC_MAIN, S:8, A:1.0 | The real-space (linear) correlation coefficient RSCC, as described by Jones et al., evaluated over all atoms in the main chain of the monomer. |
RSCC Side C:RSCC_SIDE, S:8, A:1.0 | The real-space (linear) correlation coefficient RSCC, as described by Jones et al., evaluated over all atoms in the side chain of the monomer.
|
RSR All C:RSR_ALL, S:8, A:1.0 | The real-space residual RSR, as described by Branden and Jones, evaluated over all atoms in the monomer.
sum|p~obs~ - p~calc~|
RSR = ---------------------
sum|p~obs~ + p~calc~|
p~obs~ = the density in an "experimental" map
p~calc~ = the density in a "calculated" map
sum is taken over the specified grid points
The details of how these maps were calculated should be described in _struct_mon_details.RSR. The sums are taken over all map grid points near the relevant atoms.
The radius for including grid points in the calculation should also be given in _struct_mon_details.RSR.
Ref: Branden, C.-I. & Jones, T. A. (1990). Nature, 343, 687-689.
|
RSR Main C:RSR_MAIN, S:8, A:1.0 | The real-space residual RSR, as described by Branden and Jones, (1990) evaluated over all atoms in the main chain of the monomer.
|
RSR Side C:RSR_SIDE, S:8, A:1.0 | The real-space residual RSR, as described by Branden and Jones, (1990) evaluated over all atoms in the side chain of the monomer.
|
Serial C:SERIAL, S:10, A:3.0 | Serial identifier of the residue in the chain. This is generated uniformly and consistently.
It does not always correspond to the PDB SEQ because new chains are identified or fixed.
There is no reason to use insert code any more, residue serial uniquely identifies a residue in a chain |
Sheet Id C:SHEET_ID, S:10, A:2.0 | The database identifier of the Sheet |
Sheet Serial C:SHEET_SERIAL, S:10, A:2.0 | Serial identifier of the sheet that the residue belongs |
Strand Id C:STRAND_ID, S:10, A:1.0 | The database identifier of the Strand |
Strand Serial C:STRAND_SERIAL, S:10, A:1.0 | Serial identifier of the strand that the residue belongs |
Tco C:TCO, S:0, A:10.0 | Cosine of angle between c=o of residue i and c=o of residue i-1. for alpha-helices, tco is near +1, for beta-sheets tco is near -1. not used for structure definition.
|
of organism | |
2nd hydrogen acceptor | |
1st hydrogen acceptor | |
of | |
of | |
kinked | |
of | |
of | |
of | |
of | |
2nd strand end of | |
2nd strand begin of | |
1st strand end of | |
1st strand begin of | |
of | |
of | |
2nd oxygen donor | |
1st oxygen donor | |
|
Reference attributes:Strand Id - Naming attributes:Accession Code,Assembly Serial,Chain Code,Strand Serial |
C:STRAND_ID, S:10, A:5.0 | The database identifier of the Strand |
C:ACCESSION_CODE, S:255, A:4.0 | The PDB accession code of the entry |
C:ASSEMBLY_SERIAL, S:3, A:2.0 | The serial identifier of the assembly in the entry |
C:CHAIN_CODE, S:8, A:2.0 | The standard code of the chain that uniquely identifies it in the assembly. It is an extension of the PDB chain Id.
In cases where symmetry operations have been applied to a chain, these chains are named with a numeric suffix, ie. A,A1,A2,A3 ...
The chain id specified in the PDB file is also ignored for waters and bound molecules, and their codes are derived from the name of the chain that they are bound to.
