Molecular Orbital Calculations on Polypeptides and Proteins III. Conformation of Side Chains

The conformations of side chains in polypeptides have been discussed on the basis of predictions from extended Huckel theory. For certain backbone conformations, carbon atoms at α , β, and \(\gamma\) posi­tions in the side chain can have a fairly strong interaction with the atoms in the backbone and consequently such conformations become unstable with brapching of side chains, or when bulky groups are present in β-positions. Beyond \(\delta\)-carbon atom, the side chain conformation is independent of the backbone structure. The nature of side chain affects the relative energies for right handed a-helix and collagen structures. The right handed cc-helix appear to be most stable when the side chain contains a secondary β-carbon. For all the side chains studied, the energy difference between the two structures is very small. However, such structures are fairly stable compared to left handed α-helix or extended chains.