Secondary Structure Section

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

HELIX

Overview

HELIX records are used to identify the position of helices in the molecule. Helices are named, numbered, and classified by type. 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 of the helix is the N-terminal residue.
Helices are classified as follows:

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

Relationships to Other Record Types

There may be related information in the REMARKs.

Example

     1     2     3     4    5     6     7     8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
HELIX  1 HA GLY A  86 GLY A  94 1                  9  
HELIX  2 HB GLY B  86 GLY B  94 1                  9 
 
HELIX  21 21 PRO J 385 LEU J 388 5                  4  
HELIX  22 22 PHE J 397 PHE J 402 5                  6

SHEET

Overview

SHEET records are used to identify the position of sheets in the molecule. Sheets are both named and numbered. The residues where the sheet begins and ends are noted.

Record Format

COLUMNS    DATA TYPE   FIELD     DEFINITION
-------------------------------------------------------------------------------------
 1 - 6    Record name  "SHEET "
 8 - 10    Integer    strand     Strand number which starts at 1 for each
 strand within a sheet and increases by one.
12 - 14    LString(3)  sheetID    Sheet identifier.
15 - 16    Integer    numStrands   Number of strands in sheet.
18 - 20    Residue name initResName  Residue name of initial residue.
22      Character   initChainID  Chain identifier of initial residue 
 in strand. 
23 - 26    Integer    initSeqNum   Sequence number of initial residue
 in strand.
27      AChar     initICode   Insertion code of initial residue
 in strand.
29 - 31    Residue name endResName   Residue name of terminal residue.
33      Character   endChainID   Chain identifier of terminal residue.
34 - 37    Integer    endSeqNum   Sequence number of terminal residue.
38      AChar     endICode    Insertion code of terminal residue.
39 - 40    Integer    sense     Sense of strand with respect to previous
 strand in the sheet. 0 if first strand,
 1 if parallel,and -1 if anti-parallel.
42 - 45    Atom     curAtom    Registration. Atom name in current strand.
46 - 48    Residue name curResName   Registration. Residue name in current strand
50      Character   curChainId  Registration. Chain identifier in
 current strand.
51 - 54    Integer    curResSeq   Registration. Residue sequence number
 in current strand.
55      AChar     curICode    Registration. Insertion code in
 current strand.
57 - 60    Atom     prevAtom    Registration. Atom name in previous strand.
61 - 63    Residue name prevResName  Registration. Residue name in
 previous strand.
65       Character   prevChainId  Registration. Chain identifier in
 previous strand.
66 - 69    Integer    prevResSeq   Registration. Residue sequence number
 in previous strand.
70       AChar     prevICode   Registration. Insertion code in
 previous strand.

Details

The initial residue for a strand is its N-terminus. Strand registration information is provided in columns 39 - 70. Strands are listed starting with one edge of the sheet and continuing to the spatially adjacent strand.
The sense in columns 39 - 40 indicates whether strand n is parallel (sense = 1) or anti-parallel (sense = -1) to strand n-1. Sense is equal to zero (0) for the first strand of a sheet.
The registration (columns 42 - 70) of strand n to strand n-1 may be specified by one hydrogen bond between each such pair of strands. This is done by providing the hydrogen bonding between the current and previous strands. No register information should be provided for the first strand.
Split strands, or strands with two or more runs of residues from discontinuous parts of the amino acid sequence, are explicitly listed. Detail description can be included in the REMARK 700 .

Relationships to Other Record Types

If the entry contains bifurcated sheets or beta-barrels, the relevant REMARK 700 records must be provided. See the REMARK section for details.

Examples

     1     2     3     4     5     6     7     8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
SHEET  1  A 5 THR A 107 ARG A 110 0
SHEET  2  A 5 ILE A 96 THR A 99 -1 N LYS A 98  O THR A 107
SHEET  3  A 5 ARG A 87 SER A 91 -1 N LEU A 89  O TYR A 97
SHEET  4  A 5 TRP A 71 ASP A 75 -1 N ALA A 74  O ILE A 88
SHEET  5  A 5 GLY A 52 PHE A 56 -1 N PHE A 56  O TRP A 71
SHEET  1  B 5 THR B 107 ARG B 110 0
SHEET  2  B 5 ILE B 96 THR B 99 -1 N LYS B 98  O THR B 107
SHEET  3  B 5 ARG B 87 SER B 91 -1 N LEU B 89  O TYR B 97
SHEET  4  B 5 TRP B 71 ASP B 75 -1 N ALA B 74  O ILE B 88
SHEET  5  B 5 GLY B 52 ILE B 55 -1 N ASP B 54  O GLU B 73

The sheet presented as BS1 below is an eight-stranded beta-barrel. This is represented by a nine-stranded sheet in which the first and last strands are identical.

SHEET  1 BS1 9 VAL  13 ILE  17 0                
SHEET  2 BS1 9 ALA  70 ILE  73 1 O TRP  72  N ILE  17 
SHEET  3 BS1 9 LYS 127 PHE  132 1 O ILE  129  N ILE  73 
SHEET  4 BS1 9 GLY 221 ASP  225 1 O GLY  221  N ILE  130 
SHEET  5 BS1 9 VAL 248 GLU  253 1 O PHE  249  N ILE  222 
SHEET  6 BS1 9 LEU 276 ASP  278 1 N LEU  277  O GLY  252 
SHEET  7 BS1 9 TYR 310 THR  318 1 O VAL  317  N ASP  278 
SHEET  8 BS1 9 VAL 351 TYR  356 1 O VAL  351  N THR  318 
SHEET  9 BS1 9 VAL  13 ILE  17 1 N VAL  14  O PRO  352

The sheet structure of this example is bifurcated. In order to represent this feature, two sheets are defined. Strands 2 and 3 of BS7 and BS8 are identical.

SHEET  1 BS7 3 HIS 662 THR  665 0                
SHEET  2 BS7 3 LYS 639 LYS  648 -1 N PHE  643  O HIS  662 
SHEET  3 BS7 3 ASN 596 VAL  600 -1 N TYR  598  O ILE  646 
SHEET  1 BS8 3 ASN 653 TRP  656 0                
SHEET  2 BS8 3 LYS 639 LYS  648 -1 N LYS  647  O THR  655 
SHEET  3 BS8 3 ASN 596 VAL  600 -1 N TYR  598  O ILE  646