Finally there are no "null" chain codes and in cases where no id was specified in the PDB file, then arbitrary chain codes are assigned (i.e. A,B) |
C:STRAND_SERIAL, S:10, A:3.0 | |
Assembly Id C:ASSEMBLY_ID, S:10, A:4.0 | The database identifier of the Assembly |
Chain Id C:CHAIN_ID, S:10, A:5.0 | The database identifier of the Chain |
Entry Id C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
Library C:LIBRARY, S:255, A:4.0 | The library (method or program) that determined the structure |
Model Id C:MODEL_ID, S:10, A:4.0 | The database identifier of the Model |
Model Serial C:MODEL_SERIAL, S:10, A:2.0 | The serial identifier of the model in the entry |
Strand Type Details C:STRAND_TYPE_DETAILS, S:4000, A:1.0 | |
Strand Pdb Code C:STRAND_PDB_CODE, S:765, A:1.0 | |
Partner 1Strand Id C:PARTNER_1_STRAND_ID, S:10, A:5.0 | The database identifier of the Partner 1Strand |
Strand Details C:STRAND_DETAILS, S:4000, A:1.0 | |
Partner 1Strand Serial C:PARTNER_1_STRAND_SERIAL, S:10, A:3.0 | |
Strand Cif Conf Id C:STRAND_CIF_CONF_ID, S:60, A:1.0 | |
Partner 2Strand Id C:PARTNER_2_STRAND_ID, S:10, A:3.0 | The database identifier of the Partner 2Strand |
Strand Classification C:STRAND_CLASSIFICATION, S:90, A:1.0 | |
Partner 2Strand Serial C:PARTNER_2_STRAND_SERIAL, S:10, A:2.0 | |
Partner 3Strand Id C:PARTNER_3_STRAND_ID, S:10, A:2.0 | The database identifier of the Partner 3Strand |
Partner 3Strand Serial C:PARTNER_3_STRAND_SERIAL, S:10, A:2.0 | |
Partner 4Strand Id C:PARTNER_4_STRAND_ID, S:10, A:1.0 | The database identifier of the Partner 4Strand |
Partner 4Strand Serial C:PARTNER_4_STRAND_SERIAL, S:10, A:1.0 | |
Strand Begin Residue Id C:STRAND_BEG_RESIDUE_ID, S:10, A:5.0 | |
Sheet Id C:SHEET_ID, S:10, A:4.0 | The database identifier of the Sheet |
Sheet Name C:SHEET_NAME, S:8, A:2.0 | The name of the sheet that the strand belongs in |
Strand Begin Serial C:STRAND_BEG_RESIDUE_SERIAL, S:10, A:3.0 | |
Sheet Serial C:SHEET_SERIAL, S:10, A:3.0 | |
Strand Beg Chain Code C:STRAND_BEG_CHAIN_CODE, S:8, A:2.0 | The standard code of the Strand Beg Chain |
Strand Begin Chain PDB Code C:STRAND_BEG_CHAIN_PDB_CODE, S:2, A:1.0 | PDB code of the chain of the begining residue of the strand |
Strand begin code C:STRAND_BEG_CHEM_COMP_CODE, S:12, A:6.0 | The aminoacid (ligand) molecule code of the first residue of the strand |
Begin Insert Code C:STRAND_BEG_PDB_INSERT_CODE, S:2, A:1.0 | The insertion code of the first residue of the strand |
Strand Beg Residue Data Id C:STRAND_BEG_RESIDUE_DATA_ID, S:10, A:5.0 | The database identifier of the Strand Beg Residue Data |
Strand Beg Residue PDB Code C:STRAND_BEG_RESIDUE_PDB_CODE, S:10, A:3.0 | |
Strand End Residue Id C:STRAND_END_RESIDUE_ID, S:10, A:5.0 | |
Strand Beg Residue PDB Seq C:STRAND_BEG_RESIDUE_PDB_SEQ, S:38, A:3.0 | |
Strand End Serial C:STRAND_END_RESIDUE_SERIAL, S:10, A:3.0 | |
Cross C:STRAND_CROSS_1, S:2, A:1.0 | Richardson nomenclature for the topology of the orientation of Strand to the next strand in the sequence |
Orientation of 1st partner C:STRAND_DIRECTIONS_1, S:2, A:1.0 | The sign giving the orientation of the 1st partner relative to the current strand. |
Orientation of 2nd partner C:STRAND_DIRECTIONS_2, S:2, A:1.0 | The sign giving the orientation of the 2nd partner relative to the current strand. |
Orientation of 3rd partner C:STRAND_DIRECTIONS_3, S:2, A:1.0 | The sign giving the orientation of the 3rd partner relative to the current strand. |
Orientation of 4th partner C:STRAND_DIRECTIONS_4, S:2, A:1.0 | The sign giving the orientation of the 4th partner relative to the current strand. |
