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                                 SISC

                Sequence Identity & Structure Comparison

                            version 12/1999


 Adam Zemla 
 Email: adamz@llnl.gov

 THE WEB BASED FACILITY IS UNDER CONSTRUCTION!

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 The following data files are updated every week:

   - PDB_list             The list of current set of structures downloaded 
                          from Protein Data Bank (PDB files).

   - SEQRES.all_list      The list of all chains of sequences of amino acids
                          that are extracted from SEQRES records of PDB files.

   - SEQRES.unique        The set of unique residue sequences. The set of 
                          basic (primitive) clusters of sequences.

   - SEQRES.unique_list   The list of unique residue sequences (clusters).

   - PDB_seq_ss.all       The set of all residue sequences extracted from
                          ATOM records (coordinates) of PDB files. Each 
                          residue sequence (chain) is reported together with 
                          its secondary structure element assignment generated 
                          by DSSP program.


The DSSP code 

      H = alpha helix 
      I = 5 helix (pi helix) 
      G = 3-helix (3/10 helix) 

      E = extended strand, participates in beta ladder 
      B = residue in isolated beta-bridge 

      T = hydrogen bonded turn 
      S = bend 
      C = others 

--------------- FILES FORMAT DESCRIPTION --------------------------------------

1. Example of the SEQRES.unique file:

>Cluster_name  Cluster_sequence_length  number_of_chains
# si chain_name  percent_of_coordinates  pdb_length  resolution
SequenceOfAminoAcidsExtractedFromSEQRESrecords

>1boy     219   6
# si  1boy       96.35   211     2.20
# si  1tfh_A     92.24   202     2.40
# si  1ahw_C     91.32   200     3.00
# si  1ahw_F     91.32   200     3.00
# si  1jps_T     91.32   200     1.85
# si  1tfh_B     83.11   182     2.40
SGTTNTVAAYNLTWKSTNFKTILEWEPKPVNQVYTVQISTKSGDWKSKCF
YTTDTECDLTDEIVKDVKQTYLARVFSYPAGNVESTGSAGEPLYENSPEF
TPYLETNLGQPTIQSFEQVGTKVNVTVEDERTLVRRNNTFLSLRDVFGKD
LIYTLYYWKSSSSGKKTAKTNTNEFLIDVDKGENYCFSVQAVIPSRTVNR
KSTDSPVECMGQEKGEFRE


2. Example of the PDB_seq_ss.all file:

>Chain_name  cluster_name  cluster_sequence_length
# xxxxx: xxxxx
#  ---- " ----
# xxxxx: xxxxx
SequenceOfAminoAcidsExtractedFromRecords-ATOM
TheSecondaryStructureElementAssignmentBy-DSSP

>1tfh_A  1boy    219
# Header:     COAGULATION FACTOR
# Title:      EXTRACELLULAR DOMAIN OF HUMAN TISSUE FACTOR
# Keywds:     BLOOD COAGULATION,  TISSUE FACTOR,  COAGULATION FACTOR,
# Keywds:     GLYCOPROTEIN
# Date:       10-APR-97
# Revdate:    19-AUG-98
# Resolution:   2.40
# Residues:    92.24  202  203
# Author:     M.HUANG, R.SYED, E.A.STURA, M.J.STONE, R.S.STEFANKO, W.RUF,
# Author:     T.S.EDGINGTON, I.A.WILSON
# Compnd:     MOL_ID: 1;
# Compnd:     MOLECULE: HUMAN TISSUE FACTOR;
# Compnd:     CHAIN: A,  B;
# Compnd:     FRAGMENT: EXTRACELLULAR DOMAIN;
# Compnd:     SYNONYM: TF,  THROMBOPLASTIN,  COAGULATION FACTOR III;
# Compnd:     ENGINEERED: YES
# Cryst1:      64.393   85.828  112.901  90.00  90.00  90.00 P 21 21 21    8
NTVAAYNLTWKSTNFKTILEWEPKPVNQVYTVQISTKSGDWKSKCFYTTD
CCCCCEEEEEEEETTEEEEEEECCCSSEEEEEEEEETTSCCEEEEEEESC

TECDLTDEIVKDVKQTYLARVFSYPAGNV-AGEPLYENSPEFTPYLETNL
SEEECHHHHTTCTTSCEEEEEEEEECSCC-CCSCEEEECCCBCHHHHSBC

GQPTIQSFEQVGTKVNVTVEDERTLVRRNNTFLSLRDVFGKDLIYTLYYW
CCCCEEEEEEETTEEEEEECCCEEEEEETTEEEEHHHHHGGGCEEEEEEE

KSSSSGKKTAKTNTNEFLIDVDKGENYCFSVQAVIPSRTVNRKSTDSPVE
ETTCCCCEEEEESSSEEEEECCTTCCEEEEEEEECTTCSSSCBCCCCCCE

CMG
ECC