Many surveys showed that the computationally derived energy differences between the cis and trans isomers are only partially reflected in their frequency of occurrence in the PDB. (1990 ) characterized 17 cis X-Xnp and 99 cis X-Pro peptides and MacArthur & Thornton (1991 ) analysed 58 cis X-Pro residues in a set of nonhomologous structures. In the early 1990s the number of structures deposited in the PDB allowed the first studies of the local protein environment of cis peptides. Therefore, characterization of cis-peptide geometry in protein crystal structures was very difficult. In the early days of protein crystallography cis peptides were almost completely absent in the available protein crystal structures (Ramachandran & Mitra, 1976 ). The cis imide bond X-Pro is more frequently observed than the cis amide bond X-Xnp (where Xnp is any residue except Pro) because the C α i−1 and O i−1 atoms have similar third neighbours in either X-Pro conformation (Ramachandran & Sasisekharan, 1968 ). The trans conformation is energetically preferred over the cis conformation owing to unfavourable nonbonded interactions between the two C α-H α moieties flanking the peptide bond (Zimmerman & Scheraga, 1976 Stewart et al., 1990 and references therein Jabs et al., 1999 and references therein). The C α i–1-C α i distance is around 3.81 Å in the trans conformation and around 2.94 Å in the cis conformation.

The dihedral angle ω (C α i−1-C i−1-N i-C α i) typically has values around 180° ( trans) or 0° ( cis), although exceptions are possible (Berkholz et al., 2012 ). The partial double-bond character of the peptide bond restricts its torsion.

Peptide bonds connect adjacent amino acids in proteins.

Amide plane of peptide backbone