Extended PROSITE Syntax for Residue Groups

The syntax for defining a residue group is an extended form of the PROSITE syntax, which allows you to specify secondary structure and some properties:

• Standard IUPAC one-letter (upper case) codes are used for all amino acids.

• Lower case x is used for any amino acid.

• Each element of a pattern is separated with a - symbol.

• Residues that are permitted at a given position are listed between square brackets, e.g. [ACT] means one of Ala, Cys, or Thr, or in other words, only Ala, Cys, or Thr can appear at this position.

• Residues that are not permitted at a given position are listed between curly brackets, e.g. {GP} means not Gly and not Pro, or in other words, any residue but Gly or Pro can appear at this position.

• Repetition is indicated using parentheses, e.g. A(3) means Ala-Ala-Ala, G(2,4) means between 2 to 4 Gly residues.

• The following lower case characters can be used for residue types:

  • a—acidic residue: [DE]
  • b—basic residue: [KR]
  • o—hydrophobic residue: [ACFILPWVY]
  • p—aromatic residue: [WYF]

• The following lower case characters can be used to restrict residue types by property:

  • s—solvent-exposed residue
  • h—residue in helical region
  • e—residue in extended (beta strand) region
  • f—flexible residue, defined as having a B-factor above the average over all residues

  These four characters can be appended to a residue type to restrict the type of residue, e.g. Ah means Ala in a helical region.

Some examples of valid and invalid patterns are given below, with comments.