A peptide bond links successive amino acids in a polypeptide chain. The mere linking of amino acids to form a polypeptide chain, however, is insufficient to ensure that the joined amino acids will adopt a particular three-dimensional structure. The peptide bond possesses two extraordinarily important properties that facilitate folding of a polypeptide into a particular structure.

First, as a consequence of the partial double-bond character of the peptide bond between the carbonyl carbon and nitrogen, the unit bounded by the alpha carbon atoms of two successive amino acids is constrained to lie in a plane. Therefore, energy need not be consumed from other interactions to generate the “proper” orientation about the C-N bond in each amino acid. Rotation is possible about each of the two peptide backbone bonds from the Cα atom of each amino acid (Fig. 1). Angles of rotation about these two bonds are called φ and ψ, and their specification for each of the amino acids in a polypeptide completely describes the path of the polypeptide backbone. Of course, the side chains of the amino acids are free to rotate and may adopt a number of conformations so that the φ and ψ angles do not completely specify the structure of a protein.

The second consequence of the peptide bond is that the amide hydrogen from one amino acid may be shared with the carbonyl oxygen from another amino acid in a hydrogen bond. Since each amino acid in a polypeptide chain possesses both a hydrogen bond donor and an acceptor, many hydrogen bonds may be formed, and in fact are formed in a polypeptide. Due to their positions on the amino acids these bonds have to be between different amino acids in the protein. Therefore they provide many stabilizing and structure-forming interactions. Although the individual hydrogen bonds are weak, the large number that can form in a protein contributes substantially to maintaining the three-dimensional structure of a protein.

Fig1. Two amino acid units in a polypeptide chain illustrating the planar structure of the peptide bond, the two degrees of rotational freedom for each amino acid unit in a polypeptide, and the angles ϕ and ψ.