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Residue-by-residue listing
Part 1. Residue information
Explanatory notes
The first page gives some explanatory notes about the stereochemical
parameters used.
Residue-by-residue listing for 1abc Page 1
----------------------------------------
This listing highlights the residues in the structure which may need investigation.
The ideal values and standard deviations against which the structure has been compared are shown in the following table:
<------------------------------- I D E A L V A L U E S ------------------------------->
Chi-1 dihedral Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality
g(-) trans g(+) Chi-2 phi helix psi rt-hand lf-hand bond dihedral en. C-alpha
------------------------------------------------------------------------------------------
Ideal value 64.1 183.6 -66.7 177.4 -65.4 -65.3 -39.4 96.8 -85.8 2.0 180.0 -2.0 33.9
Standard deviation 15.7 16.8 15.0 18.5 11.2 11.9 11.3 14.8 10.7 0.1 5.8 0.8 3.5
------------------------------------------------------------------------------------------
In the listing below, properties that deviate from these values are highlighted by asterisks and plus-signs. Each asterisk
represents one standard deviation, and each plus-sign represents half a standard deviation. So, a highlight such as +***, indicates
that the value of the parameter is between 3.5 and 4.0 standard deviations from the ideal value shown above.
Where the deviation is greater than 4.5 standard deviations its numerical value is shown; for example, *5.5*.
The final column gives the maximum deviation in each row, while the maximum column deviations are shown at the end of the listing.
Also at the end are the keys to the codes used for the secondary structure and Ramachandran plot assignments.
These notes include the "ideal" values, and
corresponding standard deviations, against which the values calculated
for your structure are compared. The "ideals" used here
come from an analysis of 118 high-resolution structures performed by
Morris et al. (1992).
Residue-by-residue information
The explanatory text is followed by an analysis of each of the
stereochemical parameters for each residue in the structure.
Full print-out.
...................................................................................................................................
Residue Kabsch Region
--------- Sander of
No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max
Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev
-----------------------------------------------------------------------------------------------------------------------------------
1A PRO 1 e - - - - - - - - - - - 178.3 - 38.6 -
* *
2A GLN 2 E B - 145.4 - 172.2 - - - - - - 179.9 - 24.3 -
** +** +**
3A ILE 3 E B - - -67.1 128.2 - - - - - - 182.6 -2.1 31.0 -
+** +**
4A THR 4 B 76.0 - - - - - - - - - 188.6 - 34.9 -
* *
5A LEU 5 S A - - -47.7 174.4 - - - - - - 177.4 - 27.8 -
* +* +*
Each value is
highlighted by asterisks and plus-signs if it deviates from the
"ideal" by more than 1 standard deviation. An asterisk
represents one standard deviation, and a plus-sign represents
half a standard deviation. So, a highlight such as +***
indicates that the value of the parameter is between 3.5 and
4.0 standard deviations from the ideal. Where the deviation is more
than 4.5 standard deviations, its numerical value is shown instead:
for example, *5.5* represents 5.5 standard deviations.
The information shown for each residue is as follows:
-
1. Residue number
- as given in the original coordinates
file.
-
2. Chain identifier
- where relevant, picked up from the original
coordinates file.
-
3. Sequential number
- starting at 1 for the first residue and
numbering the residues sequentially from then on. This may differ from the
residue numbering given in the original coordinates file.
-
4. Kabsch & Sander secondary structure assignment
-
assignment of secondary structure according to the method of Kabsch
& Sander (1983). The codes used are as follows:
B - residue in isolated beta-bridge S - bend
E - extended strand, participates T - hydrogen-bonded turn
in beta-ladder e - extension of beta-strand
G - 3-helix (3/10 helix) g - extension of 3/10 helix
H - 4-helix (alpha-helix) h - extension of alpha-helix
I - 5-helix (pi-helix)
The lower-case assignments are our extensions of the Kabsch & Sander
definition and are obtained by slightly relaxing their criteria.
-
5. Region of Ramachandran plot
- a single letter code identifies
which region of the Ramachandran plot the residue is in. For end residues
and glycines this assignment does not apply, so is shown by a hyphen,
"-".