Strand End Chain Code C:STRAND_END_CHAIN_CODE, S:8, A:2.0 | The standard code of the Strand End Chain |
Strand Ending Chain PDB Code C:STRAND_END_CHAIN_PDB_CODE, S:2, A:1.0 | PDB code of the chain of the ending residue of the strand |
Strand end code C:STRAND_END_CHEM_COMP_CODE, S:12, A:7.0 | The aminoacid (ligand) molecule code of the last residue of the strand |
End Insert Code C:STRAND_END_PDB_INSERT_CODE, S:2, A:1.0 | The insertion code of the last residue of the strand |
Strand End Residue Data Id C:STRAND_END_RESIDUE_DATA_ID, S:10, A:5.0 | The database identifier of the Strand End Residue Data |
Strand End Residue PDB Code C:STRAND_END_RESIDUE_PDB_CODE, S:10, A:3.0 | |
Strand End Residue PDB Seq C:STRAND_END_RESIDUE_PDB_SEQ, S:38, A:3.0 | |
1st join C:STRAND_JOIN_1, S:10, A:3.0 | Richardson nomenclature for the topology of the connection to the next strand in the sequence for the strand begining (99 means that the next strand is in a different sheet) |
2nd join C:STRAND_JOIN_2, S:10, A:1.0 | Richardson nomenclature for the topology of the connection to the next strand in the sequence for the strand end |
Strand Length C:STRAND_LENGTH, S:10, A:2.0 | The number residues in the strand |
Number of Partners C:STRAND_NUM_PARTNERS, S:10, A:2.0 | |
Valid In Assymetric Unit C:NON_ASSEMBLY_VALID, S:1, A:1.0 | This item is to be used not only in an assembly context, but also to represent the original asymmetric unit |
of | |
has | |
of | |
1st strand of | |
1st strand of | |
4th | |
3rd | |
2nd | |
1st | |
2nd strand of | |
2nd strand of | |
1st strand of | |
2nd strand of | |
2nd strand of | |
1st strand of | |
4th | |
3rd | |
2nd | |
1st | |
in | |
of | |
of | |
|
Reference attributes:Bulge Id - Naming attributes:Accession Code,Assembly Serial,Bulge Serial |
C:BULGE_ID, S:10, A:4.0 | The database identifier of the Bulge |
C:ACCESSION_CODE, S:255, A:4.0 | The PDB accession code of the entry |
C:ASSEMBLY_SERIAL, S:0, A:2.0 | The serial identifier of the assembly in the entry |
C:BULGE_SERIAL, S:10, A:1.0 | |
Assembly Id C:ASSEMBLY_ID, S:10, A:4.0 | The database identifier of the Assembly |
Type C:BULGE_TYPE, S:20, A:3.0 | The classification of the beta bulge. The bulge type is described using two letters: the first letter is P or A depending on whether the bulge involves parallel or antiparallel beta strands; the second letter can be C(lassic), W(ide), G(1), B(ent) or S(pecial). |
Entry Id C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
Library C:LIBRARY, S:255, A:4.0 | The library (method or program) that determined the structure |
Model Id C:MODEL_ID, S:10, A:4.0 | The database identifier of the Model |
Model Serial C:MODEL_SERIAL, S:10, A:2.0 | The serial identifier of the model in the entry |
Bulge Name C:BULGE_NAME, S:765, A:1.0 | (obsolete) |
Bulge Type Details C:BULGE_TYPE_DETAILS, S:4000, A:1.0 | (obsolete) |
Res 1Chain Code C:RES_1_CHAIN_CODE, S:8, A:2.0 | The standard code of the Res 1Chain |
Bulge Pdb Code C:BULGE_PDB_CODE, S:765, A:1.0 | (obsolete) |
Residue 1 Chain PDB Code C:RES_1_CHAIN_PDB_CODE, S:2, A:1.0 | PDB code of chain of the first residue |
Bulge Details C:BULGE_DETAILS, S:4000, A:1.0 | (obsolete) |
1st residue code C:RES_1_CHEM_COMP_CODE, S:12, A:6.0 | The aminoacid (ligand) molecule code of the first residue of the bulge |
Bulge Cif Conf Id C:BULGE_CIF_CONF_ID, S:60, A:1.0 | (obsolete) |
1st residue insert code C:RES_1_PDB_INSERT_CODE, S:2, A:1.0 | The insertion code of the residue for the 1st residue of the bulge |
Bulge Classification C:BULGE_CLASSIFICATION, S:90, A:1.0 | (obsolete) |
