Skip to content

Commit

Permalink
Add hydroxyproline note
Browse files Browse the repository at this point in the history
  • Loading branch information
@alchemistmatt
alchemistmatt committed Mar 15, 2024
1 parent 4e534eb commit dd296a8
Showing 1 changed file with 24 additions and 22 deletions.
46 changes: 24 additions & 22 deletions src/main/java/edu/ucsd/msjava/msutil/AminoAcid.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -275,30 +275,32 @@ public int hashCode() {
// }

private static Hashtable<Character, AminoAcid> residueMap;
// Static table containing Predefined Amino Acids
// Static table containing Predefined Amino Acids, sorted by increasing mass
private static final AminoAcid[] standardAATable =
{
new AminoAcid('G', "Glycine", new Composition(2, 3, 1, 1, 0)),
new AminoAcid('A', "Alanine", new Composition(3, 5, 1, 1, 0)),
new AminoAcid('S', "Serine", new Composition(3, 5, 1, 2, 0)),
new AminoAcid('P', "Proline", new Composition(5, 7, 1, 1, 0)),
new AminoAcid('V', "Valine", new Composition(5, 9, 1, 1, 0)),
new AminoAcid('T', "Threonine", new Composition(4, 7, 1, 2, 0)),
new AminoAcid('C', "Cystine", new Composition(3, 5, 1, 1, 1)),
new AminoAcid('L', "Leucine", new Composition(6, 11, 1, 1, 0)),
new AminoAcid('I', "Isoleucine", new Composition(6, 11, 1, 1, 0)),
new AminoAcid('N', "Asparagine", new Composition(4, 6, 2, 2, 0)),
new AminoAcid('D', "Aspartate", new Composition(4, 5, 1, 3, 0)),
new AminoAcid('Q', "Glutamine", new Composition(5, 8, 2, 2, 0)),
new AminoAcid('K', "Lysine", new Composition(6, 12, 2, 1, 0)),
new AminoAcid('E', "Glutamate", new Composition(5, 7, 1, 3, 0)),
new AminoAcid('M', "Methionine", new Composition(5, 9, 1, 1, 1)),
new AminoAcid('H', "Histidine", new Composition(6, 7, 3, 1, 0)),
new AminoAcid('F', "Phenylalanine", new Composition(9, 9, 1, 1, 0)),
// new AminoAcid('U', "Selenocysteine", 150.0379),
new AminoAcid('R', "Arginine", new Composition(6, 12, 4, 1, 0)),
new AminoAcid('Y', "Tyrosine", new Composition(9, 9, 1, 2, 0)),
new AminoAcid('W', "Tryptophan", new Composition(11, 10, 2, 1, 0)),
// C H N O S
new AminoAcid('G', "Glycine", new Composition(2, 3, 1, 1, 0)), // 57.0215
new AminoAcid('A', "Alanine", new Composition(3, 5, 1, 1, 0)), // 71.0371
new AminoAcid('S', "Serine", new Composition(3, 5, 1, 2, 0)), // 87.032
new AminoAcid('P', "Proline", new Composition(5, 7, 1, 1, 0)), // 97.0528
new AminoAcid('V', "Valine", new Composition(5, 9, 1, 1, 0)), // 99.0684
new AminoAcid('T', "Threonine", new Composition(4, 7, 1, 2, 0)), // 101.0477
new AminoAcid('C', "Cystine", new Composition(3, 5, 1, 1, 1)), // 103.0092
// new AminoAcid('O', "Hydroxyproline", new Composition(5, 7, 1, 2, 0)), // 113.0477; note that O could be Hydroxyproline, Ornithine, or Pyrrolysine
new AminoAcid('L', "Leucine", new Composition(6, 11, 1, 1, 0)), // 113.0841
new AminoAcid('I', "Isoleucine", new Composition(6, 11, 1, 1, 0)), // 113.0841
new AminoAcid('N', "Asparagine", new Composition(4, 6, 2, 2, 0)), // 114.0429
new AminoAcid('D', "Aspartate", new Composition(4, 5, 1, 3, 0)), // 115.0269
new AminoAcid('Q', "Glutamine", new Composition(5, 8, 2, 2, 0)), // 128.0586
new AminoAcid('K', "Lysine", new Composition(6, 12, 2, 1, 0)), // 128.095
new AminoAcid('E', "Glutamate", new Composition(5, 7, 1, 3, 0)), // 129.0426
new AminoAcid('M', "Methionine", new Composition(5, 9, 1, 1, 1)), // 131.0405
new AminoAcid('H', "Histidine", new Composition(6, 7, 3, 1, 0)), // 137.0589
new AminoAcid('F', "Phenylalanine", new Composition(9, 9, 1, 1, 0)), // 147.0684
// new AminoAcid('U', "Selenocysteine", 150.0379), // 150.9536
new AminoAcid('R', "Arginine", new Composition(6, 12, 4, 1, 0)), // 156.1011
new AminoAcid('Y', "Tyrosine", new Composition(9, 9, 1, 2, 0)), // 163.0633
new AminoAcid('W', "Tryptophan", new Composition(11, 10, 2, 1, 0)), // 186.0793
};

// public static final AminoAcid N_TERN = new AminoAcid('[', "N-terminus", new Composition(0,0,0,0,0));
Expand Down

0 comments on commit dd296a8

Please sign in to comment.