| interface

## Function

Reads CCF files (clean coordinate files) and writes CON files (contact files) of inter-chain residue-residue contact data

## Description

This program is part of a suite of EMBOSS applications that directly or indirectly make use of the protein structure databases pdb and scop. This program is part of an experimental analysis pipeline described in an accompanying document. We provide the software in the hope that it will be useful. The applications were designed for specific research purposes and may not be useful or reliable in contexts other than the described pipeline. The development of the suite was coordinated by Jon Ison to whom enquiries and bug reports should be sent (email jison@hgmp.mrc.ac.uk).

Knowledge of the physical contacts that amino acid residues in two different polypeptide chains of a protein make with one another is required for several different analyses. interface calculates inter-chain residue-residue contact data from clean protein coordinate files.

interface reads a protein coordinate file and writes a file of inter-chain residue-residue contact data in embl-like format. The file contains residue contact data for all pairs of chains in each model in the coordinate file. The input and output files are specified by the user. A log file is also written.

## Algorithm

Contact between two residues is defined as when the van der Waals surface of any atom of the first residue comes within the threshold contact distance of the van der Waals surface of any atom of the second residue. The threshold contact distance is a user-defined distance with a default value of 1 Angstrom.

## Usage

Here is a sample session with interface

    % interface
    Reads CCF files (clean coordinate files) and writes CON files (contact
    files) of inter-chain residue-residue contact data.
    Name of protein CCF file (clean coordinate file) (input): interface/2hhb.ccf
    Threshold contact distance [1.0]: 1
    Name of CON file (contact file) (output) [test.con]: 2hhb.con
    Name of log file for the build [interface.log]:

    2hhb

Go to the input files for this example
Go to the output files for this example

## Command line arguments

       Standard (Mandatory) qualifiers:
      [-infile]            infile     This option specifies the name of the
                                      protein CCF file (clean coordinate file)
                                      (input). A 'clean cordinate file' contains
                                      protein coordinate and derived data for a
                                      single PDB file ('protein clean coordinate
                                      file') or a single domain from SCOP or CATH
                                      ('domain clean coordinate file'), in CCF
                                      format (EMBL-like). The files, generated by
                                      using PDBPARSE (PDB files) or DOMAINER
                                      (domains), contain 'cleaned-up' data that is
                                      self-consistent and error-corrected.
                                      Records for residue solvent accessibility
                                      and secondary structure are added to the
                                      file by using PDBPLUS.
       -thresh             float      This option specifies the threshold contact
                                      distance. Contact between two residues is
                                      defined as when the van der Waals surface of
                                      any atom of the first residue comes within
                                      the threshold contact distance of the van
                                      der Waals surface of any atom of the second
                                      residue. The threshold contact distance is a
                                      user-defined distance with a default value
                                      of 1 Angstrom.
      [-outfile]           outfile    This option specifies the name of CON file
                                      (contact file) (output). A 'contact file'
                                      contains contact data for a protein or a
                                      domain from SCOP or CATH, in the CON format
                                      (EMBL-like). The contacts may be intra-chain
                                      residue-residue, inter-chain
                                      residue-residue or residue-ligand. The files
                                      are generated by using CONTACTS, INTERFACE
                                      and FUNKY.
       -conerrfile         outfile    This option specifies the name of the log
                                      file for the build. The log file contains
                                      messages about any errors arising while
                                      INTERFACE ran.

       Additional (Optional) qualifiers: (none)
       Advanced (Unprompted) qualifiers:
       -vdwfile            datafile   This option specifies the name of data file
                                      with van der Waals radii. The file of van
                                      der Waals radii for atoms in amino acid
                                      residues is part of the emboss distribution.
       -ignore             float      This option specifies the threshold ignore
                                      distance. If any two atoms from two
                                      different residues are at least this
                                      distance apart then no futher inter-atomic
                                      contacts will be checked for for that
                                      residue pair . This speeds the calculation
                                      up considerably.

