Peptide Sequence Notation: How Amino Acid Sequences Are Written
For in vitro laboratory research use only. This is a chemistry reference on how peptide sequences are written. It makes no claims about the effects of any material.
A peptide is a chain of amino acids joined by peptide bonds. Its sequence is the order of those amino acids, and there is a standard way to write it down. This guide explains that notation so you can read sequences in reference databases, supplier specifications and certificates of analysis.
Direction: N-terminus to C-terminus
Every linear peptide has two ends. The N-terminus carries the free amino group, and the C-terminus carries the free carboxyl group. By convention, sequences are always written from left to right, starting at the N-terminus and ending at the C-terminus. So Gly-Ala-Ser and Ser-Ala-Gly are two different peptides, even though they contain the same three amino acids.
Three-letter and one-letter codes
Each of the 20 standard amino acids has a three-letter code and a one-letter code, set out in the IUPAC-IUB recommendations on amino acid and peptide nomenclature. Three-letter codes are joined with hyphens (Gly-Ala-Ser). One-letter codes are written as a continuous string (GAS).
| Amino acid | Three-letter | One-letter |
|---|---|---|
| Alanine | Ala | A |
| Arginine | Arg | R |
| Asparagine | Asn | N |
| Aspartic acid | Asp | D |
| Cysteine | Cys | C |
| Glutamic acid | Glu | E |
| Glutamine | Gln | Q |
| Glycine | Gly | G |
| Histidine | His | H |
| Isoleucine | Ile | I |
| Leucine | Leu | L |
| Lysine | Lys | K |
| Methionine | Met | M |
| Phenylalanine | Phe | F |
| Proline | Pro | P |
| Serine | Ser | S |
| Threonine | Thr | T |
| Tryptophan | Trp | W |
| Tyrosine | Tyr | Y |
| Valine | Val | V |
Several one-letter codes don’t match the first letter of the name (for example, K for lysine, W for tryptophan and Y for tyrosine), so it’s worth checking the table rather than guessing. When a position is ambiguous, B stands for Asx (Asp or Asn), Z for Glx (Glu or Gln), and X for an unknown or unspecified amino acid.
End groups and modifications
Some sequences show what sits at each end:
- H- at the start marks a free N-terminal amino group, as in H-Gly-Ala-Ser-OH.
- -OH at the end marks a free C-terminal carboxylic acid.
- -NH2 at the end marks a C-terminal amide.
- Ac- at the start marks an N-terminal acetyl group.
A “D-” prefix (for example D-Ala) marks the D-form of an amino acid. Without a prefix, the L-form is assumed. These details change the expected molecular formula and mass, so two entries with the same letters but different end groups are different compounds.
Sequence length and molecular weight
Sequence length is simply the number of amino acid residues. For example, our specifications comparison lists BPC-157 at 15 amino acids and thymosin beta-4 at 43.
The molecular weight of a linear peptide is the sum of its residue masses plus one molecule of water (about 18.02 g/mol) for the free ends. Using average residue masses, Gly-Ala-Ser works out to about 57.05 + 71.08 + 87.08 + 18.02 = about 233.2 g/mol. Published molecular weights in databases such as PubChem are reference figures for the compound, not measurements of a specific lot. See the research peptide glossary for the related terms.
Where notation shows up on a COA
The expected mass used in an identity check is worked out from the sequence and its end groups. LC-MS then compares the measured mass with that expected mass. Our LC-MS identity guide explains what that result confirms. It confirms identity, not purity; purity is a separate HPLC-UV result.
Each lot of our BPC-157 10 mg has a third-party certificate on our peptide COA lookup page. A certificate reports results for the sample tested. It is not a guarantee for other lots.
For research use only. Not for human or animal use.
