The secondary structure section of a PDB file describes helices, sheets, and turns found in protein and polypeptide structures.
Overview
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
COLUMNS DATA TYPE FIELD DEFINITION --------------------------------------------------------------------------------- 1 - 6 Record name "HELIX " 8 - 10 Integer serNum Serial number of the helix. This starts at 1 and increases incrementally. 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 residue. 26 AChar initICode Insertion code of the initial residue. 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 residue. 38 AChar endICode Insertion code of the terminal residue. 39 - 40 Integer helixClass Helix class (see below). 41 - 70 String comment Comment about this helix. 72 - 76 Integer length Length of this helix.
Details
* 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.
Example
1 2 3 4 5 6 7 1234567890123456789012345678901234567890123456789012345678901234567890123456 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.