       Associated qualifiers:

       "-outfile" associated qualifiers
       -odirectory2        string     Output directory

       "-conerrfile" associated qualifiers
       -odirectory         string     Output directory

       General qualifiers:
       -auto               boolean    Turn off prompts
       -stdout             boolean    Write standard output
       -filter             boolean    Read standard input, write standard output
       -options            boolean    Prompt for standard and additional values
       -debug              boolean    Write debug output to program.dbg
       -verbose            boolean    Report some/full command line options
       -help               boolean    Report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose
       -warning            boolean    Report warnings
       -error              boolean    Report errors
       -fatal              boolean    Report fatal errors
       -die                boolean    Report deaths

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---

[-infile]
(Parameter 1)

This option specifies the name of the protein CCF file (clean coordinate file) (input). A 'clean cordinate file' contains protein coordinate and derived data for a single PDB file ('protein clean coordinate file') or a single domain from SCOP or CATH ('domain clean coordinate file'), in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS.

Input file

Required

-thresh | This option specifies the threshold contact distance. Contact between two residues is defined as when the van der Waals surface of any atom of the first residue comes within the threshold contact distance of the van der Waals surface of any atom of the second residue. The threshold contact distance is a user-defined distance with a default value of 1 Angstrom. | Any numeric value | 1.0
[-outfile] (Parameter 2) | This option specifies the name of CON file (contact file) (output). A 'contact file' contains contact data for a protein or a domain from SCOP or CATH, in the CON format (EMBL-like). The contacts may be intra-chain residue-residue, inter-chain residue-residue or residue-ligand. The files are generated by using CONTACTS, INTERFACE and FUNKY. | Output file | test.con
-conerrfile | This option specifies the name of the log file for the build. The log file contains messages about any errors arising while INTERFACE ran. | Output file | interface.log
Additional (Optional) qualifiers | Allowed values | Default
(none)
Advanced (Unprompted) qualifiers | Allowed values | Default
-vdwfile | This option specifies the name of data file with van der Waals radii. The file of van der Waals radii for atoms in amino acid residues is part of the emboss distribution. | Data file | Evdw.dat
-ignore | This option specifies the threshold ignore distance. If any two atoms from two different residues are at least this distance apart then no futher inter-atomic contacts will be checked for for that residue pair . This speeds the calculation up considerably. | Any numeric value | 20.0

## Input file format

interface reads any normal sequence USAs.

### Input files for usage example

### File: interface/2hhb.ccf

    ID   2hhb
    XX
    DE   HEMOGLOBIN (DEOXY)
    XX
    OS   HUMAN (HOMO SAPIENS)
    XX
    EX   METHOD xray; RESO 1.74; NMOD 1; NCHN 4; NGRP 0;
    XX
    CN   [1]
    XX
    IN   ID A; NR 141; NL 1; NH 0; NE 0;
    XX
    SQ   SEQUENCE   141 AA;  15127 MW;  5EC7DB1E CRC32;
         VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK
         KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA
         VHASLDKFLA SVSTVLTSKY R
    XX
    CN   [2]
    XX
    IN   ID B; NR 146; NL 1; NH 0; NE 0;
    XX
    SQ   SEQUENCE   146 AA;  15868 MW;  EC9744C9 CRC32;
         VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV
         KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK
         EFTPPVQAAY QKVVAGVANA LAHKYH
    XX
    CN   [3]
    XX
    IN   ID C; NR 141; NL 1; NH 0; NE 0;
    XX
    SQ   SEQUENCE   141 AA;  15127 MW;  5EC7DB1E CRC32;
         VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK
         KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA
         VHASLDKFLA SVSTVLTSKY R
    XX
    CN   [4]
    XX
    IN   ID D; NR 146; NL 2; NH 0; NE 0;
    XX
    SQ   SEQUENCE   146 AA;  15868 MW;  EC9744C9 CRC32;
         VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV
         KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK
         EFTPPVQAAY QKVVAGVANA LAHKYH
    XX
    CO   1    1    .    P    1     1     .    .    .    .    .    .    V    VAL    N      6.130   16.559    4.905    7.00   41.29    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    1     1     .    .    .    .    .    .    V    VAL    CA     6.870   17.784    4.702    6.00   41.33    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    1     1     .    .    .    .    .    .    V    VAL    C      8.377   17.548    4.913    6.00   31.64    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    1     1     .    .    .    .    .    .    V    VAL    O      8.820   16.980    5.922    8.00   38.31    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    1     1     .    .    .    .    .    .    V    VAL    CB     6.345   18.763    5.731    6.00   52.26    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    1    .    P    1     1     .    .    .    .    .    .    V    VAL    CG1    6.745   20.188    5.356    6.00   52.75    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00

