Peptides can be modified
at the N-terminus e.g. N-acetylation: H-Ala-Gly-… -> Ac-Ala-Gly-… (Ac-AG…)
at the C-terminus e.g. amidation: …-Gly-Ala-OH -> …-Gly-Ala-NH2 (…GA-NH2)
Both modifications are widespread in nature.
at the side-chains of amino acids e.g. acetylation of lysine..-Lys-.. -> ..-Lys(Ac)-.. (…K(Ac)…)
NOTE: -Cys- stands for a cysteine residue containing a free thiol group, unless disulfide formation is mentioned explicitly
at the backbone of the peptide e.g. by incorporation of D-amino acids …-Ala-Leu-D-Phe-Tyr-… (…ALfY…)
Abbreviations have been defined for most modifications, others are written out in full e.g. H-Phe-pyrrolidide, H-Lys(isopropyl)-OH
Our notation does not distinguish between temporary -protecting groups- and permanent modifications of peptides. Not all modifications can be transformed unambiguously into one-letter code, but terminal modifications such as Ac or NH2 or D-amino acids (lowercase letters) or simple side-chain modifications (put in brackets) do not cause difficulties.