Res 1Phi C:RES_1_PHI, S:0, A:10.0 | The value in degrees of the main chain torsion angle phi. for residue 1st residue of the beta bulge. |
Res 1Psi C:RES_1_PSI, S:0, A:10.0 | The value in degrees of the main chain torsion angle psi. for residue 1 of the beta bulge. |
1st Residue Id C:RES_1_RESIDUE_ID, S:10, A:1.0 | |
Res 1Residue Data Id C:RES_1_RESIDUE_DATA_ID, S:10, A:5.0 | The database identifier of the Res 1Residue Data |
1st Residue Serial C:RES_1_RESIDUE_SERIAL, S:10, A:3.0 | The serial number in the chain of the 1st residue of the bulge |
1st Residue PDB Code C:RES_1_RESIDUE_PDB_CODE, S:10, A:3.0 | |
1st Residue PDB Seq C:RES_1_RESIDUE_PDB_SEQ, S:38, A:3.0 | |
Res 2Chain Code C:RES_2_CHAIN_CODE, S:8, A:2.0 | The standard code of the Res 2Chain |
Residue 2 Chain PDB Code C:RES_2_CHAIN_PDB_CODE, S:2, A:1.0 | PDB code of chain of the second residue |
2nd residue code C:RES_2_CHEM_COMP_CODE, S:12, A:7.0 | The aminoacid (ligand) molecule code of the 2nd residue of the bulge |
2nd residue insert code C:RES_2_PDB_INSERT_CODE, S:2, A:1.0 | The insertion code of the residue for the 2nd residue of the bulge |
2nd Residue Phi C:RES_2_PHI, S:0, A:10.0 | |
2nd Residue Psi C:RES_2_PSI, S:0, A:10.0 | |
Res 2Residue Data Id C:RES_2_RESIDUE_DATA_ID, S:10, A:5.0 | The database identifier of the Res 2Residue Data |
2nd Residue PDB Code C:RES_2_RESIDUE_PDB_CODE, S:10, A:3.0 | |
2nd Residue Id C:RES_2_RESIDUE_ID, S:10, A:1.0 | |
2nd Residue PDB Seq C:RES_2_RESIDUE_PDB_SEQ, S:38, A:3.0 | |
2nd Residue Serial C:RES_2_RESIDUE_SERIAL, S:10, A:3.0 | The serial number in the chain of the 2nd residue of the bulge |
Res 3Chain Code C:RES_3_CHAIN_CODE, S:8, A:2.0 | The standard code of the Res 3Chain |
Residue 3 Chain PDB Code C:RES_3_CHAIN_PDB_CODE, S:2, A:1.0 | PDB code of chain of the third residue |
3rd residue code C:RES_3_CHEM_COMP_CODE, S:12, A:6.0 | The aminoacid (ligand) molecule code of the 3rd residue of the bulge |
3rd residue insert code C:RES_3_PDB_INSERT_CODE, S:2, A:1.0 | The insertion code of the residue for the 3rd residue of the bulge |
3rd Residue Phi C:RES_3_PHI, S:0, A:10.0 | |
3rd Residue Psi C:RES_3_PSI, S:0, A:9.0 | |
Res 3Residue Data Id C:RES_3_RESIDUE_DATA_ID, S:10, A:5.0 | The database identifier of the Res 3Residue Data |
3rd Residue PDB Code C:RES_3_RESIDUE_PDB_CODE, S:10, A:3.0 | |
3rd Residue PDB Seq C:RES_3_RESIDUE_PDB_SEQ, S:38, A:3.0 | |
Res 4Chain Code C:RES_4_CHAIN_CODE, S:8, A:2.0 | The standard code of the Res 4Chain |
3rd Residue Id C:RES_3_RESIDUE_ID, S:10, A:1.0 | |
Residue 4 Chain PDB Code C:RES_4_CHAIN_PDB_CODE, S:2, A:1.0 | PDB code of chain of the fourth residue |
3rd Residue Serial C:RES_3_RESIDUE_SERIAL, S:10, A:3.0 | The serial number in the chain of the 3rd residue of the bulge |
4th residue code C:RES_4_CHEM_COMP_CODE, S:12, A:2.0 | The aminoacid (ligand) molecule code of the 4th residue of the bulge |
4th residue insert code C:RES_4_PDB_INSERT_CODE, S:2, A:1.0 | The insertion code of the residue for the 4th residue of the bulge |
4th Residue Phi C:RES_4_PHI, S:0, A:2.0 | |
4th Residue Psi C:RES_4_PSI, S:0, A:2.0 | |
Res 4Residue Data Id C:RES_4_RESIDUE_DATA_ID, S:10, A:2.0 | The database identifier of the Res 4Residue Data |
4th Residue PDB Code C:RES_4_RESIDUE_PDB_CODE, S:10, A:2.0 | |
4th Residue PDB Seq C:RES_4_RESIDUE_PDB_SEQ, S:38, A:2.0 | |
Res 5Chain Code C:RES_5_CHAIN_CODE, S:8, A:2.0 | The standard code of the Res 5Chain |
Residue 5 Chain PDB Code C:RES_5_CHAIN_PDB_CODE, S:2, A:1.0 | PDB code of chain of the fifth residue |
5th residue code C:RES_5_CHEM_COMP_CODE, S:12, A:2.0 | The aminoacid (ligand) molecule code of the 5th residue of the bulge |
