Ramachandran plot
- 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