How to read a peptide sequence (one-letter codes)

A peptide sequence is a string of amino acid symbols read from left to right, starting at the N-terminus (the end with a free amino group) and finishing at the C-terminus (the end with a free carboxyl group). Each standard amino acid has a three-letter code such as Gly and a one-letter code such as G, so the copper-binding tripeptide glycyl-histidyl-lysine can be written Gly-His-Lys or simply GHK. Prefixes and suffixes such as Ac- and -NH2 record changes to the two ends, and non-standard residues such as Aib get their own abbreviations. This guide gives the full code table and walks through real examples from our peptide library.

The 20 standard amino acid codes

The one-letter and three-letter codes are set by the IUPAC-IUBMB nomenclature recommendations. IUPAC notes that the initial letter of the amino acid name was used wherever it was unambiguous, which is why glycine is G and alanine is A. Where several names share a letter, a different letter was assigned, which is why lysine is K, tryptophan is W and tyrosine is Y. U and O were avoided because U is easily confused with V in handwriting.

IUPAC also defines three ambiguity codes you may meet in older literature or sequencing data: B (Asx) for aspartic acid or asparagine, Z (Glx) for glutamic acid or glutamine, and X (Xaa) for an unknown or "other" amino acid. On a synthetic peptide's certificate of analysis these should not appear; a defined product has a defined sequence.

N-terminus to C-terminus: why direction matters

By universal convention, sequences are written from the amino terminus on the left to the carboxyl terminus on the right. IUPAC states this directly for one-letter strings: the left-hand letter is the residue with the free amino group and the right-hand letter is the residue with the free carboxyl group. The American Peptide Society points out that reversing a sequence produces a different molecule. GHK and KHG contain the same three amino acids but are not the same peptide.

Two more conventions help with longer chains:

• Three-letter strings use hyphens to show peptide bonds: Thr-Lys-Pro-Arg-Pro-Gly-Pro. One-letter strings drop them: TKPRPGP.
• Explicit free ends can be written as H- (free amine) and -OH (free acid), as in H-GRGDS-OH. When nothing is written, a free end is usually implied, but good documentation states it.

Terminal modifications: Ac-, -NH2 and lipid tails

Many synthetic peptides are modified at one or both ends. The American Peptide Society notes that when termini are acetylated, amidated or cyclized, the modification should be stated explicitly. The common forms are:

End groups change the molecular formula and weight, so they matter at the bench. A peptide written Ac-...-NH2 is not the same compound as the unmodified chain, and molarity calculations must use the weight of the modified molecule. Our peptide calculator works from the weight you enter, so take that figure from the certificate for the exact form you hold.

Non-standard residues such as Aib

Residues outside the standard 20 have no single letter of their own. The American Peptide Society notes they receive convention-based abbreviations defined at first use. A widely used example is Aib, α-aminoisobutyric acid. In sequence strings it is usually written as Aib in brackets or with hyphens, for example H-Aib-E... rather than as a single letter, because no IUPAC one-letter code exists for it.

Worked examples from the library

The sequences below are taken from the cited primary or reference sources.

Semaglutide shows how analog notation works. It is described against human GLP-1 rather than written from scratch. RCSB PDB-101 describes the changes as an alanine-to-Aib substitution at position 8, a lysine-to-arginine substitution at position 34, and acylation of the lysine at position 26 with a spacer and C-18 fatty diacid side chain. This is often shortened to [Aib8, Arg34]. The position numbers refer to native human GLP-1, which is why analog notation only makes sense next to the parent sequence. Health Canada's Ozempic monograph gives the molecular formula C187H291N45O59 and a weight of 4113.6 Da. See our semaglutide profile for more.

How to check a sequence on a label or COA

• Compare residue by residue against a primary source, such as a journal paper, a regulator's product information or a structure database.
• Check both ends. A missing -NH2 or Ac- is a different compound with a different weight.
• Check the mass. Mass spectrometry results on a certificate should match the calculated mass of the stated sequence, including modifications.
• Watch for salts and counterions, which change the weight per milligram of powder without changing the sequence.

Our guide to verifying a peptide COA covers purity and mass checks in more detail, and what are peptides? explains the chemistry behind the peptide bond.

Frequently asked questions

Sources

1. IUPAC-IUBMB: Nomenclature and symbolism for amino acids and peptides, one-letter symbols (3AA-21.2)
2. IUPAC-IUBMB: Nomenclature and symbolism for amino acids and peptides, one-letter code rules
3. American Peptide Society: Nomenclature, naming conventions, one-letter and three-letter codes
4. RCSB PDB-101: Semaglutide
5. Health Canada: Ozempic product monograph (revised 21 August 2020)
6. PubMed 18498523: A synthetic hexapeptide (Argireline) with antiwrinkle activity
7. Pickart L et al. GHK peptide as a natural modulator of multiple cellular pathways in skin regeneration. BioMed Res Int (2015)
8. PubMed 20919548: Experimental optimization of learning and memory processes by Selank (2010)
9. Palmitoyl pentapeptide-4 (reference entry with primary citations)