4th Residue Id C:RES_4_RESIDUE_ID, S:10, A:1.0 | |
5th residue insert code C:RES_5_PDB_INSERT_CODE, S:2, A:1.0 | The insertion code of the residue for the 5th residue of the bulge |
5th Residue Phi C:RES_5_PHI, S:0, A:2.0 | |
4th Residue Serial C:RES_4_RESIDUE_SERIAL, S:10, A:2.0 | The serial number in the chain of the 4th residue of the bulge |
5th Residue Psi C:RES_5_PSI, S:0, A:2.0 | |
Res 5Residue Data Id C:RES_5_RESIDUE_DATA_ID, S:10, A:2.0 | The database identifier of the Res 5Residue Data |
5th Residue PDB Code C:RES_5_RESIDUE_PDB_CODE, S:10, A:2.0 | |
5th Residue PDB Seq C:RES_5_RESIDUE_PDB_SEQ, S:38, A:2.0 | |
5th Residue Serial C:RES_5_RESIDUE_SERIAL, S:10, A:2.0 | The serial number in the chain of the 5th residue of the bulge |
Valid In Assymetric Unit C:NON_ASSEMBLY_VALID, S:1, A:1.0 | This item is to be used not only in an assembly context, but also to represent the original asymmetric unit |
of | |
of | |
of | |
|
Reference attributes:Turn Id - Naming attributes:Accession Code,Assembly Serial,Chain Code,Turn Serial |
C:TURN_ID, S:10, A:5.0 | The database identifier of the Turn |
C:ACCESSION_CODE, S:255, A:4.0 | The PDB accession code of the entry |
C:ASSEMBLY_SERIAL, S:3, A:2.0 | The serial identifier of the assembly in the entry |
C:CHAIN_CODE, S:8, A:1.0 | The standard code of the chain that uniquely identifies it in the assembly. It is an extension of the PDB chain Id.
In cases where symmetry operations have been applied to a chain, these chains are named with a numeric suffix, ie. A,A1,A2,A3 ...
The chain id specified in the PDB file is also ignored for waters and bound molecules, and their codes are derived from the name of the chain that they are bound to.
Finally there are no "null" chain codes and in cases where no id was specified in the PDB file, then arbitrary chain codes are assigned (i.e. A,B) |
C:TURN_SERIAL, S:10, A:1.0 | |
Assembly Id C:ASSEMBLY_ID, S:10, A:4.0 | The database identifier of the Assembly |
Beta Turn Promotif Type C:BETA_TURN_PROMOTIF_TYPE, S:10, A:2.0 | |
Beta Turn Serial C:BETA_TURN_SERIAL, S:10, A:2.0 | Beta turn serial identifier. Valid only for beta turns |
C alpha-C aplha distance C:CA_CA_DIST, S:0, A:9.0 | The Calpha(i) to Calpha(i+3) distance for the turn |
Chain Id C:CHAIN_ID, S:10, A:5.0 | The database identifier of the Chain |
Efimov classification C:EFIVOM, S:2, A:1.0 | Classify turns according to the wilmot definitions Efimov, A. V. (1991) Structure of alpha-alpha hairpins with short connections. Protein Engineering 4, 245-250. |
Entry Id C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
Gamma Turn Serial C:GAMMA_TURN_SERIAL, S:10, A:2.0 | Gamma turn serial identifier. Valid only for beta turns |
Gamma turn type C:GAMMA_TURN_TYPE, S:255, A:2.0 | A Gamma turn is defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees of one of the following 2 classes (Rose et al., 1985, Milner-White et al, 1988): a) classic: phi(i+1)=75.0 - psi(i+1)=-64.0 , a) classic: phi(i+1)=-79.0 - psi(i+1)=69.0 |
Hydrogen bonded C:H_BONDED_FLAG, S:2, A:1.0 | Flag to indicate whether or not residue i donates a hydrogen bond to residues i+3 |
Library C:LIBRARY, S:255, A:4.0 | The library (method or program) that determined the structure |
1st Residue Id C:RES_1_RESIDUE_ID, S:10, A:0.0 | |
Model Id C:MODEL_ID, S:10, A:4.0 | The database identifier of the Model |
1st Residue Serial C:RES_1_RESIDUE_SERIAL, S:10, A:0.0 | The serial of the 1st residue of the turn |
Model Serial C:MODEL_SERIAL, S:10, A:2.0 | The serial identifier of the model in the entry |
Res 1Chain Code C:RES_1_CHAIN_CODE, S:8, A:2.0 | The standard code of the Res 1Chain |
