Amino acid one-letter and three-letter codes

The twenty standard amino acids

Residue formulas and masses are for the amino acid as it sits inside a chain, which is the free amino acid minus one water. A linear peptide's mass is the sum of its residues plus one water for the free termini — the arithmetic the molecular weight calculator performs.

Codes beyond the standard twenty

IUPAC also defines symbols for residues that are ambiguous or outside the standard set:

• B (Asx): asparagine or aspartic acid, where the analysis cannot tell them apart.
• Z (Glx): glutamine or glutamic acid, for the same reason.
• X (Xaa): an unknown or unspecified residue.
• U (Sec): selenocysteine, and O (Pyl): pyrrolysine — genetically encoded but outside the standard twenty.

None of these describe a modification. A D-amino acid, an acetylated N-terminus, a C-terminal amide or a non-natural residue has to be stated alongside the sequence, which is why several compound references here explain why no one-letter sequence is published for them.

Why some letters do not match the name

Where two amino acids share a first letter, only one can have it: A, C, G, H, I, L, M, P, S, T and V take their initial. The others were assigned by other means and are commonly remembered by sound or by elimination — F for phenylalanine ("fenylalanine"), R for arginine ("aRginine"), Y for tyrosine ("tYrosine"), W for tryptophan, D and E for the two acids, N and Q for their amides, and K for lysine, one of the letters left over.

Using the codes

One-letter strings are what sequence databases, mass spectrometry software and the peptide molecular weight calculator accept. Written N-terminus first, BPC-157 is GEPPPGKPADDAGLV: fifteen residues, formula C62H98N16O22.

Common questions

What is the one-letter code for each amino acid?

A alanine, R arginine, N asparagine, D aspartic acid, C cysteine, Q glutamine, E glutamic acid, G glycine, H histidine, I isoleucine, L leucine, K lysine, M methionine, F phenylalanine, P proline, S serine, T threonine, W tryptophan, Y tyrosine, V valine.

What do B, Z and X mean in a sequence?

They are IUPAC ambiguity codes: B is asparagine or aspartic acid, Z glutamine or glutamic acid, and X an unknown or unspecified residue.

What is the difference between residue mass and amino acid mass?

A residue is the amino acid minus the water released when it forms a peptide bond, so each residue is about 18.011 Da (monoisotopic) lighter than the free amino acid.

References

• 3AA-21: One-letter symbols for amino acids — IUPAC-IUBMB nomenclature recommendations, hosted by Queen Mary University of London
• Nomenclature and symbolism for amino acids and peptides (IUPAC-IUB JCBN recommendations 1983) — IUPAC-IUB Joint Commission on Biochemical Nomenclature, Biochemical Journal, 1984
• Standard Atomic Weights — Commission on Isotopic Abundances and Atomic Weights (CIAAW), IUPAC