The other codes are as follows:
A - Core alpha L - Core left-handed alpha
a - Allowed alpha l - Allowed left-handed alpha
~a - Generous alpha ~l - Generous left-handed alpha
B - Core beta p - Allowed epsilon
b - Allowed beta ~p - Generous epsilon
~b - Generous beta XX - Outside major areas
(ie disallowed)
-
6. Chi-1 dihedral angle
- three separate columns are given for
the three possible conformations of chi-1: gauche minus, trans, and gauche
plus.
-
7. Chi-2 dihedral angle
- only the values for the chi-2 dihedral
angles in the trans conformation are shown.
-
8. Proline phi
- the phi torsion angle for proline residues only.
-
9. Phi helix
- the phi torsion angle for all residues
identified as being in an alpha-helix by the H of the Kabsch &
Sander secondary structure assignment code.
-
10. Helix psi
- as above, but for the psi torsion angle.
-
11. Chi-3 dihedral angle
- being the torsion angle defined by the S-S
bridge in a disulphide bond, with separate columns for the right- and
left-handed conformations.
-
12. Disulph bond
- sulphur-sulphur distance, in Å, between
paired cysteine residues.
-
13. H-bond en.
- estimated strength of the main-chain hydrogen
bond (in kcal/mol), where applicable, calculated using the method of
Kabsch & Sander (1983).
-
14. Chirality C-alpha
- value of the zeta "virtual"
torsion angle, defined by the atoms Calpha, N, C, and Cbeta. This is a
"virtual" torsion angle as it is not defined along an actual
bond.
-
15. Bad contacts
- number of bad contacts for this residue,
as defined by non-bonded atoms at a distance of <= 2.6Å. The
bad contacts are listed at the end of the print-out (see Part 3
below).
-
16. Max dev
- this shows the maximum deviation (in terms of
asterisks, etc) of all the columns in the current row.
At the end of this print-out, the column totals show the maximum deviation
in each column, the column's mean value and standard deviation, and number
of values it contains. If the mean values themselves deviate significantly
from the "ideals", they too are highlighted by asterisks.
Part 2. Main-chain bond lengths and bond angles
The second part of the listing analyses the main-chain bond lengths
and bond angles of your protein structure. The "ideal" values
are shown in a table at the start of the listing and come from the analysis of
small-molecule data by Engh & Huber (1991).
Residue-by-residue listing for 1abc Page 9
----------------------------------------
M A I N C H A I N B O N D L E N G T H S A N D B O N D A N G L E S
..................................... Small molecule data .........................................
<---------- Bond lengths ----------> <---------------------- Bond angles ---------------------->
C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N
---------------------------------------------------------------------------------------------------
Any - 1.231 - - - - - - - - - -
( 0.020)
Pro 1.341 - - - 1.466 122.60 116.90 - - 111.80 103.00 122.00
( 0.016) ( 0.015) ( 5.00) ( 1.50) ( 2.50) ( 1.10) ( 1.40)
Except Pro 1.329 - - - - - - - - - - 123.00
( 0.014) ( 1.60)
Gly - - 1.516 - 1.451 120.60 116.40 120.80 - 112.50 - -
( 0.018) ( 0.016) ( 1.70) ( 2.10) ( 2.10) ( 2.90)
Except Gly - - 1.525 - - - - 120.80 - - - -
( 0.021) ( 1.70)
Ala - - - 1.521 - - - - 110.50 - 110.40 -
( 0.033) ( 1.50) ( 1.50)
Ile,Thr,Val - - - 1.540 - - - - 109.10 - 111.50 -
( 0.027) ( 2.20) ( 1.70)
Except Gly,Pro - - - - 1.458 121.70 116.20 - - 111.20 - -
( 0.019) ( 1.80) ( 2.00) ( 2.80)
The rest - - - 1.530 - - - - 110.10 - 110.50 -
( 0.020) ( 1.90) ( 1.70)
Note. The table above shows the mean values obtained from small molecule data by Engh & Huber (1991). The values shown in brackets
are standard deviations
...................................................................................................................................
