Question

4. a. What is the diagram shown below called? What is the significance of the blue regions on the diagram? (4 pts) +180 120 (degrees) +180 • (degrees) b. Below is an actual plotted protein on the same axes. Why are there large portions of dots in those specific areas? (4 pts) c. What is important about the series of dots in the lower right quadrant (-180°< ' < 0°. 0°< < 180°)? What is most likely the identity of these amino acids? (4 pts)

Answer 1

a its a ramachandran plot

dark blue represent conformations that involve no steric overlap

Medium blue indicates conformations permitted if atoms are allowed to approach each other by an additional 0.1 nm, a slight clash

The lightest blue indicates conformations that are permissible if a very modest flexibility (a few degrees) is allowed in the ω dihedral angle peptide bond itself (generally constrained to 180°)

The white regions are conformations that are not allowed

b.The asymmetry of the plot results from the L stereochemistry of the amino acid residues and with the increased branching the plotted area decreases

c. lower right quadrant shows the least favourable conformations as can be seen in question A

The only amino acid residue found in a conformation outside the blue regions is glycine. Because its side chain is a single hydrogen atom so Gly residue can take part in many conformations
that are sterically forbidden for other amino acids