      [Part of this file has been deleted for brevity]

    CO   1    .    .    W    .     174   .    .    .    .    .    .    .    HOH    O     -4.764   -6.228    5.515    8.00   40.89    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     175   .    .    .    .    .    .    .    HOH    O     23.809   19.925    1.758    8.00   39.37    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     176   .    .    .    .    .    .    .    HOH    O     -7.871   -9.078    2.406    8.00   43.37    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     177   .    .    .    .    .    .    .    HOH    O      4.693   12.083    7.558    8.00   40.24    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     178   .    .    .    .    .    .    .    HOH    O      8.775  -23.438   16.055    8.00   42.33    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     179   .    .    .    .    .    .    .    HOH    O     -7.480  -10.898   17.998    8.00   38.06    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     180   .    .    .    .    .    .    .    HOH    O     -4.731   16.453    2.295    8.00   36.37    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     181   .    .    .    .    .    .    .    HOH    O     -1.055   11.866   -0.448    8.00   43.19    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     182   .    .    .    .    .    .    .    HOH    O    -27.610  -10.991    5.353    8.00   43.46    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     183   .    .    .    .    .    .    .    HOH    O     26.015   11.766    5.159    8.00   40.95    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     184   .    .    .    .    .    .    .    HOH    O    -18.517   -8.355   15.267    8.00   35.55    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     185   .    .    .    .    .    .    .    HOH    O    -14.034    2.806  -30.367    8.00   41.77    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     186   .    .    .    .    .    .    .    HOH    O    -32.905   -9.033    0.480    8.00   43.68    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     187   .    .    .    .    .    .    .    HOH    O    -28.749  -13.315    1.938    8.00   45.36    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     188   .    .    .    .    .    .    .    HOH    O      0.516   -8.074  -26.354    8.00   41.53    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     189   .    .    .    .    .    .    .    HOH    O    -20.080   -9.873  -22.862    8.00   36.25    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     190   .    .    .    .    .    .    .    HOH    O    -13.442    9.778  -13.572    8.00   39.70    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     191   .    .    .    .    .    .    .    HOH    O    -24.804   -2.608  -15.488    8.00   37.79    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     192   .    .    .    .    .    .    .    HOH    O      6.547    9.706   16.296    8.00   41.86    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     193   .    .    .    .    .    .    .    HOH    O      0.029   22.606   14.164    8.00   43.02    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     194   .    .    .    .    .    .    .    HOH    O    -11.367    0.306   28.463    8.00   44.30    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     195   .    .    .    .    .    .    .    HOH    O    -19.950  -10.635   14.301    8.00   40.17    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     196   .    .    .    .    .    .    .    HOH    O     -7.047   -6.324   20.098    8.00   36.98    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     197   .    .    .    .    .    .    .    HOH    O    -23.876    1.108   14.102    8.00   33.31    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     198   .    .    .    .    .    .    .    HOH    O    -34.199    8.033   11.037    8.00   40.72    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     199   .    .    .    .    .    .    .    HOH    O    -14.173   13.393   -8.778    8.00   43.21    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     200   .    .    .    .    .    .    .    HOH    O     11.388  -11.044   24.763    8.00   39.34    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     201   .    .    .    .    .    .    .    HOH    O      3.735   -3.643    2.734    8.00   42.17    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     202   .    .    .    .    .    .    .    HOH    O      3.149   -0.692    2.083    8.00   41.40    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     203   .    .    .    .    .    .    .    HOH    O      4.511  -25.886   13.006    8.00   39.83    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     204   .    .    .    .    .    .    .    HOH    O      8.712  -21.655    3.577    8.00   43.08    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     205   .    .    .    .    .    .    .    HOH    O     22.926   -4.304   24.079    8.00   38.10    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     206   .    .    .    .    .    .    .    HOH    O     11.435    9.654   20.618    8.00   40.23    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     207   .    .    .    .    .    .    .    HOH    O     18.099    5.542   27.744    8.00   39.03    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     208   .    .    .    .    .    .    .    HOH    O     12.174    9.951    9.804    8.00   44.34    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     209   .    .    .    .    .    .    .    HOH    O     24.745   -2.501   15.270    8.00   39.78    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     210   .    .    .    .    .    .    .    HOH    O     24.231    0.100   14.764    8.00   42.94    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     211   .    .    .    .    .    .    .    HOH    O     23.324  -18.136   10.981    8.00   53.60    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     212   .    .    .    .    .    .    .    HOH    O     25.576  -22.211    6.309    8.00   45.18    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     213   .    .    .    .    .    .    .    HOH    O     14.639   24.823   -4.300    8.00   41.35    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     214   .    .    .    .    .    .    .    HOH    O     14.903    5.393  -23.047    8.00   37.45    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     215   .    .    .    .    .    .    .    HOH    O     16.650   -5.137  -16.717    8.00   39.12    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     216   .    .    .    .    .    .    .    HOH    O      7.424   -6.700  -20.085    8.00   38.62    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     217   .    .    .    .    .    .    .    HOH    O     -1.263   -2.837  -21.251    8.00   45.10    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     218   .    .    .    .    .    .    .    HOH    O     23.120   -3.118  -12.992    8.00   37.05    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     219   .    .    .    .    .    .    .    HOH    O     23.664    0.968  -14.389    8.00   36.25    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     220   .    .    .    .    .    .    .    HOH    O     25.698    7.981  -15.362    8.00   35.85    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     221   .    .    .    .    .    .    .    HOH    O     30.009   16.347   -6.794    8.00   37.62    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     222   .    .    .    .    .    .    .    HOH    O     27.728   16.677   -1.376    8.00   42.54    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    CO   1    .    .    W    .     223   .    .    .    .    .    .    .    HOH    O      8.142   18.836    1.041    8.00   39.90    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00
    //

