Sequence file

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Contents

Basic format

GLY    11
SER    12
ILE    13
PRO    14
CYSS   15
LEU    16
LEU    17
SER    18
cPRO   19
TRP    20
SER    21
GLU    22
TRP    23
CYSS   24

This sequence consists of 14 amino acid residues that are numbered consequtively 11-24.

Residue names are case-sensitive.

Reduced cysteine residues are denoted by CYS, oxidized cystine residues (involved in disulfide bridges) are denoted by CYSS, if the standard residue library is used.

By default, OMEGA torsion angles, e.g. in the peptide bonds in proteins, are kept fixed in the trans position, ω = 180°. Optionally, OMEGA angles can be fixed in the cis position, ω = 0°, by adding a lower case 'c' in front of the residue name, as in the case of PRO 19 above.

Equivalent forms

Residue numbers can be omitted if they are equal to the residue number of the previous residue plus 1. The first residue number can be omitted if it is equal to 1.

GLY    11
SER
ILE
PRO
CYSS
LEU
LEU
SER
cPRO
TRP
SER
GLU
TRP
CYSS

Multiple residues can be written on a line:

GLY 11 SER ILE PRO CYSS LEU LEU SER cPRO TRP SER GLU TRP CYSS

Multiple molecules

Multiple molecules must be separated by a stretch of "invisible" linker residues:

GLY  11 SER ILE PRO CYSS LEU LEU SER cPRO TRP SER GLU TRP CYSS      # molecule 1
PL   51 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LL2 LP  # linker
GLY 111 SER ILE PRO CYSS LEU LEU SER cPRO TRP SER GLU TRP CYSS      # molecule 2

The standard residue library provides the following linker residues:

  • PL: Linker from a protein amino acid residue to a linker residue
  • LL: Linker residue with a virtual bond length of 1 Å
  • LL2: Linker residue with a virtual bond length of 2 Å
  • LL5: Linker residue with a virtual bond length of 5 Å
  • LP: Linker from a linker residue to a protein amino acid residue

Non-standard covalent links

A non-standard covalent link can be declared by a link statement. For instance, for a cyclic peptide:

GLY    11
SER    12
ILE    13
PRO    14
CYSS   15
LEU    16
LEU    17
SER    18
cPRO   19
TRP    20
SER    21
GLU    22
TRP    23
CYSS   24

link N 11 C 24

The purpose of the link statement is to eliminate the steric repulsion between the two covalently bound atoms and the atoms directly bound to them. The link statement will not enforce the formation of a covalent bond between the two atoms. This must be made by explicit distance constraints.

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