Connectivity Annotation Section

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

SSBOND

Overview

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

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 oper for 1st resid
67 - 72        SymOP           sym2         Symmetry oper for 2nd resid

Details

Bond distances between the sulfur atoms must be close to expected values.

sym1 and sym2 are given as blank when the identity operator (and no cell translation) is to be applied to the residue.

Verification/Validation/Value Authority Control

PDB 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            
123456789012345678901234567890123456789012345678901234567890123456789012          
SSBOND   1 CYS E   48    CYS E   51                          2555                 
SSBOND   2 CYS E  252    CYS E  285

SSBOND   1 CYS A  250    CYS A  277                          1555   1555
SSBOND   2 CYS B  250    CYS B  277                          1555   1555

Known Problems

If SG of cysteine is disordered then there are possible alternate linkages. PDB's 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. 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 for 1st atom.
67 - 72      SymOP            sym2         Symmetry operator for 2nd atom.

Details

The atoms involved in bonds between HET groups or between a HET group and standard residue are listed.

Interresidue 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 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.

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
123456789012345678901234567890123456789012345678901234567890123456789012
LINK         O1  DDA     1                 C3  DDL     2      
LINK        MN    MN   391                 OE2 GLU   217            2565

LINK         C   LYS A 296                 N   CME A 297     1555   1555
LINK         C   CME A 297                 N   MET A 298     1555   1555
LINK        CA    CA A 997                 O   GLN A 262     1555   1555
LINK        CA    CA A 997                 O   TRP A 240     1555   1555
LINK        CA    CA A 997                 O   HOH Z 169     1555   1555
LINK        CA    CA A 997                 O   PRO A 249     1555   1555

CISPEP

Overview

CISPEP records specify the prolines and other peptides found to be in the cis conformation. This record replaces the use of footnote records to list cis peptides.

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       Measure of the angle in degrees.

Details

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

Each cis peptide is listed on a separate line, with an incrementally ascending sequence number.

Verification/Validation/Value Authority Control

PDB generates these records automatically.

Relationships to Other Record Types

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

Example

         1         2         3         4         5         6         7            
1234567890123456789012345678901234567890123456789012345678901234567890            
CISPEP   1 GLY A  116    GLY A  117          0        18.50                 
CISPEP   2 THR D   92    PRO D   93          0       359.80

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