The format of the clean protein coordinate file is described in pdbparse

## Output file format

### Output files for usage example

### File: 2hhb.con

    XX   Inter-chain residue-residue contact data.
    XX
    TY   INTER
    XX
    EX   THRESH 1.0; IGNORE 20.0; NMOD 1; NCHA 4
    XX
    NE   6
    XX
    EN   [1]
    XX
    ID   PDB 2hhb; DOM .; LIG .
    XX
    CN   MO 1; CN1 1; CN2 2; ID1 A; ID2 B; NRES1 141; NRES2 146
    XX
    S1   SEQUENCE   141 AA;  15127 MW;  5EC7DB1E CRC32;
         VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK
         KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA
         VHASLDKFLA SVSTVLTSKY R
    XX
    S2   SEQUENCE   146 AA;  15868 MW;  EC9744C9 CRC32;
         VHLTPEEKSA VTALWGKVNV DEVGGEALGR LLVVYPWTQR FFESFGDLST PDAVMGNPKV
         KAHGKKVLGA FSDGLAHLDN LKGTFATLSE LHCDKLHVDP ENFRLLGNVL VCVLAHHFGK
         EFTPPVQAAY QKVVAGVANA LAHKYH
    XX
    NC   SM 48; LI .
    XX
    SM   GLU 30 ; PRO 124
    SM   ARG 31 ; PHE 122
    SM   ARG 31 ; THR 123
    SM   ARG 31 ; PRO 124
    SM   ARG 31 ; GLN 127
    SM   LEU 34 ; PRO 124
    SM   LEU 34 ; PRO 125
    SM   LEU 34 ; ALA 128
    SM   SER 35 ; GLN 127
    SM   SER 35 ; ALA 128
    SM   SER 35 ; GLN 131
    SM   PHE 36 ; GLN 131
    SM   HIS 103 ; ASN 108
    SM   HIS 103 ; VAL 111
    SM   HIS 103 ; CYS 112
    SM   HIS 103 ; GLN 127
    SM   HIS 103 ; GLN 131
    SM   CYS 104 ; GLN 127
    SM   LEU 106 ; CYS 112
    SM   VAL 107 ; VAL 111
    SM   VAL 107 ; CYS 112
    SM   VAL 107 ; ALA 115
    SM   VAL 107 ; PHE 122
    SM   VAL 107 ; GLN 127

      [Part of this file has been deleted for brevity]

