Connectivity Annotation Section

The connectivity annotation section allows the depositors to specify the existence and location of disulfide bonds and other linkages.

SSBOND

The SSBOND record identifies each disulfide bond in protein and polypeptide structures by identifying the two residues involved in the bond.

The disulfide bond distance is included after the symmetry operations at the end of the SSBOND record.

Record Format

COLUMNS    DATA TYPE   FIELD      DEFINITION
--------------------------------------------------------------------------------
 1 - 6    Record name  "SSBOND"
 8 - 10    Integer    serNum      Serial number.
12 - 14    LString(3)   "CYS"  Residue name.
16       Character   chainID1     Chain identifier.
18 - 21    Integer    seqNum1     Residue sequence number.
22       AChar     icode1      Insertion code.
26 - 28    LString(3)   "CYS"  Residue name.
30       Character   chainID2     Chain identifier.
32 - 35    Integer    seqNum2     Residue sequence number.
36       AChar     icode2      Insertion code.
60 - 65    SymOP     sym1       Symmetry operator for residue 1.
67 - 72    SymOP     sym2       Symmetry operator for residue 2.
74 – 78    Real(5.2)   Length      Disulfide bond distance

Details

Bond distances between the sulfur atoms must be close to expected value.
sym1 and sym2 are right justified and are always given even when identity operator (no cell translation) is to be applied to the residue.

Verification/Validation/Value Authority Control

wwPDB processing programs generate these records automatically.

Relationships to Other Record Types

CONECT records are generated for the disulfide bonds when SG atoms of both cysteines are present in the coordinate records.

Example

     1     2     3    4     5     6     7     8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
SSBOND  1 CYS A  6  CYS A 127             1555  1555 2.03 
SSBOND  2 CYS A  30  CYS A 115             1555  1555 2.07 
SSBOND  3 CYS A  64  CYS A 80             1555  1555 2.06 
SSBOND  4 CYS A  76  CYS A 94             1555  1555 2.04

Known Problems

If SG of cysteine is disordered then there are possible alternate linkages. wwPDB practice is to put together all possible SSBOND records. This is problematic because the alternate location identifier is not specified in the SSBOND record.

LINK

Overview

The LINK records specify connectivity between residues that is not implied by the primary structure. Connectivity is expressed in terms of the atom names. They also include the distance associated with the each linkage following the symmetry operations at the end of each record.

This record supplements information given in CONECT records and is provided here for convenience in searching.

Record Format

COLUMNS     DATA TYPE   FIELD      DEFINITION
------------------------------------------------------------------------------------
 1 - 6     Record name  "LINK "
13 - 16     Atom      name1      Atom name.
17       Character   altLoc1     Alternate location indicator.
18 - 20     Residue name  resName1    Residue name.
22       Character   chainID1    Chain identifier.
23 - 26     Integer    resSeq1     Residue sequence number.
27       AChar     iCode1     Insertion code.
43 - 46     Atom      name2      Atom name.
47       Character   altLoc2     Alternate location indicator.
48 - 50     Residue name  resName2    Residue name.
52       Character   chainID2    Chain identifier.
53 - 56     Integer    resSeq2     Residue sequence number.
57       AChar     iCode2     Insertion code.
60 - 65     SymOP     sym1      Symmetry operator atom 1.
67 - 72     SymOP     sym2      Symmetry operator atom 2.
74 – 78     Real(5.2)   Length     Link distance

Details

The atoms involved in bonds between HET groups or between a HET group and standard residue are listed.
Inter-residue linkages not implied by the primary structure are listed (e.g., reduced peptide bond).
Non-standard linkages between residues, e.g., side-chain to side-chain, are listed.
Each LINK record specifies one linkage.
These records do not specify connectivity within a HET group (see CONECT) or disulfide bridges (see SSBOND).
sym1 and sym2 are right justified and are given as blank when the identity operator (and no cell translation) is to be applied to the atom.

- For NMR entries, only one set (or model) of LINK records will be supplied. 
- Coordinate bonds are also listed as LINKs

Verification/Validation/Value Authority Control

The distance between the pair of atoms listed must be consistent with the bonding.

Relationships to Other Record Types

CONECT records are generated from LINKs when both atoms are present in the entry. If symmetry operators are given to generate one of the residues involved in the bond, REMARK 290 defines the symmetry transformation.

Example

     1     2     3     4     5     6     7     8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
LINK     O  GLY A 49        NA  NA A6001  1555  1555 2.98 
LINK     OG1 THR A 51        NA  NA A6001  1555  1555 2.72 
LINK     OD2 ASP A 66        NA  NA A6001  1555  1555 2.72 
LINK     NE ARG A 68        NA  NA A6001  1555  1555 2.93 
LINK NE ARG A 68 NA NA A6001 1555 1555 2.93
LINK C21 2EG A 7 C22 2EG B 19 1555 1555 1.56

CISPEP

Overview

CISPEP records specify the prolines and other peptides found to be in the cis conformation. Each cis peptide is listed on a separate line, with a consecutive numbering sequence.

Record Format

COLUMNS    DATA TYPE  FIELD     DEFINITION
-------------------------------------------------------------------------
 1 - 6    Record name  "CISPEP"
 8 - 10    Integer    serNum    Record serial number.
12 - 14    LString(3)  pep1     Residue name.
16      Character   chainID1   Chain identifier.
18 - 21    Integer    seqNum1    Residue sequence number.
22      AChar     icode1    Insertion code.
26 - 28    LString(3)  pep2     Residue name.
30      Character   chainID2   Chain identifier.
32 - 35    Integer    seqNum2    Residue sequence number.
36      AChar     icode2    Insertion code.
44 - 46    Integer    modNum    Identifies the specific model.
54 - 59    Real(6.2)   measure    Angle measurement in degrees.

Details

Cis peptides are those with omega angles of 0°±30°. Deviations larger than 30° are listed in REMARK 500.

Verification/Validation/Value Authority Control

These records are generated automatically.

Relationships to Other Record Types

Peptide bonds which deviate significantly from either the cis or trans conformation are annotated in REMARK 500.

Example

 1     2     3     4     5     6     7     8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
CISPEP  1 SER A 58  GLY A  59     0    20.91  
CISPEP  1 GLY A 116  GLY A 117     0    18.50 
CISPEP  1 MET A  1  SER A  2     0    -3.69