Residue 1 Chain PDB Code C:RES_1_CHAIN_PDB_CODE, S:2, A:1.0 | PDB code of chain of the first residue |
1st residue code C:RES_1_CHEM_COMP_CODE, S:12, A:7.0 | The aminoacid (ligand) molecule code of the first residue of the turn |
1st residue insert code C:RES_1_PDB_INSERT_CODE, S:2, A:1.0 | The insertion code of the residue for the 1st residue of the turn |
Res 1Residue Data Id C:RES_1_RESIDUE_DATA_ID, S:10, A:5.0 | The database identifier of the Res 1Residue Data |
1st Residue PDB Code C:RES_1_RESIDUE_PDB_CODE, S:10, A:3.0 | |
1st Residue PDB Seq C:RES_1_RESIDUE_PDB_SEQ, S:38, A:3.0 | |
2nd Residue Id C:RES_2_RESIDUE_ID, S:10, A:0.0 | |
Res 2Chain Code C:RES_2_CHAIN_CODE, S:8, A:2.0 | The standard code of the Res 2Chain |
2nd Residue Serial C:RES_2_RESIDUE_SERIAL, S:10, A:0.0 | The serial of the 2nd residue of the turn |
Residue 2 Chain PDB Code C:RES_2_CHAIN_PDB_CODE, S:2, A:1.0 | PDB code of chain of the second residue |
2nd residue code C:RES_2_CHEM_COMP_CODE, S:12, A:6.0 | The aminoacid (ligand) molecule code of the 2nd residue of the turn |
Second residue chi1 C:RES_2_CHI1, S:0, A:9.0 | The value in degrees of the side chain torsion angle chi1, for those residues containing such an angle for residue i+1 of the gamma turn. |
2nd residue insert code C:RES_2_PDB_INSERT_CODE, S:2, A:1.0 | The insertion code of the residue for the 2nd residue of the turn |
Second residue phi C:RES_2_PHI, S:0, A:10.0 | The value in degrees of the main chain torsion angle phi. for residue i+1 of the gamma turn. |
Second residue psi C:RES_2_PSI, S:0, A:10.0 | The value in degrees of the main chain torsion angle psi. for residue i+1 of the gamma turn. |
Res 2Residue Data Id C:RES_2_RESIDUE_DATA_ID, S:10, A:5.0 | The database identifier of the Res 2Residue Data |
2nd Residue PDB Code C:RES_2_RESIDUE_PDB_CODE, S:10, A:3.0 | |
3rd Residue Id C:RES_3_RESIDUE_ID, S:10, A:0.0 | |
2nd Residue PDB Seq C:RES_2_RESIDUE_PDB_SEQ, S:38, A:3.0 | |
3rd Residue Serial C:RES_3_RESIDUE_SERIAL, S:10, A:0.0 | The serial of the 3rd residue of the turn |
Res 3Chain Code C:RES_3_CHAIN_CODE, S:8, A:2.0 | The standard code of the Res 3Chain |
Residue 3 Chain PDB Code C:RES_3_CHAIN_PDB_CODE, S:2, A:1.0 | PDB code of chain of the third residue |
3rd residue code C:RES_3_CHEM_COMP_CODE, S:12, A:6.0 | The aminoacid (ligand) molecule code of the 3rd residue of the turn |
Third residue chi1 C:RES_3_CHI1, S:0, A:7.0 | The value in degrees of the side chain torsion angle chi1, for those residues containing such an angle for residue i+2 of the gamma turn. |
3rd residue insert code C:RES_3_PDB_INSERT_CODE, S:2, A:1.0 | The insertion code of the residue for the 3rd residue of the turn |
Third residue phi C:RES_3_PHI, S:0, A:9.0 | The value in degrees of the main chain torsion angle phi. for residue i+2 of the gamma turn. |
Third residue psi C:RES_3_PSI, S:0, A:9.0 | The value in degrees of the main chain torsion angle psi. for residue i+2 of the gamma turn. |
Res 3Residue Data Id C:RES_3_RESIDUE_DATA_ID, S:10, A:5.0 | The database identifier of the Res 3Residue Data |
4th Residue Id C:RES_4_RESIDUE_ID, S:10, A:0.0 | |
3rd Residue PDB Code C:RES_3_RESIDUE_PDB_CODE, S:10, A:3.0 | |
4th Residue Serial C:RES_4_RESIDUE_SERIAL, S:10, A:0.0 | The serial of the 4th residue of the turn |
3rd Residue PDB Seq C:RES_3_RESIDUE_PDB_SEQ, S:38, A:3.0 | |
Res 4Chain Code C:RES_4_CHAIN_CODE, S:8, A:2.0 | The standard code of the Res 4Chain |
Residue 4 Chain PDB Code C:RES_4_CHAIN_PDB_CODE, S:2, A:1.0 | PDB code of chain of the fourth residue |
