
                          INTERFACE documentation
                                      
   

CONTENTS

   1.0 SUMMARY 
   2.0 INPUTS & OUTPUTS 
   3.0 INPUT FILE FORMAT 
   4.0 OUTPUT FILE FORMAT 
   5.0 DATA FILES 
   6.0 USAGE 
   7.0 KNOWN BUGS & WARNINGS 
   8.0 NOTES 
   9.0 DESCRIPTION 
   10.0 ALGORITHM 
   11.0 RELATED APPLICATIONS 
   12.0 DIAGNOSTIC ERROR MESSAGES 
   13.0 AUTHORS 
   14.0 REFERENCES 

1.0 SUMMARY

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

2.0 INPUTS & OUTPUTS

   INTERFACE reads a protein CCF file (clean coordinate file) and writes
   a CON file (contacts file) of inter-chain residue-residue contact
   data. The file contains residue contact data for all pairs of chains
   in each model in the CCF file. The input and output files are
   specified by the user. A log file is also written.

3.0 INPUT FILE FORMAT

   The format of the protein CCF file is described in the PDBPARSE
   documentation.

  Input files for usage example

  File: ../pdbplus-keep/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 7; 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 8; 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 7; 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 8; 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
RE   1    1    1    1     V VAL   .    .    .    .    .    C      360.00  130.5
7  137.00  142.86   94.30  113.45   99.30   29.40   79.10  113.56   98.30   29.
29   81.40
RE   1    1    2    2     L LEU   .    .    .    .    .    C      -80.50  121.9
4   16.80   18.20   10.20    7.73    5.50   10.48   27.90    7.73    5.40   10.
48   28.80
RE   1    1    3    3     S SER   1    AA   H    1    .    C      -71.32  164.7
8   44.40   44.59   38.30   44.42   56.90    0.17    0.40   39.26   80.90    5.
34    7.90
RE   1    1    4    4     P PRO   1    AA   H    1    1    H      -62.31  -35.0
5   99.60  105.25   77.30  103.02   85.90    2.23   13.70  103.65   85.70    1.
60   10.50
RE   1    1    5    5     A ALA   1    AA   H    1    1    H      -65.00  -41.5
2   59.80   65.59   60.80   64.35   92.70    1.24    3.20   64.35   90.20    1.
24    3.40
RE   1    1    6    6     D ASP   1    AA   H    1    1    H      -56.29  -42.8
4   13.60   13.83    9.90   13.80   13.40    0.03    0.10    0.44    0.90   13.
39   14.70


  [Part of this file has been deleted for brevity]

