Ramachandran Plot: Difference between revisions
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<StructureSection load='' size='450' pspeed='8' side='right' scene='Ramachandran_Plots/Plot_1rnh/2' caption=''> | <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]] | [[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 (φ)and psi (ψ)]] - of the residues (amino acids) contained in a peptide. In sequence order, φ is the | The Ramachandran plot is a plot of the torsional angles - [[Psi_and_Phi_Angles|phi (φ)and psi (ψ)]] - of the residues (amino acids) contained in a peptide. In sequence order, φ is the C(i),Ca(i),N(i),C(i+1) torsion angle and ψ 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 φ values on the x-axis and the ψ 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== | ==Secondary structure plot regions== | ||
Secondary structures of a peptide are segments of the peptide that have ordered and repetitive structure, and the repetitive structure is due to a repetitive conformation of the residues and, ultimately, repetitive values of φ and ψ. | Secondary structures of a peptide are segments of the peptide that have ordered and repetitive structure, and the repetitive structure is due to a repetitive conformation of the residues and, ultimately, repetitive values of φ and ψ. The different secondary structures can be distinguished by their range of φ and ψ values with the values of different secondary structures mapping to different regions of the Ramachandran plot. Two common examples of secondary structure are illustrated below. | ||
=== α-helix === | === α-helix === | ||
The <scene name='Ramachandran_Plots/Helix_first/1'>scene on the right</scene> shows the axis of the α-helix rotating in the y-plane. When viewing the helix on end, observe the open center of the helix. <scene name='Ramachandran_Plots/Helix_planes/2'>Planes</scene> are drawn on some of the peptide bonds to emphasize that in an α-helix the planar peptide bonds rotate about the axis of the helix. The <scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot1/3'>Ramachandran plot</scene> of this peptide has points clustered about the values of φ= -57<sup>o</sup> and ψ= -47<sup>o</sup> which are the average values for α-helices. <scene name='38/381225/Plot2/4'>Adding the values</scene> of two other helical segments demonstrates that data from all three appear in one large cluster and that the helical segments can not be distinguished by the differences in their φ and ψ values. | The <scene name='Ramachandran_Plots/Helix_first/1'>scene on the right</scene> shows the axis of the α-helix rotating in the y-plane. When viewing the helix on end, observe the open center of the helix. <scene name='Ramachandran_Plots/Helix_planes/2'>Planes</scene> are drawn on some of the peptide bonds to emphasize that in an α-helix the planar peptide bonds rotate about the axis of the helix. The <scene name='User:Karl_Oberholser/Ramachandran_Plots/Plot1/3'>Ramachandran plot</scene> of this peptide has points clustered about the values of φ= -57<sup>o</sup> and ψ= -47<sup>o</sup> which are the average values for α-helices. <scene name='38/381225/Plot2/4'>Adding the values</scene> of two other helical segments demonstrates that data from all three appear in one large cluster and that the helical segments can not be distinguished by the differences in their φ and ψ values. | ||