N U C P L O T manual

Appendix B - The *.bond file format

The table below shows the NUCPLOT file format for the *.bond file containing the list of hydrogen bonds, non bonded contacts and covalent bonds to be plotted. The file is automatically produced when the HBPLUS files are used as inputs.

Example file:

                             10         20         30         40  
                    12345678790123456787901234567879012345678790123
                    ===============================================
     
     Line 1:        NUCPLOT v.1.0  -  Bond file (pdb1zaa.bond)
     Line 2:        -----------------------------------------------
       |  
     Line 4:        **** Hydrogen Bonds ***************************
       |                  Donor               Acceptor     Distance
       |            ARG C   70    NH2      G A    2    O1P   2.87
       |            ARG C   80    NH2      G A    2    N7    2.86
       |            ARG C   80    NH1      G A    2    O6    2.99
     Line X:        HOH    319    O        G B    4    O6    2.60
       |  
       |  
     Line X+3:      **** Non Bonded Contacts **********************
       |                 protein                DNA        Distance
       |            THR C   56    CG2      C A    3    P     3.63
       |            THR C   56    CG2      C A    3    O1P   3.82
     Line Y:        THR C   56    CB       C A    3    O2P   3.38
       |  
       |  
     Line Y+3:      **** Covalent Bonds ***************************
       |                 protein                DNA        Distance

Explanation of columns:

       ------------------------------------------------------------
        Field |    Column    |   Description
          No. |     range    |              
       ------------------------------------------------------------
           1. |     1 - 3    |   Donor residue 3-letter code
           -  |     4 - 4    |   Blank
           2. |     5 - 5    |   Donor chain ID
           -  |     6 - 7    |   Blank
           3. |     8 - 10   |   Donor residue number
           -  |    11 - 13   |   Blank
           4. |    14 - 17   |   Donor residue atom name
           -  |    18 - 21   |   Blank
           5. |    22 - 24   |   Acceptor residue 3-letter code 
           -  |    25 - 25   |   Blank
           6. |    26 - 26   |   Acceptor chain ID
           -  |    27 - 28   |   Blank
           7. |    29 - 31   |   Acceptor residue number
           -  |    32 - 34   |   Blank
           8. |    35 - 38   |   Acceptor residue name
           -  |    39 - 41   |   Blank
           9. |    42 - 45   |   H-bond distance
       ------------------------------------------------------------