Connectivity Section

This section provides information on atomic connectivity. LINK, SSBOND, and CISPEP are found in the Connectivity Annotation section.

CONECT

Overview

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

Record Format

COLUMNS       DATA  TYPE      FIELD        DEFINITION
-------------------------------------------------------------------------
 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

Details

CONECT records are present for:

- Intra-residue connectivity within  non-standard (HET) residues (excluding water).
- Inter-residue connectivity of HET  groups to standard groups (including water) or to other HET groups. 
- Disulfide bridges specified in the  SSBOND records have corresponding records.

No differentiation is made between atoms with delocalized charges (excess negative or positive charge).
Atoms specified in the CONECT records have the same numbers as given in the coordinate section.
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 non-salt bridges, 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 hydrogen bonds, when the hydrogen atom is present in the coordinates, a CONECT record between the hydrogen atom and its acceptor atom is generated.
For NMR entries, CONECT records for one model are generated describing heterogen connectivity and others for LINK records assuming that all models are homogeneous models.

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.

Example

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
CONECT 1179  746 1184 1195 1203                    
CONECT 1179 1211 1222                              
CONECT 1021  544 1017 1020 1022

Known Problems

CONECT records involving atoms for which the coordinates are not present in the entry (e.g., symmetry-generated) are not given.

CONECT records involving atoms for which the coordinates are missing due to disorder, are also not provided.