Ramachandran Plot: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Karl Oberholser, Joel L. Sussman, Eran Hodis, Wayne Decatur, Shelly Livne, Jaime Prilusky, Jane S. Richardson, Alexander Berchansky, Angel Herraez, Eric Martz, Norbert Sträter

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 <StructureSection load='' size='450' pspeed='8' side='right' scene='Ramachandran_Plots/Plot_1rnh/2' caption=''>
 [[Image:Ramachandran plot general 100K.jpg|thumb|left|240px|Ramachandran plot and contours from 100,000 high-quality general-case datapoints]]
-The Ramachandran plot is a plot of the torsional angles - [[Psi_and_Phi_Angles|phi (&phi;)and psi (&psi;)]] - of the residues (amino acids) contained in a peptide. In sequence order, &phi; is the C(i),Ca(i),N(i),C(i+1) torsion angle and &psi; is the N(i-1),C(i),Ca(i),N(i) torsion angle. The plot was developed in 1963 by G. N. Ramachandran, et. al.<ref>Ramachandran GN, Ramakrishnan C, Sasisekharan V (July 1963). "Stereochemistry of polypeptide chain configurations". J. Mol. Biol. 7: 95–9. PMID 13990617</ref> by plotting the &phi; values on the x-axis and the &psi; values on the y-axis, as for the image at left<ref>doi:10.1002/prot.10286</ref>. Plotting the torsional angles in this way graphically shows which combination of angles are possible. The torsional angles of each residue in a peptide define the geometry of its attachment to its two adjacent residues by positioning its planar peptide bond relative to the two adjacent planar peptide bonds, thereby the torsional angles determine the conformation of the residues and the peptide. Many of the angle combinations, and therefore the conformations of residues, are not possible because of steric hindrance. By making a Ramachandran plot, protein structural scientists can determine which torsional angles are permitted and can obtain insight into the structure of peptides. The scene on the right is the Ramachandran plot of ribonuclease H.
+The Ramachandran plot is a plot of the torsional angles - [[Psi_and_Phi_Angles|phi (&phi;)and psi (&psi;)]] - of the residues (amino acids) contained in a peptide. In sequence order, &phi; is the C(i-1),N(i),Ca(i),C(i) torsion angle and &psi; is the N(i),Ca(i),C(i),N(i+1) torsion angle. The plot was developed in 1963 by G. N. Ramachandran, et. al.<ref>Ramachandran GN, Ramakrishnan C, Sasisekharan V (July 1963). "Stereochemistry of polypeptide chain configurations". J. Mol. Biol. 7: 95–9. PMID 13990617</ref> by plotting the &phi; values on the x-axis and the &psi; values on the y-axis, as for the image at left<ref>doi:10.1002/prot.10286</ref>. Plotting the torsional angles in this way graphically shows which combination of angles are possible. The torsional angles of each residue in a peptide define the geometry of its attachment to its two adjacent residues by positioning its planar peptide bond relative to the two adjacent planar peptide bonds, thereby the torsional angles determine the conformation of the residues and the peptide. Many of the angle combinations, and therefore the conformations of residues, are not possible because of steric hindrance. By making a Ramachandran plot, protein structural scientists can determine which torsional angles are permitted and can obtain insight into the structure of peptides. The scene on the right is the Ramachandran plot of ribonuclease H.
 ==Secondary structure plot regions==