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