Then comes the listing itself
Residue
------------- <---------- Bond lengths ----------> <---------------------- Bond angles ---------------------->
No. Type Seq Max
Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev
-----------------------------------------------------------------------------------------------------------------------------------
1A PRO 1 - 1.242 1.516 1.515 1.464 - 116.17 116.50 110.93 111.72 102.81 127.32
+** +*** +***
2A GLN 2 1.320 1.237 1.503 1.462 1.487 117.31 115.43 122.24 125.94 100.74 112.42 122.03
* *** +* ** *8.3* +*** * *8.3*
3A ILE 3 1.300 1.225 1.543 1.551 1.485 121.53 112.50 124.70 116.35 100.85 112.29 122.80
** * +* ** *** +*** +***
4A THR 4 1.285 1.233 1.521 1.556 1.461 133.90 115.15 116.07 120.21 108.60 99.88 128.50
*** *6.8* +** *5.0* *6.8* *** *6.8*
5A LEU 5 1.350 1.243 1.492 1.538 1.455 117.59 115.86 112.72 120.03 119.98 104.38 131.23
+* +* ** *4.8* *5.2* *** +*** *5.1* *5.2*
As before, any deviations
in the actual bond-lengths and bond angles from the "ideal"
values are highlighted with asterisks and plus signs.
At the end of this print-out, the different bond lengths and bond angles
are summarised in two tables giving the minimum, maximum, and mean values
of each type, together with their standard deviations.
Residue-by-residue listing for 1abc Page 18
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A N A L Y S I S O F M A I N C H A I N B O N D L E N G T H S A N D B O N D A N G L E S
+------------------+
| BOND LENGTHS |
+------------------+
-------------------------------------------------------------------------------------------------------------
(Small molecule data) Number of Min Max Mean Standard
Bond X-PLOR labelling Mean St. dev values value value value deviation
-------------------------------------------------------------------------------------------------------------
C-N C-NH1 (except Pro) 1.329 0.014 182 1.275 1.368 1.317 0.018
+*** +**
C-N (Pro) 1.341 0.016 12 1.304 1.339 1.321 0.011
** *
C-O C-O 1.231 0.020 202 1.200 1.460 1.244 0.024
+* *11.5*
CA-C CH1E-C (except Gly) 1.525 0.021 175 1.492 1.589 1.529 0.016
+* ***
CH2G*-C (Gly) 1.516 0.018 26 1.491 1.548 1.520 0.014
* +*
CA-CB CH1E-CH3E (Ala) 1.521 0.033 6 1.511 1.546 1.533 0.013
CH1E-CH1E (Ile,Thr,Val) 1.540 0.027 56 1.505 1.599 1.562 0.018
* **
CH1E-CH2E (the rest) 1.530 0.020 113 1.462 1.583 1.524 0.021
*** +**
N-CA NH1-CH1E (except Gly,Pro)1.458 0.019 160 1.416 1.515 1.468 0.018
** +**
NH1-CH2G* (Gly) 1.451 0.016 26 1.417 1.513 1.464 0.022
** +***
N-CH1E (Pro) 1.466 0.015 15 1.443 1.500 1.467 0.013
+* **
-------------------------------------------------------------------------------------------------------------
Residue-by-residue listing for 1abc Page 19
----------------------------------------
+-----------------+
| BOND ANGLES |
+-----------------+
-------------------------------------------------------------------------------------------------------------
(Small molecule data) Number of Min Max Mean Standard
Angle X-PLOR labelling Mean St. dev values value value value deviation
-------------------------------------------------------------------------------------------------------------
CA-C-N CH1E-C-NH1 (except Gly,Pro)116.2 2.0 154 105.58 128.38 115.05 4.14
*5.3* *6.1*
