Ramachandran plot

6,603 views
5,929 views

Published on

Published in: Technology
0 Comments
1 Like
Statistics
Notes
  • Be the first to comment

No Downloads
Views
Total views
6,603
On SlideShare
0
From Embeds
0
Number of Embeds
2
Actions
Shares
0
Downloads
231
Comments
0
Likes
1
Embeds 0
No embeds

No notes for slide

Ramachandran plot

  1. 1.  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
  2. 2.  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
  3. 3. 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
  4. 4. Peptide Bond & Phi-Psi Angles Phi is the angle around the N-Ca bond Psi is the angle around the Ca-C’ bond
  5. 5. 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
  6. 6. The red, brown, and yellow regions represent the favored, allowed, and "generously allowed" regions
  7. 7. 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
  8. 8. 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.
  9. 9. Thank you

×