Amino Acid Sequence Notation

The twenty proteinogenic amino acids have both a three-letter code (Ala, Gly, Lys) and a one-letter code (A, G, K). Three-letter codes are usual for short sequences and where modifications must be shown; one-letter codes are usual for longer sequences.

Sequences are written from the N-terminus on the left to the C-terminus on the right. This direction is a convention rather than a notation choice, and reversing it describes a different molecule.

An acetylated N-terminus is written as a leading Ac-, and an amidated C-terminus as a trailing -NH2. Both remove a terminal charge and both are frequently used to reduce susceptibility to exopeptidase cleavage.

A free acid C-terminus, the unmodified state, is sometimes written explicitly as -OH where the distinction matters.

D-amino acids are indicated by a D- prefix (D-Ala) or by a lower-case one-letter code, and are used where resistance to proteolysis is required. Ornithine (Orn), norleucine (Nle) and aminoisobutyric acid (Aib) appear as three-letter codes with no one-letter equivalent.

Disulfide bonds are shown by identifying the paired cysteine positions, for example Cys3-Cys11, since connectivity is not deducible from sequence alone.

Acylation, PEGylation and similar conjugations are written as the attached group at its point of attachment — a fatty-acid chain on a lysine side chain, for instance. Modifications of this kind alter mass, hydrophobicity and chromatographic retention, and so appear in both the mass spectrum and the chromatogram.