Short answer: Every common amino acid has two standard abbreviations: a three-letter symbol such as Ala, and a one-letter symbol such as A [1]. The three-letter symbol is usually the first three letters of the amino acid's trivial name, written with one capital and two lower-case letters [2]. The one-letter code was built for long sequences, where brevity matters [5]. A few extra letters cover cases the original 20 did not: B, Z and X for ambiguous or unknown residues [5], U for selenocysteine [6] and O for pyrrolysine [7].
This article is an educational guide to chemical notation for laboratory readers. It does not describe biological effects, and it is not guidance for use in people or animals.
The 20 common amino acids and their codes
OpenStax's organic chemistry text lists the 20 amino acids commonly found in proteins with both abbreviations, grouped by side-chain type [1]. Here they are in the same order, written as name, three-letter symbol, one-letter symbol.
Neutral amino acids (15) [1]:
- Alanine: Ala, A
- Asparagine: Asn, N
- Cysteine: Cys, C
- Glutamine: Gln, Q
- Glycine: Gly, G
- Isoleucine: Ile, I
- Leucine: Leu, L
- Methionine: Met, M
- Phenylalanine: Phe, F
- Proline: Pro, P
- Serine: Ser, S
- Threonine: Thr, T
- Tryptophan: Trp, W
- Tyrosine: Tyr, Y
- Valine: Val, V
- Aspartic acid: Asp, D
- Glutamic acid: Glu, E
- Arginine: Arg, R
- Histidine: His, H
- Lysine: Lys, K
The extra letters: B, Z, X, U, O (and J)
Beyond the 20 standard letters, a handful of symbols handle uncertainty and rarer residues:
- B (Asx): aspartic acid or asparagine, when the two have not been distinguished [5].
- Z (Glx): glutamic acid or glutamine, or substances such as 4-carboxyglutamic acid and 5-oxoproline that yield glutamic acid on acid hydrolysis of peptides [5].
- X (Xaa): an amino acid whose identity is undetermined, or one that is atypical [5].
- U (Sec): selenocysteine. The 1999 JCBN/NC-IUBMB Newsletter recommended Sec and U, noting that J was already used in NMR work for signals that could be either leucine or isoleucine [6].
- O (Pyl): pyrrolysine, found in proteins of certain archaea. The 2009 nomenclature newsletter recommended Pyl and O for representing it in sequence databases [7].
- J: Mascot treats J as leucine or isoleucine by default, but Matrix Science notes that this use of J is not standardised, and that UniProtKB does not use the letter J even once [8].
Why the one-letter codes look the way they do
Only some letters match an obvious initial. The IUPAC-IUB note on the choice of symbols explains the logic [5]:
- Six direct initials: cysteine (C), histidine (H), isoleucine (I), methionine (M), serine (S) and valine (V) had no ambiguity, so they got their first letters.
- Shared initials: where several amino acids share A, G, L, P or T, the letter went to the most frequently occurring and structurally simplest one: alanine, glycine, leucine, proline and threonine.
- Sound-alikes: F for phenylalanine and R for arginine are phonetic associations.
- Shape: W was chosen for tryptophan because its double ring is associated with the bulky letter W.
- Pairs: N and Q went to asparagine and glutamine; D and E to aspartic and glutamic acids.
- Leftovers: K and Y went to lysine and tyrosine because they were close alphabetically to the initial letters of the names.
- Letters avoided at first: U (easily confused with V in handwriting), O (confused with G, Q, C, D and zero in poor print-outs) and J (absent from several languages).
A short history
The IUPAC-IUB text traces the idea back several decades [5]:
1. Gamow and Yčas mentioned the possibility of one-letter symbols in 1958.
2. Šorm and colleagues systematized the idea in 1961.
3. Dayhoff and Eck used one-letter symbols, derived partly from Šorm's code, in their protein sequence compilations.
4. IUB-IUPAC recommendations were approved in 1968, based on proposals from a subcommittee of W. E. Cohn, M. O. Dayhoff, R. V. Eck and B. Keil.
The IUPAC-IUB text says it gives those recommendations "with no substantial change" [5].
Three-letter rules worth knowing
The three-letter system has a few formal conventions [2]:
- Capitalisation: one capital followed by two lower-case letters, such as Gln, not GLN or gln, regardless of position in a sentence.
- Configuration: a symbol means the L form of a chiral amino acid unless D or DL is placed before it with a hyphen.
