Ramachandran plot

Ramachandran plot

It is also called as Ramachandran diagram discoverd by G.N.Ramachandran in 1963. It displays to visualize the distribution of conformational angle (dihedral angles ψ and φ) of amino acid residues in protein structure except glycine and proline.

The rotations of the polypeptide backbone around the bonds between N-Cα (called Phi, φ) and Cα-C (called Psi, ψ, see below for the graphics view of the angles). A special way for plotting protein torsion angles was also introduced by Ramachandran and co-authors, and was subsequently named the Ramachandran plot. The Ramachandran plot provides an easy way to view the distribution of torsion angles in a protein structure. It also provides an overview of excluded regions that show which rotations of the polypeptide are not allowed due to steric hindrance (collisions between atoms). The Ramachandran plot of a particular protein may also serve as an important indicator of the quality of its three-dimensional structures .

Torsion angles are among the most important local structural parameters that control protein folding - essentially, if we would have a way to predict the Ramachandran angles for a particular protein, we would be able to predict its fold. The torsion angles phi and psi provide the flexibility required for the polypeptide backbone to adopt a certain fold, since the third possible torsion angle within the protein backbone (called omega, ω) is essentially flat and fixed to 180 degrees. This is due to the partial double-bond character of the peptide bond, which restricts rotation around the C-N bond, placing two successive α-carbons and C, O, N and H between them in one plane. Thus, rotation of the protein chain can be described as rotation of the peptide bond planes relative to each other.

Since Gly is more flexible ψ and φ combinations not tolerated. Proline, with the sidechain covalently linked to the preceding backbone N, is more tightly constrained than general  residues.  In the plot the φ values on the x-axis and the ψ values on the y-axis. The torsional angles determine the conformation of the residues and the peptide. Many of the angle  conformations are not possible because of steric hindrance.

  - C is ψ and  N- is φ

Image source https://en.wikipedia.org/wiki/Ramachandran_plot

The  axis of the α-helix rotating in the y-plane. The Ramachandran plot of  peptide has points clustered about the values of φ= -57^o and ψ= -47^o which are the average values for α-helices. 

 Most β-sheets in globular proteins are twisted sheets which do not have flat parallel pleats. The Ramachandran plot of twisted sheet has points clustered about the values of φ= -130^o and ψ= +140^o which are the average values for twisted sheets.  

                     Image sourcehttps://www.studyblue.com/notes/note/n/protein-structure/deck/7778686
1.The area of allowed regions in the Ramachandran map will bw least for -
a.Gly                                c.L-ala
b.L-pro                             d.alpha-methylL-valine

Ans.L-pro 

2.JUNE 2017 CSIR 
The amino acids with Phi and psi values (-60,-40),(-59,-47) and (-80,120) will be adaopting which of the following confirmation ?
a.Helix-Helix-extended
b.Heix-coil-extended
c.Extended-extended-loop
d.Loop-loop-coil                                          Ans.A (Helix-Helix-extended)

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