2.  Ramachandran plot – to visualize the
backbone of aminoacid residues
 Used for structural validation and to
calculate the possible phi and psi angles that
accounts for the aminoacid residues
 Done by several software namely
WHATIF RAMACHANDRAN PLOT

3.  Work of Ramachandran
 Initially proposed a modelled structure on
collagen as a two bonded system based on
the formation of two inter hydrogen bonds
between their structures

4. Basics of map
 Parameter – torsion angle
 System used – protein chain consisting
of aminoacid side chains
 Ramachandran angles
– phi and psi
A B C D
B C
A D

5. Peptide Bond & Phi-Psi Angles
Phi is the angle around the N-Ca bond
Psi is the angle around the Ca-C’ bond

6. Principle within the
formation
 Using the analysis of crystal structure
data two limiting condition was
approached
-normal limits
-outer limits
 Using phi and psi angles conformation
of linked peptide units are calculated
 This results in 3 conditions

7. The red, brown, and yellow regions represent the
favored, allowed, and "generously allowed" regions

8. Distribution over the map
 The distribution of phi and psi angles
for a total of 9,156 amino acid
residues from 4,413 protein chains,
based on crystallographic data
 2 areas where the density of points is
high
(1) Around phi= -60 and psi= -60
corresponds to the a-helix
(2) Around phi= -90 and psi= -120
corresponds to the b-structure

9. Aminoacid preferences
 Usually glycine and proline are not
peffered in ramachandran plot.
 The aminoacids with larger side chains
will show less number of allowed region
within the ramachandran plot.
 Proline gives a very less number of phi
and psi values since the possess five
carbon ring.

10. Thank you