Protein Structure - 6
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
).