    SM   GLU 27 ; PRO 124
    SM   GLU 30 ; PRO 124
    SM   ARG 31 ; PHE 122
    SM   ARG 31 ; THR 123
    SM   ARG 31 ; PRO 124
    SM   ARG 31 ; GLN 127
    SM   LEU 34 ; PRO 124
    SM   LEU 34 ; PRO 125
    SM   LEU 34 ; ALA 128
    SM   SER 35 ; GLN 127
    SM   SER 35 ; ALA 128
    SM   SER 35 ; GLN 131
    SM   PHE 36 ; GLN 131
    SM   HIS 103 ; ASN 108
    SM   HIS 103 ; VAL 111
    SM   HIS 103 ; CYS 112
    SM   HIS 103 ; GLN 127
    SM   HIS 103 ; GLN 131
    SM   CYS 104 ; GLN 127
    SM   LEU 106 ; CYS 112
    SM   VAL 107 ; VAL 111
    SM   VAL 107 ; CYS 112
    SM   VAL 107 ; ALA 115
    SM   VAL 107 ; PHE 122
    SM   VAL 107 ; GLN 127
    SM   ALA 110 ; CYS 112
    SM   ALA 110 ; ALA 115
    SM   ALA 110 ; HIS 116
    SM   ALA 111 ; ALA 115
    SM   ALA 111 ; GLY 119
    SM   LEU 113 ; HIS 116
    SM   PRO 114 ; HIS 116
    SM   PHE 117 ; ARG 30
    SM   PHE 117 ; CYS 112
    SM   PHE 117 ; HIS 116
    SM   THR 118 ; ARG 30
    SM   PRO 119 ; ARG 30
    SM   PRO 119 ; VAL 33
    SM   PRO 119 ; VAL 34
    SM   PRO 119 ; MET 55
    SM   ALA 120 ; VAL 33
    SM   ALA 120 ; PRO 51
    SM   HIS 122 ; ARG 30
    SM   HIS 122 ; VAL 34
    SM   HIS 122 ; VAL 109
    SM   HIS 122 ; CYS 112
    SM   ALA 123 ; VAL 33
    SM   ALA 123 ; VAL 34
    SM   ASP 126 ; VAL 34
    SM   ASP 126 ; TYR 35
    //

### File: interface.log

    2hhb

The embl-like format used for the contact files (below) uses the following records:

(1) ID - the 4-character PDB identifier code.

(2) DE - bibliographic information. The text "Residue-residue contact data" is always given.

(3) EX - experimental information. The value of the threshold contact distance is given as a floating point number after 'THRESH'. The number of models and number of polypeptide chains are given after 'NMOD' and 'NCHA' respectively. domain coordinate files a 1 is always given. Following the EX record, the file will have a section containing a PA, IN and SM records (see below) for each chain pair. The sections for each chain pair of a model are given after the MO record.

(4) MO - model number. The number given in brackets after this record indicates the start of a section of model-specific data.

(5) PA - chain pair number. The numbers given either side of the ':' after this record indicate the start of a section of chain pair-specific data.

(6) IN - chain specific data. The characters given after ID1 and ID2 are the PDB chain identifiers for the pair taken from the input file, (a '.` given in cases where a chain identifier was not specified in the original pdb file). The number of amino acid residues comprising each chain is given after NR1 and NR2 respectively. The number of residue-residue contacts is given after NSMCON.

(7) SM - Line of residue contact data. Pairs of amino acid identifiers and residue numbers are delimited by a ';'. Residue numbers are taken from the clean coordinate file and give a correct index into the sequence (i.e. they are not necessarily the same as the original pdb file). The first residue belongs to the first partner of the chain-pair, the second residue belongs to the second partner.

(8) XX - used for spacing.

(9) // - given on the last line of the file only.

Note - SM records are used for contacts between either either side-chain or main-chain atoms as defined above. In a future implementation, SS will be used for side-chain only contacts, MM will be used for main-chain only contacts, and there will probably be several other forms of contact too.

