Editing Ramachandran plot (section)

{{Short description|Visual representation of allowable protein conformations}}
[[Image:Ramachandran plot original outlines.jpg|thumb|right|220px|Original hard-sphere, reduced-radius, and relaxed-tau φ,ψ regions from Ramachandran, with updated labels and axes]]
[[Image:Protein backbone PhiPsiOmega drawing.svg|thumb|left|140px|Backbone dihedral angles φ and ψ (and ω). All three angles are at 180° in the conformation shown]]
In [[biochemistry]], a '''Ramachandran plot''' (also known as a '''Rama plot''', a '''Ramachandran diagram''' or a '''[φ,ψ] plot'''), originally developed in 1963 by [[Gopalasamudram Narayana Ramachandran|G. N. Ramachandran]], C. Ramakrishnan, and [[V. Sasisekharan]],<ref>{{cite journal |pages=95–9 |doi=10.1016/S0022-2836(63)80023-6 |title=Stereochemistry of polypeptide chain configurations |year=1963 |last1=Ramachandran |first1=G.N. |last2=Ramakrishnan |first2=C. |last3=Sasisekharan |first3=V. |journal=Journal of Molecular Biology |volume=7 |pmid=13990617}}</ref> is a way to visualize energetically allowed regions for backbone [[dihedral angle]]s ( also called as torsional angles , phi and psi angles ) ψ against φ of [[amino acid]] residues in [[protein structure]]. The figure on the left illustrates the definition of the φ and ψ backbone dihedral angles<ref>{{cite book |year=1981 |last1=Richardson |first1=J.S. |title=Anatomy and Taxonomy of Protein Structures |chapter=The Anatomy and Taxonomy of Protein Structure |volume=34 |pages=167–339 |doi=10.1016/S0065-3233(08)60520-3 |pmid=7020376 |series=Advances in Protein Chemistry |isbn=9780120342341}}</ref> (called φ and φ' by Ramachandran). The ω angle at the [[peptide bond]] is normally 180°, since the partial-double-bond character keeps the peptide bond planar.<ref>{{cite journal | year= 1951 |last1= Pauling |first1=L. |last2=Corey |first2=H.R. |last3=Branson |title= The Structure of Proteins: Two Hydrogen-Bonded Helical Configurations of the Polypeptide Chain |journal= Proceedings of the National Academy of Sciences of the United States of America|volume= 37|pages= 205–211 |pmc = 1063337 |pmid=14816373 |issue=4 |doi=10.1073/pnas.37.4.205 | first3= H. R.|bibcode=1951PNAS...37..205P |doi-access= free }}</ref> The figure in the top right shows the allowed φ,ψ backbone conformational regions from the Ramachandran et al. 1963 and 1968 hard-sphere calculations: full radius in solid outline, reduced radius in dashed, and relaxed tau (N-Cα-C) angle in dotted lines.<ref>{{cite book |last1=Ramachandran |first1=G.N. |last2= Sasiskharan |first2=V. |year=1968 |title= Conformation of polypeptides and proteins |volume=23 |pages=283–437 |doi=10.1016/S0065-3233(08)60402-7 |series=Advances in Protein Chemistry |isbn=9780120342235 |pmid=4882249}}</ref> Because [[dihedral angle]] values are circular and 0° is the same as 360°, the edges of the Ramachandran plot "wrap" right-to-left and bottom-to-top. For instance, the small strip of allowed values along the lower-left edge of the plot are a continuation of the large, extended-chain region at upper left. 
[[Image:1axc PCNA ProCheck Rama.jpg|thumb|200px|right| A Ramachandran plot generated from human [[PCNA]], a trimeric [[DNA clamp]] protein that contains both [[Beta sheet|β-sheet]] and [[Alpha helix|α-helix]] ([[Protein Data Bank|PDB]] ID 1AXC). The red, brown, and yellow regions represent the favored, allowed, and "generously allowed" regions, respectively, as defined by ProCheck]]