Question

Why is the Ramachandran Plot for Glycine symmetric and why is the plot asymmetric for all amino acids except (glycine, proline, pre-proline)?

Answer 1

GENERALLY the Ramachandran plot originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, is a way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure.

1. The one might be expect that larger side chains would result in more restrictions and consequently a smaller allowable region in the Ramachandran plot.
2. In exercise, the major effect seen is that of the presence or absence of the methylene group at Cβ. Glycine has only a hydrogen atom for its side chain, with a much smaller van der Waals radius than the CH₃, CH₂, or CH group that starts the side chain of all other amino acids.
3. From now it is least restricted, and this is apparent in the Ramachandran plot for glycine for which the allowable area is considerably larger.
4. In gap, the Ramachandran plot for proline, with its 5-membered-ring side chain connecting Cα to backbone N, shows a limited number of possible combinations of ψ and φ
5. A large set of high-resolution structures and outlines for favored and for allowed conformational regions for the general case (all amino acids except Gly, Pro, and pre-Pro), for Gly, and for Pro.The most common regions are labeled: α for α helix, Lα for lefthanded helix, β for β-sheet, and ppII for polyproline II.