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