Connectivity Annotation Section

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

SSBOND (updated)

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 (updated)

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