
                                 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.
