5. Secondary Structure Section

The secondary structure section of a PDB file describes helices, sheets, and turns found in protein and polypeptide structures.



HELIX records are used to identify the position of helices in the molecule. Helices are both named and numbered. The residues where the helix begins and ends are noted, as well as the total length.

Record Format

 1 -  6        Record name     "HELIX "

 8 - 10        Integer         serNum          Serial number of the helix.
                                               This starts at 1 and increases

12 - 14        LString(3)      helixID         Helix identifier.  In addition
                                               to a serial number, each helix is
                                               given an alphanumeric character
                                               helix identifier.

16 - 18        Residue name    initResName     Name of the initial residue.

20             Character       initChainID     Chain identifier for the chain
                                               containing this helix.

22 - 25        Integer         initSeqNum      Sequence number of the initial

26             AChar           initICode       Insertion code of the initial

28 - 30        Residue name    endResName      Name of the terminal residue of
                                               the helix.

32             Character       endChainID      Chain identifier for the chain
                                               containing this helix.

34 - 37        Integer         endSeqNum       Sequence number of the terminal

38             AChar           endICode        Insertion code of the terminal

39 - 40        Integer         helixClass           Helix class (see below).

41 - 70        String          comment         Comment about this helix.

72 - 76        Integer         length          Length of this helix.


* Additional HELIX records with different serial numbers and identifiers occur if more than one helix is present.

* The initial residue is the N-terminal residue of the helix.

* Helices are classified as follows:

           TYPE OF HELIX             CLASS NUMBER (COLUMNS 39 - 40)
     Right-handed alpha (default)                1
     Right-handed omega                          2
     Right-handed pi                             3
     Right-handed gamma                          4
     Right-handed 310                            5
     Left-handed alpha                           6
     Left-handed omega                           7
     Left-handed gamma                           8
     27 ribbon/helix                             9
     Polyproline                                10

Verification/Validation/Value Authority Control

HELIX records are now being generated automatically by PDB using the Kabsch and Sander algorithm [Kabsch and Sander, Biopolymers 22: 2577-2637 (1983)], although they may be provided by the depositor instead. PDB verifies that named residues exist in the ATOM records.

Relationships to Other Record Types

There may be related information in the REMARKs.


         1         2         3         4         5         6         7
HELIX    1  HA GLY A   86  GLY A   94  1                                   9
HELIX    2  HB GLY B   86  GLY B   94  1                                   9

Known Problems

PDB is considering addition of some new information related to HELIX, in order to present more complete structural information. Please comment on the suggestion of adding a new record which would present the various domain types found in the molecule, e.g., Residues 12 --> 120: alpha/beta.