4th residue code C:RES_4_CHEM_COMP_CODE, S:12, A:6.0 | The aminoacid (ligand) molecule code of the 4th residue of the turn |
4th residue insert code C:RES_4_PDB_INSERT_CODE, S:2, A:1.0 | The insertion code of the residue for the 4th residue of the turn |
Res 4Residue Data Id C:RES_4_RESIDUE_DATA_ID, S:10, A:5.0 | The database identifier of the Res 4Residue Data |
4th Residue PDB Code C:RES_4_RESIDUE_PDB_CODE, S:10, A:3.0 | |
4th Residue PDB Seq C:RES_4_RESIDUE_PDB_SEQ, S:38, A:3.0 | |
Turn Type C:TURN_TYPE, S:255, A:5.0 | |
Wilmot class C:WILMOT_CLASS, S:10, A:2.0 | Classify turns according to the wilmot definitions Efimov, A. V. (1991) Structure of alpha-alpha hairpins with short connections. Protein Engineering 4, 245-250. |
Valid In Assymetric Unit C:NON_ASSEMBLY_VALID, S:1, A:0.0 | This item is to be used not only in an assembly context, but also to represent the original asymmetric unit |
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Reference attributes:Sheet Hbond Id - Naming attributes:Accession Code,Assembly Serial,Sheet Serial,Strand 1Serial,Strand 2Serial |
C:SHEET_HBOND_ID, S:10, A:4.0 | The database identifier of the Sheet Hbond |
C:ACCESSION_CODE, S:255, A:4.0 | The PDB accession code of the entry |
C:ASSEMBLY_SERIAL, S:3, A:2.0 | The serial identifier of the assembly in the entry |
C:SHEET_SERIAL, S:10, A:3.0 | |
C:STRAND_1_SERIAL, S:10, A:1.0 | |
C:STRAND_2_SERIAL, S:10, A:1.0 | |
Assembly Id C:ASSEMBLY_ID, S:10, A:4.0 | The database identifier of the Assembly |
Entry Id C:ENTRY_ID, S:10, A:4.0 | The database identifier of the Entry |
Library C:LIBRARY, S:255, A:4.0 | The library (method or program) that determined the structure |
Model Id C:MODEL_ID, S:10, A:4.0 | The database identifier of the Model |
Model Serial C:MODEL_SERIAL, S:10, A:2.0 | The serial identifier of the model in the entry |
Sheet Id C:SHEET_ID, S:10, A:1.0 | The database identifier of the Sheet |
Strand 1Beg Atom Data Id C:STRAND_1_BEG_ATOM_DATA_ID, S:10, A:6.0 | The database identifier of the Strand 1Beg Atom Data |
Strand 1Beg Chain Code C:STRAND_1_BEG_CHAIN_CODE, S:8, A:2.0 | The standard code of the Strand 1Beg Chain |
Strand 1 Begin Chain PDB Code C:STRAND_1_BEG_CHAIN_PDB_CODE, S:2, A:1.0 | PDB code of the chain of the begining residue of the first strand |
1st strand begin code C:STRAND_1_BEG_CHEM_COMP_CODE, S:12, A:6.0 | The aminoacid (ligand) molecule code of the first interacting residue of the 1st strand |
1st strand Begin Serial C:STRAND_1_BEG_RESIDUE_SERIAL, S:10, A:0.0 | |
Begin element of 1st partner C:STRAND_1_BEG_PDB_ELEMENT, S:3, A:1.0 | Atom element for the first partner of the first hydrogen bond between two residue ranges in a sheet |
1st strand begin insert code C:STRAND_1_BEG_PDB_INSERT_CODE, S:2, A:1.0 | The insertion code of the last residue of the 1st strand |
Strand 1Beg Residue Data Id C:STRAND_1_BEG_RESIDUE_DATA_ID, S:10, A:5.0 | The database identifier of the Strand 1Beg Residue Data |
Strand 1Beg Residue PDB Code C:STRAND_1_BEG_RESIDUE_PDB_CODE, S:10, A:3.0 | |
Strand 1Beg Residue PDB Seq C:STRAND_1_BEG_RESIDUE_PDB_SEQ, S:38, A:3.0 | |
Strand 1End Atom Data Id C:STRAND_1_END_ATOM_DATA_ID, S:10, A:6.0 | The database identifier of the Strand 1End Atom Data |
Strand 1End Chain Code C:STRAND_1_END_CHAIN_CODE, S:8, A:2.0 | The standard code of the Strand 1End Chain |
Strand 1 End Chain PDB Code C:STRAND_1_END_CHAIN_PDB_CODE, S:2, A:1.0 | PDB code of the chain of the ending residue of the first strand |
1st strand end code C:STRAND_1_END_CHEM_COMP_CODE, S:12, A:7.0 | The aminoacid (ligand) molecule code of the last interacting residue of the 1st strand |