CH2G*-C-NH1 (Gly) 116.4 2.1 24 108.68 122.98 115.74 3.51
+*** ***
CH1E-C-N (Pro) 116.9 1.5 15 109.51 121.84 117.08 3.61
*4.9* ***
O-C-N O-C-NH1 (except Pro) 123.0 1.6 179 107.65 133.44 124.50 3.92
* 9.6* *6.5*
O-C-N (Pro) 122.0 1.4 15 116.69 127.92 122.37 2.95
+*** ****
C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 158 114.47 135.11 123.03 4.76
**** *7.4*
C-NH1-CH2G* (Gly) 120.6 1.7 24 114.63 133.63 123.55 4.68
+*** *7.7* +*
C-N-CH1E (Pro) 122.6 5.0 12 118.38 128.07 122.48 2.93
*
CA-C-O CH1E-C-O (except Gly) 120.8 1.7 175 104.73 131.27 120.21 4.54
* 9.5* *6.2*
CH2G*-C-O (Gly) 120.8 2.1 26 110.25 130.04 119.71 4.61
*5.0* ****
CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 6 107.31 124.02 111.99 5.81
** * 9.0*
CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 56 102.39 127.48 113.17 5.61
*** *8.4* +*
CH2E-CH1E-C (the rest) 110.1 1.9 113 100.42 125.94 111.62 5.04
*5.1* *8.3*
N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 160 96.93 123.60 108.57 5.32
*5.1* ****
NH1-CH2G*-C (Gly) 112.5 2.9 26 98.93 124.24 112.72 5.95
*4.7* ****
N-CH1E-C (Pro) 111.8 2.5 15 101.33 121.30 112.55 5.39
**** +***
N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 6 102.73 118.03 111.09 5.14
*5.1* *5.1*
NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 56 96.67 130.94 112.14 6.59
*8.7* *11.4*
N-CH1E-CH2E (Pro) 103.0 1.1 15 94.19 107.88 103.37 3.11
*8.0* ****
NH1-CH1E-CH2E (the rest) 110.5 1.7 98 100.31 128.67 111.76 6.07
*6.0* *10.7*
-------------------------------------------------------------------------------------------------------------
The small molecule data used in the above analysis is from Engh & Huber (1991). The atom labelling follows that used in the
X-PLOR dictionary, with some additional atoms (marked with an asterisk) as defined by Engh & Huber.
Part 3. Bad contacts listing
The bad contacts listing shows the
atom-pairs involved, the type of contact, and the separation between the
two atoms. As already mentioned, bad contacts are defined here as any pair
of non-bonded atoms that are at a distance of <=2.6Å from
one another.
Residue-by-residue listing for 1abc Page 20
----------------------------------------
B A D C O N T A C T S L I S T I N G
.......................................................................
Residue Residue
----------- -----------
No. Type No. Type Contact Distance
Chain Atom Chain Atom type (Angstroms)
-----------------------------------------------------------------------
1. 26 A THR O --> 305 HOH O Main-Het 2.6
2. 27 A GLY O --> 358 HOH O Main-Het 2.6
3. 46 A MET O --> 378 HOH O Main-Het 2.4
4. 50 A ILE O --> 342 HOH O Main-Het 2.6
5. 65 A GLU OE1 --> 309 HOH O Side-Het 2.3
6. 66 A ILE C --> 67 A ABA CA Main-Het 2.4
7. 67 A ABA O --> 68 A GLY N Het-Main 2.2
8. 88 A ASN O --> 337 HOH O Main-Het 2.5
9. 90 A LEU O --> 95 A ABA N Main-Het 2.6
10. 94 A GLY C --> 95 A ABA CA Main-Het 2.4
11. 95 A ABA O --> 96 A THR N Het-Main 2.3
12. 95 A ABA O --> 317 HOH O Het-Het 2.6
13. 7 B GLN OE1 --> 310 HOH O Side-Het 2.4
14. 17 B GLY O --> 319 HOH O Main-Het 2.4
15. 26 B THR O --> 304 HOH O Main-Het 2.3
Part 4. Summary statistics and quality assessment
The final part of the print-out reproduces the statistics printed on
the Ramachandran
plot, the Main-chain
parameters plot and the Side-chain
parameters plot.
