                           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;  15126 MW;  34D13618E62A33C1 CRC64;
     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;  15867 MW;  EACBC707CFD466A1 CRC64;
     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;  15126 MW;  34D13618E62A33C1 CRC64;
     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;  15867 MW;  EACBC707CFD466A1 CRC64;
     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  130.57
  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  121.94
   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  164.78
   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  -35.05
   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  -41.52
   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  -42.84
   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;  15126 MW;  34D13618E62A33C1 CRC64;
     VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK
     KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA
     VHASLDKFLA SVSTVLTSKY R
XX
S2   SEQUENCE   146 AA;  15867 MW;  EACBC707CFD466A1 CRC64;
     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

Generate inter-chain CON files from CCF files.
Version: EMBOSS:6.6.0.0

   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      [1.0] 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)
  [-outfile]           outfile    [test.con] 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    [interface.log] 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   [Evdw.dat] 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      [20.0] 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)

   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 first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to 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 and exit. 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 dying program messages
   -version            boolean    Report version number and exit


  6.1 COMMAND LINE ARGUMENTS

