Brief manual on the database DCS (Database on Coordination Spheres)

Enter the database DCS here. It works under the SRS system.

Introduction

DCS contain structural and physico-chemical information on amino acid residue coordination spheres in protein 3D structures. Current release contain data from DNA-binding proteins structures selection (46 non-homologous protein chains). DCS database contains of three tables, related to residues data (DCS_RES), protein data (DCS_PROT) and environment class data.

The detailed description of the fields is given below.

Complete list of the fields

DCS_RES

ResidueIdentifier, ProteinIdentifier, ClusterIdentifier, ResidueName, AminoAcid, PDBIndex, SequenceIndex, SecondaryStructure, SolventAccessibility, DNAContact, CoordinationNumber

Fields description

ResidueIdentifier

Unique identifier of an residue entry. It has the format RESN, where N is a number

ProteinIdentifier

Link to the protein reference in the DCS_PROT table (the identifier of the corresponding entry in DCS_PROT )

ClusterIdentifier

Link to the environment class reference in the DCS_CLUST table (the identifier of the corresponding entry in DCS_CLUST  having the form ENVCLN)

ResidueName

Name of the residue. It has the format A_N, where A is amino acid type, N is a number

AminoAcid

Type of amino acid in 1-letter code

PDBIndex

Index of residue in PDB structure, ranges from 1 to number of residues in PDB entry

SequenceIndex

Index of residue in protein sequence

SecondaryStructure

Secondary structure according to DSSP (H = alpha helix, B = residue in isolated beta-bridge, E = extended strand, participates in beta ladder, G = 3-helix (3/10 helix), I = 5 helix (pi helix), T = hydrogen bonded turn, S = bend )

SolventAccessibility

Solvent accessibility according to DSSP

DNAContact

If this field is equal to 1, then residue is in contact with DNA. If this field is equal to 0, then residue is not in contact. If if 0, DNAContact=-1, then information not available (no DNA is presented in corresponded PDB file)

CoordinationNumber

Coordination number (number of contact residues within 7 A distance cutoff)

DCS_PROT

ProteinIdentifier, PDBID, ProteinSize, ResidueList

Fields description

ProteinIdentifier

Unique identifier of an protein entry. It has the format PROTN, where N is a number

PDBID

Reference to protein structure in PDB (format is ID:Chain)

ResidueList

List of residues, members of this protein (residue identifiers in DCS_RES table)

DCS_CLUST

ClassIdentifier, ClassSize, MeanAccessibility, Volume, Polarity, IsoelectricPoint, Hydrophobicity, MeanSolventAcc, ResidueList

Fields description

ClassIdentifier

Unique identifier of an environment class. It has the format ENVCLN, where N is a number

ClassSize

Size of class (number of environments of this class)

MeanAccessibility

Mean DSSP accessibility for central residues

Volume, Polarity, IsoelectricPoint, Hydrophobicity, MeanSolventAcc

Mean values for corresponding physico-chemical properties of environment residues.

ResidueList

List of residues, members of this protein (residue identifiers in DCS_RES table)