Excerpt from interface output file

    ID   2hhb
    XX
    DE   Residue-residue side-chain contact data
    XX
    EX   THRESH 1.0; IGNORE 20.0; NMOD 1; NCHA 4;
    XX
    MO   [1]
    XX
    PA   1:2
    XX
    IN   ID1 A; ID2 B; NR1 141; NR2 146; NSMCON 48;
    XX
    SM   GLU 30 ; PRO 124
    SM   ARG 31 ; PHE 122
    SM   ARG 31 ; THR 123
    SM   ARG 31 ; PRO 124
    SM   ARG 31 ; GLN 127
    SM   LEU 34 ; PRO 124
    SM   LEU 34 ; PRO 125
    **
    < data ommitted for clarity >
    **
    SM   ALA 123 ; VAL 34
    SM   ASP 126 ; VAL 34
    SM   ASP 126 ; TYR 35
    XX
    PA   1:3
    XX
    IN   ID1 A; ID2 C; NR1 141; NR2 141; NSMCON 3;
    XX
    SM   ASP 126 ; ARG 141
    SM   LYS 127 ; ARG 141
    SM   ALA 130 ; ARG 141
    XX
    PA   1:4
    XX
    IN   ID1 A; ID2 D; NR1 141; NR2 146; NSMCON 25;
    XX
    SM   PRO 37 ; HIS 146
    **
    < data ommitted for clarity >
    **
    SM   ASP 126 ; VAL 34
    SM   ASP 126 ; TYR 35
    XX
    //

## Data files

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.

To see the available EMBOSS data files, run:

    % embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:

    % embossdata -fetch -file Exxx.dat

Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".

The directories are searched in the following order:

- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata

contacts uses a data file containing van der Waals radii for atoms in proteins. The file Evdw.dat is such a data file and is part of the emboss distribution.

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

interface generates a log file an excerpt of which is shown below. If there is a problem in processing a coordinate file, three lines containing the record '//', the pdb identifier code and an error message respectively are written. The text 'WARN file open error filename', 'ERROR file read error filename' or 'ERROR file write error filename ' will be reported when an error was encountered during a file open, read or write respectively. Various other error messages may also be given (in case of difficulty email Jon Ison, jison@hgmp.mrc.ac.uk).

Excerpt of log file

    //
    DS002__
    WARN  Could not open for reading cpdb file s002.pxyz
    //

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
contactcount | Counts specific versus non-specific contacts in a directory of cleaned protein chain contact files
contacts | Reads CCF files (clean coordinate files) and writes CON files (contact files) of intra-chain residue-residue contact data
domainalign | Generates DAF files (domain alignment files) of structure-based sequence alignments for nodes in a DCF file (domain classification file)
domainrep | Reorder DCF file (domain classification file) so that the representative structure of each user-specified node is given first
domainreso | Removes low resolution domains from a DCF file (domain classification file)
libgen | Generates various types of discriminating elements for each alignment in a directory
psiphi | Calculates phi and psi torsion angles from cleaned EMBOSS-style protein co-ordinate file
rocon | Reads a DHF file (domain hits file) of hits (sequences of unknown structural classification) and a DHF file of validation sequences (known classification) and writes a 'hits file' for the hits, which are classified and rank-ordered on the basis of score
rocplot | Provides interpretation and graphical display of the performance of discriminating elements (e.g. profiles for protein families). rocplot reads file(s) of hits from discriminator-database search(es), performs ROC analysis on the hits, and writes graphs illustrating the diagnostic performance of the discriminating elements
seqalign | Reads a DAF file (domain alignment file) and a DHF file (domain hits file) and writes a DAF file extended with the hits
seqfraggle | Removes fragments from DHF files (domain hits files) or other files of sequences
seqsearch | Generate database hits (sequences) for nodes in a DCF file (domain classification file) by using PSI-BLAST
seqsort | Reads DHF files (domain hits files) of database hits (sequences) and removes hits of ambiguous classification
seqwords | Generates DHF files (domain hits files) of database hits (sequences) for nodes in a DCF file (domain classification file) by keyword search of UniProt
siggen | Generates a sparse protein signature from an alignment and residue contact data
sigscan | Generates a DHF file (domain hits file) of hits (sequences) from scanning a signature against a sequence database

A 'protein coordinate file' contains protein coordinate and other data extracted from a single pdb file. The files, generated by pdbparse, are in embl-like format and contain 'cleaned-up' data that is self-consistent and error-corrected.

## Author(s)

Jon Ison (jison © rfcgr.mrc.ac.uk)
MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

## History

Written (2003) - Jon Ison

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.