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Ramachandran plot
From Wikipedia, the free encyclopedia

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Ramachandran plot - Wikipedia, the free encyclopedia http://en.wikipedia.org/wiki/Ramachandran_plot

A peptidic bond has two degree

of freedom, the dihedral angles
named φ and ψ by
Ramachandran.

A Ramachandran plot generated from the

protein PCNA, a human DNA clamp protein that
is composed of both beta sheets and alpha
helices (PDB ID 1AXC). Points that lie on the
axes indicate N- and C-terminal residues for
each subunit. The green regions show possible
angle formations that include Glycine, while the
blue areas are for formations that don't include
Glycine.

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Ramachandran plot - Wikipedia, the free encyclopedia http://en.wikipedia.org/wiki/Ramachandran_plot

A Ramachandran plot (also known as a Ramachandran

map or a Ramachandran diagram or a [φ,ψ] plot),
developed by Gopalasamudram Narayana Ramachandran
and Viswanathan Sasisekharan is a way to visualize dihedral
angles ψ against φ of amino acid residues in protein
structure.[1] It shows the possible conformations of ψ and φ
angles for a polypeptide.

Mathematically, the Ramachandran plot is the visualization

of a function . The
domain of this function is the torus. Hence, the conventional
Ramachandran plot is a projection of the torus on the plane,
resulting in a distorted view and the presence of
discontinuities.

One would expect that larger side chains would result in

more restrictions and consequently a smaller allowable
region in the Ramachandran plot. In practice this does not
appear to be the case; only the methylene group at the α
position has an influence. Glycine has a hydrogen atom,
with a smaller van der Waals radius, instead of a methyl
group at the α position. Hence it is least restricted and this is
apparent in the Ramachandran plot for Glycine for which
the allowable area is considerably larger.
In contrast, the Ramachandran plot for proline shows only a
very limited number of possible combinations of ψ and φ.
The Ramachandran plot was calculated just before the first
protein structures at atomic resolution were determined.
Forty years later there were tens of thousands of
high-resolution protein structures determined by X-ray
crystallography and deposited in the Protein Data Bank
(PDB). From one thousand different protein chains,
Ramachandran plots of over 200 000 amino acids were
plotted, showing some significant differences, especially for
glycine (Hovmöller et al. 2002). The upper left region was
found to be split into two; one to the left containing amino
acids in beta sheets and one to the right containing the
amino acids in random coil of this conformation.
The classical version of the Ramachandran plot
for (a) alanine (but often taken as typical for all
non-glycines) and (b) glycine according to
Ramachandran & Sasisekharan (1968). The fully
allowed regions are shaded; the partially allowed
regions are enclosed by a solid line. The
connecting regions enclosed by the dashed lines
are permissible with slight flexibility of bond
angles. These plots were arrived at by stereo-
chemical modelling. Although some overall
features of these plots are correct, the details
differ from the experimentally observed
Ramachandran plots for (c) all 19 non-glycines
and (d) glycine. The most remarkable
differences are that most regions show a 45
degree slope rather than being parallel to any of
the axes, the beta sheet region is split into two
distinct maxima and the two most populated
regions (red) for glycine seen in (d) were
predicted to be only just permissible as shown in
(b). There are five areas in the glycine plot; two
with psi 0 and three with psi 180. Referenced
from Hovmöller (2002)

One can also plot the dihedral angles in polysaccharides and other polymers in this fashion. For the first two
protein side-chain dihedral angles a similar plot is the Janin Plot.

Software
Ramachandran plot 2.0 (http://dicsoft1.physics.iisc.ernet.in/rp)
Web-based tool showing Ramachandran plot of any PDB entry (http://www.fos.su.se/~pdbdna
/input_Raman.html)
STING

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Ramachandran plot - Wikipedia, the free encyclopedia http://en.wikipedia.org/wiki/Ramachandran_plot

Pymol with the DynoPlot extension

VMD, distributed with dynamic Ramachandran plot plugin
Sirius
Swiss PDB Viewer (http://ca.expasy.org/spdbv/)
TALOS (http://spin.niddk.nih.gov/NMRPipe/talos/)

See also PDB for a list of similar software.

References
1. ^ RAMACHANDRAN GN, RAMAKRISHNAN C, SASISEKHARAN V (July 1963). "Stereochemistry of
polypeptide chain configurations". J. Mol. Biol. 7: 95–9. PMID 13990617 (http://www.ncbi.nlm.nih.gov/pubmed
/13990617) .

S. Hovmöller, T. Zhou & T. Ohlson (2002) Conformations of amino acids in proteins. In: Acta Cryst. vol.
D58, p. 768-776.

External links
DynoPlot in PyMOL wiki (http://www.pymolwiki.org/index.php/DynoPlot)
Link to Ramachandran Plot Map of alpha-helix and beta-sheet locations (http://www.cryst.bbk.ac.uk
/PPS95/course/3_geometry/rama.html)
Link to Ramachandran plot calculated from protein structures determined by X-ray crystallography
compared to the original Ramachan. (http://www.fos.su.se/~svenh/index.html)
Proteopedia Ramachandran Plot (http://www.proteopedia.org/wiki/index.php/User:Karl_Oberholser
/Ramachandran_Plots#Ramachandran_Plots)
Retrieved from "http://en.wikipedia.org/wiki/Ramachandran_plot"
Categories: Biochemistry methods | Plots (graphics)

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