Conformation of the polypeptide chain

• There are three bonds for each residue in a polypeptide that about which rotation is possible
• f, y and w

• Rotation about the peptide bond (w), is limited by the partial double bond character of the bond.

• The trans configuration is energetically more stable than the cis:

• Except for proline, for which the trans and cis configurations have similar energy's.

• The Ramachandran diagram plots out the energy service for pairs of f and y angles.

• SwissPDBViewer can be used to produce Ramachandran diagrams for proteins (download pdb for flavodoxin).