The peptide bond have two resonance forms that contribute some double @-@ bond character and inhibit rotation around its axis , so that the alpha carbons are roughly coplanar . The other two dihedral angles in the peptide bond determine the local shape assumed by the protein backbone . The end of the protein with a free carboxyl group is known as the C @-@ terminus or carboxy terminus , whereas the end with a free amino group is known as the N @-@ terminus or amino terminus . The words protein , polypeptide , and peptide are a little ambiguous and can overlap in meaning . Protein is generally used to refer to the complete biological molecule in a stable conformation , whereas peptide is generally reserved for a short amino acid oligomers often lacking a stable three @-@ dimensional structure . However , the boundary between the two is not well defined and usually lie near 20 – 30 residues . Polypeptide can refer to any single linear chain of amino acids , usually regardless of length , but often imply an absence of a defined conformation .