AT   1    .    .    .    174   . HOH   W O        -4.764   -6.228    5.515    8
.00   40.89
AT   1    .    .    .    175   . HOH   W O        23.809   19.925    1.758    8
.00   39.37
AT   1    .    .    .    176   . HOH   W O        -7.871   -9.078    2.406    8
.00   43.37
AT   1    .    .    .    177   . HOH   W O         4.693   12.083    7.558    8
.00   40.24
AT   1    .    .    .    178   . HOH   W O         8.775  -23.438   16.055    8
.00   42.33
AT   1    .    .    .    179   . HOH   W O        -7.480  -10.898   17.998    8
.00   38.06
AT   1    .    .    .    180   . HOH   W O        -4.731   16.453    2.295    8
.00   36.37
AT   1    .    .    .    181   . HOH   W O        -1.055   11.866   -0.448    8
.00   43.19
AT   1    .    .    .    182   . HOH   W O       -27.610  -10.991    5.353    8
.00   43.46
AT   1    .    .    .    183   . HOH   W O        26.015   11.766    5.159    8
.00   40.95
AT   1    .    .    .    184   . HOH   W O       -18.517   -8.355   15.267    8
.00   35.55
AT   1    .    .    .    185   . HOH   W O       -14.034    2.806  -30.367    8
.00   41.77
AT   1    .    .    .    186   . HOH   W O       -32.905   -9.033    0.480    8
.00   43.68
AT   1    .    .    .    187   . HOH   W O       -28.749  -13.315    1.938    8
.00   45.36
AT   1    .    .    .    188   . HOH   W O         0.516   -8.074  -26.354    8
.00   41.53
AT   1    .    .    .    189   . HOH   W O       -20.080   -9.873  -22.862    8
.00   36.25
AT   1    .    .    .    190   . HOH   W O       -13.442    9.778  -13.572    8
.00   39.70
AT   1    .    .    .    191   . HOH   W O       -24.804   -2.608  -15.488    8
.00   37.79
AT   1    .    .    .    192   . HOH   W O         6.547    9.706   16.296    8
.00   41.86
AT   1    .    .    .    193   . HOH   W O         0.029   22.606   14.164    8
.00   43.02
AT   1    .    .    .    194   . HOH   W O       -11.367    0.306   28.463    8
.00   44.30
AT   1    .    .    .    195   . HOH   W O       -19.950  -10.635   14.301    8
.00   40.17
AT   1    .    .    .    196   . HOH   W O        -7.047   -6.324   20.098    8
.00   36.98
AT   1    .    .    .    197   . HOH   W O       -23.876    1.108   14.102    8
.00   33.31
AT   1    .    .    .    198   . HOH   W O       -34.199    8.033   11.037    8
.00   40.72
AT   1    .    .    .    199   . HOH   W O       -14.173   13.393   -8.778    8
.00   43.21
AT   1    .    .    .    200   . HOH   W O        11.388  -11.044   24.763    8
.00   39.34
AT   1    .    .    .    201   . HOH   W O         3.735   -3.643    2.734    8
.00   42.17
AT   1    .    .    .    202   . HOH   W O         3.149   -0.692    2.083    8
.00   41.40
AT   1    .    .    .    203   . HOH   W O         4.511  -25.886   13.006    8
.00   39.83
AT   1    .    .    .    204   . HOH   W O         8.712  -21.655    3.577    8
.00   43.08
AT   1    .    .    .    205   . HOH   W O        22.926   -4.304   24.079    8
.00   38.10
AT   1    .    .    .    206   . HOH   W O        11.435    9.654   20.618    8
.00   40.23
AT   1    .    .    .    207   . HOH   W O        18.099    5.542   27.744    8
.00   39.03
AT   1    .    .    .    208   . HOH   W O        12.174    9.951    9.804    8
.00   44.34
AT   1    .    .    .    209   . HOH   W O        24.745   -2.501   15.270    8
.00   39.78
AT   1    .    .    .    210   . HOH   W O        24.231    0.100   14.764    8
.00   42.94
AT   1    .    .    .    211   . HOH   W O        23.324  -18.136   10.981    8
.00   53.60
AT   1    .    .    .    212   . HOH   W O        25.576  -22.211    6.309    8
.00   45.18
AT   1    .    .    .    213   . HOH   W O        14.639   24.823   -4.300    8
.00   41.35
AT   1    .    .    .    214   . HOH   W O        14.903    5.393  -23.047    8
.00   37.45
AT   1    .    .    .    215   . HOH   W O        16.650   -5.137  -16.717    8
.00   39.12
AT   1    .    .    .    216   . HOH   W O         7.424   -6.700  -20.085    8
.00   38.62
AT   1    .    .    .    217   . HOH   W O        -1.263   -2.837  -21.251    8
.00   45.10
AT   1    .    .    .    218   . HOH   W O        23.120   -3.118  -12.992    8
.00   37.05
AT   1    .    .    .    219   . HOH   W O        23.664    0.968  -14.389    8
.00   36.25
AT   1    .    .    .    220   . HOH   W O        25.698    7.981  -15.362    8
.00   35.85
AT   1    .    .    .    221   . HOH   W O        30.009   16.347   -6.794    8
.00   37.62
AT   1    .    .    .    222   . HOH   W O        27.728   16.677   -1.376    8
.00   42.54
AT   1    .    .    .    223   . HOH   W O         8.142   18.836    1.041    8
.00   39.90
//

4.0 OUTPUT FILE FORMAT

   The CON format used for the contact files (Figure 1) is similar to
   EMBL format and is described in the CONTACTS documentation. A few of
   the records differ in the INTERFACE output compared to the CONTACTS
   output, however, so for the sake of clarity all records are described
   below.
     * XX - used for spacing and comments. The first line is
       bibliographic information and contains the text "Inter-chain
       residue-residue contact data".
     * TY - type of contact. For CON files generated by CONTACTS, 'INTER'
       is always given.
     * EX - experimental information. The value of the threshold contact
       distance is given as a floating point number after 'THRESH'. For
       CON files generated by INTERFACE, a '.' is given after 'THRESH'
       (this record is used by the CONTACTS application and can be
       disregarded). The number of models and number of polypeptide
       chains are given after 'NMOD' and 'NCHA' respectively. For domain
       CCF files a 1 is always given.
     * NE - number of entries (interfaces) in the file. For CON files
       generated by INTERFACE this is the number of interfaces (pairs of
       chains), equal to the number of models multiplied by the number of
       unique interfaces. Following the NE record, the file has a section
       for each entry containing records for entry number (EN),
       identifier codes (ID), polypeptide chain-specific data (CN), chain
       sequence information (S1 & S2) and number of contacts (NC), that
       together define the interface and its contacts.
     * EN - entry number. The number in brackets indicates the start of
       an entry (interface).
     * CN - polypeptide chain-specific data. Tokens delimiting data items
       are as follow. (1) MO: The model number (from the PDB file). (2)
       CN1: Chain number (first chain). (3) CN2: Chain number (second
       chain). (4) ID1: PDB chain identifier (first chain) (a '.` given
       in cases where a chain identifier was not specified in the
       original PDB file or, for domain CCF files, the domain is
       comprised of more than one domain). (5) ID2: Chain identifier
       (second chain). (6) NRES1: number of residues (first chain). (7)
       NRES2: number of residues (second chain).
     * NC - number of contacts: (1) SM: Number of residue-residue
       contacts; between side-chain or main-chain atoms of an amino acid
       residue in one chain and the side- or main-chain atoms of a
       residue in a different chain. (2) LI: Number of residue-ligand
       contacts; between side-chain or main-chain atoms of an amino acid
       residue and a ligand.
     * ID - identifier codes: (1) PDB: 4-character PDB identifier code.
       (2) DOM: SCOP or CATH domain identifier code. (3) LIG: Not used by
       INTERFACE, a '.' is given.
     * S1 - polypeptide chain sequence (first chain). The number of
       residues is given before AA on the first line. The sequece is
       given on subsequent lines.
     * S2 - polypeptide chain sequence (second chain).
     * SM - Line of residue contact data. Pairs of amino acid identifiers
       and residue numbers are delimited by a ';'. The left-hand term
       refers to the first chain and the right-hand term the second
       chain. Residue numbers are taken from the CCF files and give a
       correct index into the sequences (i.e. they are not necessarily
       the same as the original PDB file). These sequence is given in the
       CON file itself (S1 & S2 records).
     * // - delimiter for individual entries in the file and also given
       on the last line of the file.