End element of first partner C:STRAND_1_END_PDB_ELEMENT, S:3, A:1.0 | Atom element for the first partner of the last hydrogen bond between two residue ranges in a sheet |
2nd strand BeginResidue Serial C:STRAND_2_BEG_RESIDUE_SERIAL, S:10, A:0.0 | |
1st strand end insert code C:STRAND_1_END_PDB_INSERT_CODE, S:2, A:1.0 | The insertion code of the first residue of the 1st strand |
Strand 1End Residue Data Id C:STRAND_1_END_RESIDUE_DATA_ID, S:10, A:5.0 | The database identifier of the Strand 1End Residue Data |
Strand 1End Residue PDB Code C:STRAND_1_END_RESIDUE_PDB_CODE, S:10, A:3.0 | |
Strand 1End Residue PDB Seq C:STRAND_1_END_RESIDUE_PDB_SEQ, S:38, A:3.0 | |
Strand 1Id C:STRAND_1_ID, S:10, A:1.0 | The database identifier of the Strand 1 |
Strand 2Beg Atom Data Id C:STRAND_2_BEG_ATOM_DATA_ID, S:10, A:6.0 | The database identifier of the Strand 2Beg Atom Data |
Strand 2Beg Chain Code C:STRAND_2_BEG_CHAIN_CODE, S:8, A:2.0 | The standard code of the Strand 2Beg Chain |
Strand 2 Begin Chain PDB Code C:STRAND_2_BEG_CHAIN_PDB_CODE, S:2, A:1.0 | PDB code of the chain of the begining residue of the second strand |
2nd strand begin code C:STRAND_2_BEG_CHEM_COMP_CODE, S:12, A:7.0 | The aminoacid (ligand) molecule code of the 1st interacting residue of the 2nd strand |
Begining element 2nd partner C:STRAND_2_BEG_PDB_ELEMENT, S:3, A:1.0 | Atom element for the second partner of the first hydrogen bond between two residue ranges in a sheet |
1st strand End Serial C:STRAND_1_END_RESIDUE_SERIAL, S:10, A:0.0 | |
2nd strand begin insert code C:STRAND_2_BEG_PDB_INSERT_CODE, S:2, A:1.0 | The insertion code of the last residue of the 2nd strand |
Strand 2Beg Residue Data Id C:STRAND_2_BEG_RESIDUE_DATA_ID, S:10, A:5.0 | The database identifier of the Strand 2Beg Residue Data |
Strand 2Beg Residue PDB Code C:STRAND_2_BEG_RESIDUE_PDB_CODE, S:10, A:3.0 | |
Strand 2Beg Residue PDB Seq C:STRAND_2_BEG_RESIDUE_PDB_SEQ, S:38, A:3.0 | |
Strand 2End Atom Data Id C:STRAND_2_END_ATOM_DATA_ID, S:10, A:6.0 | The database identifier of the Strand 2End Atom Data |
Strand 2End Chain Code C:STRAND_2_END_CHAIN_CODE, S:8, A:2.0 | The standard code of the Strand 2End Chain |
Strand 2 End Chain PDB Code C:STRAND_2_END_CHAIN_PDB_CODE, S:2, A:1.0 | PDB code of the chain of the ending residue of the second strand |
2nd strand end code C:STRAND_2_END_CHEM_COMP_CODE, S:12, A:6.0 | The aminoacid (ligand) molecule code of the last interacting residue of the 2nd strand |
End element of second partner C:STRAND_2_END_PDB_ELEMENT, S:3, A:1.0 | Atom element for the second partner of the last hydrogen bond between two residue ranges in a sheet |
2nd strand end insert code C:STRAND_2_END_PDB_INSERT_CODE, S:2, A:1.0 | The insertion code of the first residue of the 2nd strand |
2nd strand End Serial C:STRAND_2_END_RESIDUE_SERIAL, S:10, A:0.0 | |
Strand 2End Residue Data Id C:STRAND_2_END_RESIDUE_DATA_ID, S:10, A:5.0 | The database identifier of the Strand 2End Residue Data |
Strand 2End Residue PDB Code C:STRAND_2_END_RESIDUE_PDB_CODE, S:10, A:3.0 | |
Strand 2End Residue PDB Seq C:STRAND_2_END_RESIDUE_PDB_SEQ, S:38, A:3.0 | |
Strand 2Id C:STRAND_2_ID, S:10, A:1.0 | The database identifier of the Strand 2 |
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:Date, 
:Unknown
The attribute is a part of the name of an instance
The attribute is a part of the reference key of an instance
The relation is the containment relation of the entity
Entity Details: A=Number of attributes of the Entity
R=Number of relations of the Entity
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I=Approximation of the number of instances of the entity