Appendix B - LIGPLOT file formats

Hydrogen-bonds file, .hhb

The table below shows the LIGPLOT file format for the .hhb file containing the listing of hydrogen bonds to be plotted.

Line 1: 'ligplot.hhb'

Line 2: (blank)

Line 3:

'   Donor                  Acceptor     Distance'

Lines 4 to end:-

---------------------------------------------------------------------------
Field |    Column    | FORTRAN |                                         
  No. |     range    | format  | Description                                   
---------------------------------------------------------------------------
   1. |    1 -  3    |   A3    | Acceptor residue standard 3 letter code
   -  |    4 -  4    |   1X    | Blank      
   2. |    5 -  5    |   A1    | Acceptor chain identifier
   -  |    6 -  6    |   1X    | Blank
   3. |    7 - 11    |   A5    | Acceptor residue sequence number 
   -  |   12 - 13    |   2X    | Blank
   4. |   14 - 16    |   A3    | Acceptor residue atom name (eg CA or ND1)
   -  |   17 - 21    |   5X    | Blank
   5. |   22 - 24    |   A3    | Donor residue standard 3 letter code
   -  |   25 - 25    |   1X    | Blank
   6. |   26 - 26    |   A1    | Donor chain identifier
   -  |   27 - 27    |   1X    | Blank
   7. |   28 - 32    |   A5    | Donor residue sequence number
   -  |   33 - 34    |   2X    | Blank
   8. |   35 - 37    |   A3    | Donor residue atom name (eg CA or ND1)
   -  |   38 - 41    |   4X    | Blank
   9. |   42 - 45    |  F4.2   | Hydrogen bond distance
---------------------------------------------------------------------------

Example of .hhb file

A sample ligplot.hhb file is given below:-

         1         2         3         4     
123456789012345678901234567890123456789012345
---------------------------------------------
ligplot.hhb output:

   Donor                  Acceptor     Distance
HIS     57   NE2     TRP C  252   OXT    3.13
GLY    193   N       TRP C  252   O      3.03
SER    195   N       TRP C  252   O      2.69
TRP C  252   N       SER    214   O      3.00
GLY    216   N       GLY C  250   O      3.15
GLY C  250   N       GLY    216   O      2.92
TRP C  252   NE1     SER    217   O      3.12

Hydrophobic contacts file, .nnb

The table below shows the LIGPLOT file format for the .nnb file containing the listing of hydrophobic contacts to be plotted.

Line 1: 'ligplot.nnb'

Line 2: (blank)

Line 3:

'   Atom 1                 Atom 2          Distance'

Lines 4 to end:-

---------------------------------------------------------------------------
Field |    Column    | FORTRAN |                                         
  No. |     range    | format  | Description                                   
---------------------------------------------------------------------------
   1. |    1 -  3    |   A3    | Atom 1: standard 3 letter code
   -  |    4 -  4    |   1X    | Blank      
   2. |    5 -  5    |   A1    | Atom 1: chain identifier
   -  |    6 -  6    |   1X    | Blank
   3. |    7 - 11    |   A5    | Atom 1: residue sequence number 
   -  |   12 - 13    |   2X    | Blank
   4. |   14 - 16    |   A3    | Atom 1: residue atom name (eg CA or ND1)
   -  |   17 - 21    |   5X    | Blank
   5. |   22 - 24    |   A3    | Atom 2: residue standard 3 letter code
   -  |   25 - 25    |   1X    | Blank
   6. |   26 - 26    |   A1    | Atom 2: chain identifier
   -  |   27 - 27    |   1X    | Blank
   7. |   28 - 32    |   A5    | Atom 2: residue sequence number
   -  |   33 - 34    |   2X    | Blank
   8. |   35 - 37    |   A3    | Atom 2: residue atom name (eg CA or ND1)
   -  |   38 - 41    |   4X    | Blank
   9. |   42 - 45    |  F4.2   | Contact distance
---------------------------------------------------------------------------

Example of .nnb file

A sample ligplot.nnb file is given below:-

         1         2         3         4     
123456789012345678901234567890123456789012345
---------------------------------------------
ligplot.nnb output

   Atom 1                 Atom 2          Distance
ALA C  251   CB      HIS     57   CD2    3.67
TRP C  252   CE3     SER    190   CB     3.52
TRP C  252   CZ3     SER    190   CB     3.58
TRP C  252   CG      CYS    191   C      3.83
TRP C  252   CD1     CYS    191   C      3.77
TRP C  252   C       SER    195   CA     3.79
TRP C  252   C       SER    195   CB     2.86
TRP C  252   CD2     TRP    215   C      3.62
TRP C  252   CE3     TRP    215   C      3.54
TRP C  252   CZ3     TRP    215   C      3.81
GLY C  250   C       TRP    215   CB     3.89
TRP C  252   CE2     GLY    216   CA     3.65
TRP C  252   CZ2     GLY    216   CA     3.29
TRP C  252   CH2     GLY    216   CA     3.48
TRP C  252   CZ2     GLY    216   C      3.60
TRP C  252   CZ3     GLY    226   CA     3.38
TRP C  252   CH2     GLY    226   CA     3.43

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