Question

What is the Ramachandran plot and how are the bond angles used to understand protein structure?

Answer 1

Ans.

Ramachandran plot is a plot that elustrate the properties of amino acids in terms to make secondary structure.

means it shows allowed region of amino acids to form perticular secondary stucture as; alpha helix, beta sheet, collagen, turns and random coil.

this is on the basis of side chain of amino acid and their intramolecular steric hindrance.

more condence structure such as alpha helix do not allow the amino acids that distrupts extensive hydrogen bonding so appropriate amino acid are allowed in the helical structure.

same for other secondary structures.

in ramachandran plot protein structures are analysed on the basis of their phi and psi angles.

amino acid favorable for perticular protein secondary structure formation commonly shares a plot area in ramachndran plot known as allowed region for perticular amino acid.

as amino acid favoring alpha helix will found in ramachandran plot with -57(phi) and -47(psi).

310 helix favoring amino acids -49(phi) and -26(psi)

anti parallel beta sheet -139(phi) and +135(psi)

parallel beta sheet -119(phi) and +113(psi) etc.

phi and psi can have any value between -180 to +180.