- Residue numbers: symbols can label positions, such as Tyr-110 for tyrosine residue 110.
- Less common residues: symbols for them should be defined in each publication, with recommended forms such as Hse for homoserine, Hcy for homocysteine and Orn for ornithine.
How to read a written peptide sequence
In the three-letter system, the hyphen stands for the peptide bond [2]. Glycylglycylglycine is written Gly-Gly-Gly [2]. (For background on the bond itself, see our peptide bond explainer.)
Direction. In a one-letter sequence, the left-hand letter is the residue carrying the free amino group and the right-hand letter is the residue carrying the free carboxyl group [5]. In other words, sequences are written from the N-terminus to the C-terminus; our N-terminus vs C-terminus guide covers why the two ends differ.
End groups and modifications [3][4]:
- Ac- marks an acetylated amino group: N-acetylglycine is Ac-Gly [3].
- -NH2 on the right marks a C-terminal amide: isoglutamine is Glu-NH2, and -Ala-NH2 shows the amide of a C-terminal alanine [3].
- H- and -OH can be added to emphasise that an end is unsubstituted, so H-Ala contrasts with Ac-Ala and Ala-OH with Ala-OMe [3].
- D- before a residue symbol marks a D residue within a sequence [4].
- cyclo(...) marks a cyclic peptide: the sequence is written in the usual way, placed in parentheses and preceded by "cyclo", as in gramicidin S, written cyclo(-Val-Orn-Leu-D-Phe-Pro-Val-Orn-Leu-D-Phe-Pro-) [4].
- Thyroliberin is written Glp-His-Pro-NH2, combining a modified N-terminal residue with a C-terminal amide.
- Angiotensin II is written Asp-Arg-Val-Tyr-Ile-His-Pro-Phe. Converting each symbol with the table above gives the one-letter string DRVYIHPF [1][4].
Which system should you use?
The IUPAC-IUB recommendations give each system a job [5]:
- One-letter code: much more concise, and helpful for summarizing large amounts of data, aligning and comparing related sequences, computer processing, and labeling residues in 3D pictures of proteins.
- Three-letter code: easier to understand for readers not familiar with the one-letter system. The one-letter code should not be used in simple text or in reporting the experimental details of sequence determination.
- Mixed papers: if the one-letter amino acid code and the single-letter nucleotide code appear in the same paper, particular care is needed to avoid confusion.
How software treats the codes
Mass spectrometry search software follows the same alphabet. Matrix Science says its Mascot software uses the IUPAC one-letter code, with the 20 standard amino acids written as the uppercase letters ACDEFGHIKLMNPQRSTVWY [8]. A few practical details from that source [8]:
- Ambiguity is expanded. If Mascot meets B, X or Z it tests the possibilities. For the example peptide PEBTIDE, it tries PEDTIDE and PENTIDE against the spectrum.
- These letters are rare. In SwissProt release 2026_02, X made up 39 ppm of residues and B and Z 1 ppm each.
- U is rarer still. UniProtKB contains about 2 ppm of U.
A note for the lab
When a sequence appears on a specification sheet or Certificate of Analysis, it is worth reading it with the conventions above in mind: which end is the N-terminus, whether an -NH2 or Ac- group is shown, and whether any residue carries a D- prefix. Our guide to reading a peptide COA covers the rest of the document.
Frequently Asked Questions
What are the amino acid abbreviations?
Each common amino acid has a three-letter symbol, such as Ala, and a one-letter symbol, such as A [1].
Why is lysine K?
L was already used for leucine. K was chosen for lysine because it is close alphabetically to the initial letter [5].
Why is phenylalanine F?
It is a phonetic association, like R for arginine [5].
What do B, Z and X mean in a sequence?
B is Asp or Asn, Z is Glu or Gln, and X is an undetermined or atypical amino acid [5].
What are U and O?
U is selenocysteine (Sec) [6] and O is pyrrolysine (Pyl) [7].
Should three-letter codes be written in capitals?
No. The standard form is one capital and two lower-case letters, such as Gln [2].
Bottom line
The three-letter and one-letter codes describe the same 20 common amino acids [1][5]. The one-letter alphabet adds B, Z and X for uncertainty [5], U for selenocysteine [6] and O for pyrrolysine [7]. Sequences run from the free amino end on the left to the free carboxyl end on the right [5], with prefixes and suffixes such as Ac-, -NH2 and D- marking modifications [3][4].
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