The primary structure of a protein is the sequence of amino acids in the peptide or protein chain, always listed from N-terminus to C-terminus. In most cases the three or one-letter abreviations for the amino acids are used. For example, the tripeptide show earlier has the primary structure alanine-serine-glycine which can be abbreviated ala-ser-gly or ASG. Notice that a peptide with the primary structure GSA would be a completely different peptide.

The primary structure supplies little information about the overall three-dimensional structure of a protein. However, the primary structure in large part determines the overall structure by influencing hydrogen bonding within the backbone (secondary structure) and interactions between sidechains (tertiary and quaternary structure).