  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

5.0 DATA FILES

   INTERFACE uses a data file containing van der Waals radii for atoms in
   proteins (see CONTACTS documentation.) The file Evdw.dat is such a
   data file and is part of the EMBOSS distribution.

6.0 USAGE

   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 SITES.
   -conlogfile         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

   "-conlogfile" 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

  6.1 COMMAND LINE ARGUMENTS

   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 SITES. Output file test.con
   -conlogfile 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

  6.2 EXAMPLE SESSION

   An example of interactive use of INTERFACE is shown below. Here is a
   sample session with interface


% interface 
Generate inter-chain CON files from CCF files.
Name of protein CCF file (clean coordinate file) (input): ../pdbplus-keep/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

7.0 KNOWN BUGS & WARNINGS

   None.

8.0 NOTES

   Types of contact 
   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, LI will be used for contacts to ligands, and there will
   probably be several other forms of contact too.
   Threshold ignore distance option
   The threshold ignore distance can be adjusted to speed-up the
   calculation of contacts considerably. 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.

  8.1 GLOSSARY OF FILE TYPES

   FILE TYPE FORMAT DESCRIPTION CREATED BY SEE ALSO
   Clean coordinate file (for protein) CCF format (EMBL-like). Protein
   coordinate and derived data for a single PDB file. The data are
   'cleaned-up': self-consistent and error-corrected. PDBPARSE Records
   for residue solvent accessibility and secondary structure are added to
   the file by using PDBPLUS.
   Clean coordinate file (for domain) CCF format (EMBL-like). Protein
   coordinate and derived data for a single domain from SCOP or CATH. The
   data are 'cleaned-up': self-consistent and error-corrected. DOMAINER
   Records for residue solvent accessibility and secondary structure are
   added to the file by using PDBPLUS.
   Contact file (intra-chain residue-residue contacts) CON format
   (EMBL-like.) Intra-chain residue-residue contact data for a protein or
   a domain from SCOP or CATH. CONTACTS N.A.
   Contact file (inter-chain residue-residue contacts) CON format
   (EMBL-like.) Inter-chain residue-residue contact data for a protein or
   a domain from SCOP or CATH. INTERFACE N.A.
   Contact file (residue-ligand contacts) CON format (EMBL-like.)
   Residue-ligand contact data for a protein or a domain from SCOP or
   CATH. SITES N.A.
   van der Waals radii A file of van der Waals radii for atoms in amino
   acid residues. Part of the emboss distribution. N.A. N.A.

   None

9.0 DESCRIPTION

   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 protein CCF files (clean
   coordinate files).

10.0 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.

11.0 RELATED APPLICATIONS

See also

    Program name                        Description
   aaindexextract Extract data from AAINDEX
   allversusall   Sequence similarity data from all-versus-all comparison
   cathparse      Generates DCF file from raw CATH files
   cutgextract    Extract data from CUTG
   domainer       Generates domain CCF files from protein CCF files
   domainnr       Removes redundant domains from a DCF file
   domainseqs     Adds sequence records to a DCF file
   domainsse      Add secondary structure records to a DCF file
   hetparse       Converts heterogen group dictionary to EMBL-like format
   pdbplus        Add accessibility & secondary structure to a CCF file
   pdbtosp        Convert swissprot:PDB codes file to EMBL-like format
   printsextract  Extract data from PRINTS
   prosextract    Build the PROSITE motif database for use by patmatmotifs
   rebaseextract  Extract data from REBASE
   scopparse      Generate DCF file from raw SCOP files
   seqnr          Removes redundancy from DHF files
   sites          Generate residue-ligand CON files from CCF files
   ssematch       Search a DCF file for secondary structure matches
   tfextract      Extract data from TRANSFAC

12.0 DIAGNOSTIC ERROR MESSAGES

   INTERFACE generates a log file an excerpt of which is shown below. If
   there is a problem in processing a CCF 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).

13.0 AUTHORS

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

14.0 REFERENCES

   Please cite the authors and EMBOSS.
   Rice P, Longden I and Bleasby A (2000) "EMBOSS - The European
   Molecular Biology Open Software Suite" Trends in Genetics, 15:276-278.
   
   See also http://emboss.sourceforge.net/

  14.1 Other useful references
