This document discusses Ramachandran plots, which are used to visualize protein backbone structures and calculate possible phi and psi bond angles in amino acid residues. Ramachandran plots show favored, allowed, and generously allowed regions for different bond angles based on analysis of crystal structure data and distributions of over 9,000 amino acid residues. Two high-density areas correspond to alpha-helices and beta-structures. Glycine and proline residues have fewer allowed regions due to their side chain properties.

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