SITES 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 residue-ligand contact data for domains in a DCF file (domain classification file)


2.0 INPUTS & OUTPUTS

SITES reads CCF files (clean coordinate file) and writes a CON files (contacts file) of residue-ligand contact data for domains in a DCF file (domain classification file). The CON file contains contact data for all ligand-domain pairs (using domain definitions from the DCF file) found in the CCF files. The input and output files are specified by the user (file extensions in the ACD file). A log file is also written.


3.0 INPUT FILE FORMAT

The format of the protein CCF file is described in the PDBPARSE documentation. Under development, no example input file(s) yet


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 SITES output compared to the CONTACTS output, however, so for the sake of clarity all records are described below. Under development, no example output file(s) yet


5.0 DATA FILES

SITES 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.

SITES uses a data file containing a dictionary of heterogen groups in PDB. This file may be generated by using HETPARSE and is part of the EMBOSS distribution. The file Ehet.dat is such a data file and is part of the EMBOSS distribution.


6.0 USAGE

6.1 COMMAND LINE ARGUMENTS

   Standard (Mandatory) qualifiers:
  [-protpath]          dirlist    This option specifies the location of the
                                  protein CCF files (clean coordinate files)
                                  (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.
  [-domaindir]         directory  This option specifies the location of the
                                  domain CCF files (clean coordinate files)
                                  (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.
   -dcffile            infile     This option specifies the name of the DCF
                                  file (domain classification file) (input). A
                                  'domain classification file' contains
                                  classification and other data for domains
                                  from SCOP or CATH, in DCF format
                                  (EMBL-like). The files are generated by
                                  using SCOPPARSE and CATHPARSE. Domain
                                  sequence information can be added to the
                                  file by using DOMAINSEQS.
   -threshold          float      This option specifies the threshold contact
                                  distance.
  [-outfile]           outfile    This option specifies the name of the output
                                  file.
   -logfile            outfile    This option specifies the name of the log
                                  file.

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -dicfile            datafile   This option specifies the dictionary of
                                  heterogen groups in PDB. This file is
                                  generated by using HETPARSE and is part of
                                  the EMBOSS distribution.
   -vdwfile            datafile   This option specifies the name of the data
                                  file with van der Waals radii for atoms in
                                  amino acid residues. This file is part of
                                  the EMBOSS distribution.

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory3        string     Output directory

   "-logfile" 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
[-protpath]
(Parameter 1)
This option specifies the location of the protein CCF files (clean coordinate files) (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. Directory with files ./
[-domaindir]
(Parameter 2)
This option specifies the location of the domain CCF files (clean coordinate files) (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. Directory ./
-dcffile This option specifies the name of the DCF file (domain classification file) (input). A 'domain classification file' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL-like). The files are generated by using SCOPPARSE and CATHPARSE. Domain sequence information can be added to the file by using DOMAINSEQS. Input file Required
-threshold This option specifies the threshold contact distance. Any numeric value 1.0
[-outfile]
(Parameter 3)
This option specifies the name of the output file. Output file SITES.con
-logfile This option specifies the name of the log file. Output file SITES.log
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
-dicfile This option specifies the dictionary of heterogen groups in PDB. This file is generated by using HETPARSE and is part of the EMBOSS distribution. Data file Ehet.dat
-vdwfile This option specifies the name of the data file with van der Waals radii for atoms in amino acid residues. This file is part of the EMBOSS distribution. Data file Evdw.dat

6.2 EXAMPLE SESSION

An example of interactive use of SITES is shown below. Under development, no final example yet Protein CCF files were read from /testdata/sites/in and domain CCF files from /testdata/sites. Ligand definitions were taken from Ehet.dat and domain definitions were taken from the DCF file testdata/sites/in/sites.dcf. A CON file of ligand-residue contacts for all domains defined in the DCF file and present in the protein CCF files, was written to testdata/sites/out/SITES.con. van der Waals radii were taken from the emboss data file Evdw.dat and the default contact distance of 1 Angstrom was used to determine contacts. The log file testdata/sites/out/SITES.log was written. The file extensions of all input and output files were specified in the ACD file.


7.0 KNOWN BUGS & WARNINGS

None.


8.0 NOTES

Types of contact
LI records are used for contacts to ligands (as defined above). In CONTACTS and INTERFACE output, SM records are used for contacts between either either side-chain or main-chain atoms. 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.

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.
Dictionary of heterogen groups A file of the dictionary of heterogen groups in PDB. HETPARSE N.A.



9.0 DESCRIPTION

Knowledge of the physical contacts that amino acid residues make with protein ligands is required for several different analyses. SITES calculates residue-ligand contact data from protein CCF files (clean coordinate files) and organises the data according to domains taken from a DCF file (domain classification file). None


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 nameDescription
aaindexextractExtract data from AAINDEX
allversusallDoes an all-versus-all global alignment for each set of sequences in an input directory and writes files of sequence similarity values
cathparseReads raw CATH classification files and writes DCF file (domain classification file)
cutgextractExtract data from CUTG
domainerReads CCF files (clean coordinate files) for proteins and writes CCF files for domains, taken from a DCF file (domain classification file)
domainnrRemoves redundant domains from a DCF file (domain classification file). The file must contain domain sequence information, which can be added by using DOMAINSEQS
domainseqsAdds sequence records to a DCF file (domain classification file)
domainsseAdds secondary structure records to a DCF file (domain classification file)
hetparseConverts raw dictionary of heterogen groups to a file in EMBL-like format
pdbparseParses PDB files and writes CCF files (clean coordinate files) for proteins
pdbplusAdd residue solvent accessibility and secondary structure data to a CCF file (clean coordinate file) for a protein or domain
pdbtospConvert raw swissprot:PDB equivalence file to EMBL-like format
printsextractExtract data from PRINTS
prosextractBuilds the PROSITE motif database for patmatmotifs to search
rebaseextractExtract data from REBASE
scopparseReads raw SCOP classification files and writes a DCF file (domain classification file)
seqnrRemoves redundancy from DHF files (domain hits files) or other files of sequences
ssematchSearches a DCF file (domain classification file) for secondary structure matches
tfextractExtract data from TRANSFAC



12.0 DIAGNOSTIC ERROR MESSAGES

SITES generates a log file an excerpt of which is shown below. The file contains a line for each protein CCF that was read containing diagnostic information is given (in case of difficulty email Jon Ison, jison@hgmp.mrc.ac.uk).

Figure 2 Excerpt from an INTERFACE log file
Excerpt of log file
CCF: 000_testdata_new/sites/in/1cs4.ccf	HETS:YES	NHETS:7	SCOP:YES	NDOMS: 1
CCF: 000_testdata_new/sites/in/1ii7.ccf	HETS:YES	NHETS:5	SCOP:YES	NDOMS: 1



13.0 AUTHORS

Waqas Awan (wawan@rfcgr.mrc.ac.uk)
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, Bleasby A.J. 2000. EMBOSS - The European Molecular Biology Open Software Suite. Trends in Genetics, 15:276-278. See also http://www.uk.embnet.org/Software/EMBOSS

14.1 Other useful references