The chief characteristic of proteins that also allow their diverse set of functions is their ability to bind other molecules specifically and tightly . The region of the protein responsible for binding another molecule is known as the binding site and is often a depression or " pocket " on the molecular surface . This binding ability is mediated by the tertiary structure of the protein , which define the binding site pocket , and by the chemical properties of the surrounding amino acids ' side chains . Protein binding can be extraordinarily tight and specific ; for example , the ribonuclease inhibitor protein binds to human angiogenin with a sub @-@ femtomolar dissociation constant ( < 10 − 15 M ) but do not bind at all to its amphibian homolog onconase ( > 1 M ) . Extremely minor chemical changes such as the addition of a single methyl group to a binding partner can sometimes suffice to nearly eliminate binding ; for example , the aminoacyl tRNA synthetase specific to the amino acid valine discriminate against the very similar side chain of the amino acid isoleucine .