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RAMACHANDRAN PLOT

In any polypeptide chain, two torsion angles also known as Ramachandran angles describes
the polypeptide backbone rotation around the bond between N-Ca (Called as Phi φ) and Ca-C
(called as Psi ψ).The fragment of the polypeptide chain which show the torsion angle phi and
psi are shown as round arrow in the below figure. This angle is defined by 3 consecutive bonds
which involve 4 atoms, this angle also called as dihedral angle. Dihedral angle describes the
chain rotation around the middle bond. The statistical distribution of the combination of the
backbone dihedral angle phi and psi is shown by the Ramachandran plot.

Fig. Illustration of Ramachandran Angle in polypeptide structure

Ramachandran Plot:

Ramachandran and co-workers suggested a special way for plotting protein torsion angle; this
plot is only known as the Ramachandran plot.

• This plot provides the distributional view of torsion angle corresponding to the two
major secondary structure of proteins (alpha helix and beta plated sheet).
• These structural elements are clearly clustered with in separate regions of the plot.
• Image of the plot shows two different structures of the same protein dot in the plot with
respect to the amino acid, with its phi and psi angles.

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Fig. Illustration of Ramachandran plot

• A computer model used by G.N. Ramachandran for small polypeptide to find the stable
confirmation the polypeptide varies between phi and psi. In this plot, for each
confirmation of poly peptide, structure was examined for the close contact between
atoms.
• In this model, atoms were treated as hard sphere according to their Vander Waals radii.
This plot is known as plot of torsional angles phi and phi which contains the residue /
amino acids of polypeptides. The angle phi and psi which are cause of colloid of sphere
and this sterically disallow the confirmation of polypeptide back bone.
• In the year 1963, Ramachandran plotted phi value on the x-axis and the psi value on
the y-axis. These torsional angles are plotted in such a way that it shows which
combination of angle are possible graphically.
• In sequence order, φ is the N(i-1),C(i),Ca(i),N(i) torsion angle and ψ is the
C(i),Ca(i),N(i),C(i+1) torsion angle. The torsional angle of each residue in polypeptide
defines the geometry of its attachment of molecules.
• In this arrangement, two adjacent residues are attached by positioning to its planar
peptide bond which is related to the two adjacent planar peptide bond so the torsional
angle is used to determine the confirmation of residue and peptide.

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• In Ramachandran plot, the scene on the right is ribonuclease H. In the secondary

structure of peptide are the segment of the poly peptide which contains ordered,
repetitive structure, and this repetitive structure is because of repetitive confirmation of
residue and the value of phi and psi is also repeated.
• So the variation in secondary structure can be characterised by the range of phi and psi
value with respect to the value of different secondary structure mapping to the different
region of Ramachandran plot, the most common example of two secondary structures
are given below;

a) Alpha-helix-

The right scene of the plot shows the axis of alpha-helix rotating in the y-plane, upon observing
the open centre of the helix by viewing the helix on the end. Planes are drawn on some of the
polypeptide bonds which emphasize that in alpha helix, planar peptide bonds rotate about the
axis of the helix. The Ramachandran plot of this given peptide has points clustered near about
the value of phi=-57º and the value of psi= -47º, these average value of alpha helix. When these
values are added with the value of two other helical segments which demonstrate the data from
the all three; it appears in one large cluster and after that helical segments cannot be
differentiated by difference in their phi and psi value.

b) Beta sheets-

In the plot, two segment of twisted beta sheet are displayed. When the plane of peptide bond is
drawn most of beta sheets in globular protein are twisted which does not have flat parallel pleat.
Upon closer view of beta sheets in the Ramachandran plot, the twisted sheet has clustered
points near about the value of phi= -130º and the value of psi= -140º, these are the average
value of twisted sheets, when these values are added to three other sheets of the segment the
area in which value for twisted sheets are located is defined with more clarity.

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Fig. Distribution of the amino acid Phi/Psi angles in the orotidine 5′-monophosphate decarboxylase.

Utility:

• Theoretically, in this plot allowed region shows the value of phi/psi angle that are
possible for amino acid. Practically phi/psi value distribution is observed and used as
structure validation of protein.
• It visualises the energetically allowed and forbidden region for the dihedral angles.
Many dihedral angles are found in the forbidden region of the Ramachandran plot for
poor quality homology models. These type of deviations indicate the problem with
structure of polypeptide.
• Earlier because of several angles, confirmation of residue was not possible to determine
because of steric hindrance. By using Ramachandran plot scientists could determine
protein structure, which torsional angle are permitted in plot and obtain the right insight
into the peptide structure.

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