Brief manual on the database ConfDB (Database on local conformations of protein chains ("conformons"))

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

Introduction

ConfDB contain structural information on conformational properties of short fragments (9 aa in length) in 3D structures of C.elegans proteins.

The detailed description of the fields is given below.

Complete list of the fields

CONFDB_RES

PeptideIdentifier, ProteinIdentifier, ClusterIdentifier, StartStructure, StartSequence

Fields description

PeptideIdentifier

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

ProteinIdentifier

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

ClusterIdentifier

Link to the environment class reference in the CONFDB_CLUST table (the identifier of the corresponding entry in CONFDB_CLUST)

StartStructure

Peptide start position in PDB structure

StartSequence

Peptide start position in protein sequence

CONFDB_PROT

ProteinIdentifier, PDBID, ChainSize, Peptide

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)

Peptide

List of peptides, members of this protein (residue identifiers in CONFDB_RES table)

CONFDB_CLUST

ClusterIdentifier, ClusterSize, Peptide

Fields description

ClusterIdentifier

Unique identifier of an conformon cluster. It has the format CONFCLN, where N is a number

ClusterSize

Size of cluster (number of environments of this class)

Peptide

List of peptides, members of this protein (residue identifiers in CONFDB_RES table)