PDB FORMAT Version 2.3
Main Index

Connectivity Section

This section provides information on chemical connectivity. LINK, HYDBND, SLTBRG, and CISPEP are found in the Connectivity Annotation section.



The CONECT records specify connectivity between atoms for which coordinates are supplied. The connectivity is described using the atom serial number as found in the entry. CONECT records are mandatory for HET groups (excluding water) and for other bonds not specified in the standard residue connectivity table which involve atoms in standard residues. These records are generated by the PDB.

Record Format

 1 -  6       Record name     "CONECT"
 7 - 11       Integer         serial        Atom serial number
12 - 16       Integer         serial        Serial number of bonded atom
17 - 21       Integer         serial        Serial number of bonded atom
22 - 26       Integer         serial        Serial number of bonded atom
27 - 31       Integer         serial        Serial number of bonded atom


  • Intra-residue connectivity within non-standard (HET) residues (excluding water) is presented on the CONECT records.
  • Inter-residue connectivity of HET groups to standard groups (including water) or to other HET groups are represented on the CONECT records.
  • Disulfide bridges specified in the SSBOND records have corresponding CONECT records.
  • No differentiation is made between donor and acceptor for hydrogen bonds.
  • No differentiation is made between atoms with excess negative or positive charge.
  • Atoms specified in the connectivity are presented by their serial numbers as found in the entry.
  • All atoms connected to the atom with serial number in columns 7 - 11 are listed in the remaining fields of the record.
  • If more than four fields are required for non-hydrogen and nonsalt-bridge bonds, a second CONECT record with the same atom serial number in columns 7 - 11 will be used.
  • These CONECT records occur in increasing order of the atom serial numbers they carry in columns 7 - 11. The target-atom serial numbers carried on these records also occur in increasing order.
  • The connectivity list given here is redundant in that each bond indicated is given twice, once with each of the two atoms involved specified in columns 7 - 11.
  • For nucleic acids, Watson-Crick hydrogen bonds between bases may be listed, but this is optional.
  • For hydrogen bonds, when the hydrogen atom is present in the coordinates, PDB generates a CONECT record between the hydrogen atom and its acceptor atom.
  • For NMR entries, CONECT records for all models are generated describing heterogen connectivity and others for LINK records.
  • Verification/Validation/Value Authority Control

    Connectivity is checked for unusual bond lengths.

    Relationships to Other Record Types

    CONECT records must be present in an entry that contains either non-standard groups or disulfide bonds.


             1         2         3         4         5         6         7
    CONECT 1179  746 1184 1195 1203                    
    CONECT 1179 1211 1222                              
    CONECT 1021  544 1017 1020 1022 1211 1222      1311

    Known Problems

    CONECTs to atoms whose coordinates are not in the entry (e.g., symmetry-generated) are not given.

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