Secondary Structure Section

The secondary structure section of a PDB formatted file describes helices and sheets 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

                                     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

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  


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