Residue-by-residue listing for 1abc Page 21
----------------------------------------
R A M A C H A N D R A N P L O T S T A T I S T I C S
Residues in most favoured regions [A,B,L] 143 89.9%
Residues in additional allowed regions [a,b,l,p] 15 9.4%
Residues in generously allowed regions [~a,~b,~l,~p] 1 0.6%
Residues in disallowed regions [XX] 0 0.0%
---- ------
Number of non-glycine and non-proline residues 159 100.0%
Number of end-residues (excl. Gly and Pro) 5
Number of glycine residues 26
Number of proline residues 15
----
Total number of residues 205
Based on the analysis of 118 structures of resolution of at least 2.0 Angstroms and R-factor no greater than 20%, a good
quality model would be expected to have over 90% in the most favoured regions [E,H,L].
S T E R E O C H E M I S T R Y O F M A I N - C H A I N
Comparison values No. of
No. of Parameter Typical Band band widths
Stereochemical parameter data pts value value width from mean
------------------------ -------- ----- ----- ----- ---------
a. %-tage residues in A, B, L 159 89.9 78.2 10.0 1.2 BETTER
b. Omega angle st dev 201 2.3 6.0 3.0 -1.2 BETTER
c. Bad contacts / 100 residues 30 14.6 9.0 10.0 0.6 Inside
d. Zeta angle st dev 179 4.1 3.1 1.6 0.6 Inside
e. H-bond energy st dev 121 0.9 0.9 0.2 0.1 Inside
f. Overall G-factor 205 -1.1 -0.6 0.3 -1.9 WORSE
S T E R E O C H E M I S T R Y O F S I D E - C H A I N
Comparison values No. of
No. of Parameter Typical Band band widths
Stereochemical parameter data pts value value width from mean
------------------------ -------- ----- ----- ----- ---------
a. Chi-1 gauche minus st dev 39 19.7 21.8 6.5 -0.3 Inside
b. Chi-1 trans st dev 32 22.3 22.0 5.3 0.1 Inside
c. Chi-1 gauche plus st dev 87 18.5 20.5 4.9 -0.4 Inside
d. Chi-1 pooled st dev 158 19.6 21.2 4.8 -0.3 Inside
e. Chi-2 trans st dev 59 20.9 22.6 5.0 -0.3 Inside
It also gives an overall assessment of the structure's quality using
the Morris et al. (1992) stereochemical classification
scheme.
M O R R I S E T A L . C L A S S I F I C A T I O N
Mean St.dev Classification
Parameter m s 1 2 3 4 Value Class
--------- ---- --- ------------------------------------ ----- -----
Phi-psi distribution - - >75.0% >65.0% >55.0% <55.0% 89.9 1
Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 18.6 3
H-bond energy st dev 0.87 0.24 <0.63 <0.87 <1.11 >1.11 0.93 3
Here a number from 1 to 4 is assigned to the structure
for each of three separate stereochemical parameters (1 being
the best and 4 the worst score).
Finally, it prints an analysis of the various overall
G-factors calculated for the structure. Any
G-factors below -1.0 may indicate properties that need
to be investigated more closely.
Residue-by-residue listing for 1abc Page 22
----------------------------------------
G - F A C T O R S
Average
Parameter Score Score
--------- ----- -----
Dihedral angles:-
Phi-psi distribution -0.63
Chi1-chi2 distribution -0.68
Chi1 only -0.41
Chi3 & chi4 0.23
Omega 0.32
------ -0.23
=====
Main-chain covalent forces:-
Main-chain bond lengths -0.33
Main-chain bond angles -4.47
------ -2.72
=====
OVERALL AVERAGE -1.14
=====
Ideally, scores should be above -0.5. Values below -1.0 may need investigation.
References
|
|
Engh RA and Huber R (1991). Accurate bond and angle
parameters for X-ray protein structure refinement. Acta Cryst.,
A47, 392-400.
|
|
Kabsch W and Sander C (1983).
Dictionary of protein secondary structure: pattern recognition of
hydrogen-bonded and geometrical features.
Biopolymers, 22, 2577-2637.
|
|
|
Morris AL, MacArthur MW, Hutchinson EG, Thornton JM (1992).
Stereochemical quality of protein structure coordinates. Proteins,
12, 345-364.
|
Sep 1995
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