RAMACHANDRAN PLOT
NYNIKA.S
DEPARTMENT OF STUDIES IN BIOCHEMISTRY
UNIVERSITY OF MYSORE
GUIDED BY
Dr N.M JAMEEL SIR
RAMACHANDRAN PLOT
INTRODUCTION:
• A Ramachandran plot is also known as Ramachandran
diagram was developed in 1963 by Gopalasamudram
Narayana Ramachandran,C.Ramakrishnan and
V.Sasishekaran.
• Ramachandran plot is a way to visualise energitically
allowed regions for backbone dihedral angle psi against phi
of amino acid residues in protein structure.
• In a polypeptide the main chain N-Cα and Cα-C bonds are
relatively free to rotate . These rotations are represented by
torsion angles phi and psi respectively.
PEPTIDE
• A Peptide is a short chain
of amino acids . The
amino acids in peptide
are connected to one
another in a sequence by
peptide bond.
• Carboxyl group of one
amino acid condenses
with amino group of
another amino acid with
an elimination of water
molecule to form peptide
bond.
CHARACTERISTICS OF PEPTIDE BOND
• Peptide bond has partial double bond character , it
is a resonance hybrid of two forms,
• The peptide bond is rigid and planar.
• The four atoms of the peptide group (C,O,N,H) lie in
a single plane in such a way that the oxygen atom of
the carbonyl group and the hydrogen atom of the
amino group are trans to each other.
TORSION ANGLES
• Torsion angles are also known
as dihedral angles which are
defined by four points in
space.
• In protein the two torsion
angles phi(Φ) and psi(Ψ)
describe the rotation of the
polypeptide chain around the
two bond on both sides of the
Cα atom.
• The bond between N-Cα is
known as phi bond and bond
between Cα- C is know as psi
bond.
RAMACHANDRAN PLOT
• G N Ramachandran used computer models of small
polypeptide to systematically vary phi and psi with an
objective of finding stable conformation of protein.
• The structure was examined for close contacts between
atoms.
• Atoms were treated as hard spheres with dimensions
corresponding to their vander waals radii .
• Therefore phi and psi angles which causes spheres to
colloid correspond to sterically disallowed
conformations of the polypeptide backbone.
RAMACHANDRAN PLOT
RAMACHANDRAN PLOT
• In the diagram the white area correspond to conformation,
where atoms in the polypeptide come closer than sum of
their vander waals radii . These regions are sterically
disallowed for all amino acid except glycine.
• The dark region correspond to conformations, where there
are no steric clashes i.e these are the allowed regions
namely alpha-helical and beta sheet conformations .
• The light area show the allowed regions if slightly shorter
vander waals radii are used in the calculation i.e the atoms
are allowed to come a little closer together . This brings
about an additional region which correspond to the left
handed –helix.
RAMACHANDRAN PLOT
• L-amino acids cannot form extended regions of left handed
helix but occasionally individual residues adopt this
conformation .These residues are usually glycine but can also
be asparagine or aspartate , where side chain forms a
hydrogen bond with the main chain and therefore stabilizes
this otherwise leads to unfavourable conformation .
• Disallowed regions generally involve steric hindrance
between the side chain C- beta methylene group and main
chain atoms.
RAMACHANDRAN PLOT
RAMACHANDRAN PLOT FOR POLY-
L GLYCINE
RAMACHANDRAN PLOT FOR POLY L GLYCINE:
• Glycine can adopt phi and psi angles in all four
quadrants of the Ramachandran plot.
• Glycine has hdrogen atom with a smaller vander
waals radius instead of a methyl group at the beta –
position .
• In Ramachandran plot the allowable area for
glycine is considerably larger.
• The Ramachandran plot for glycine resides in a
polypeptide chain differs from the other residues
with respect to its conformation.
RAMACHANDRAN PLOT
• Ramachandran plot can be constructed for polymers of
each of the 20 amino acids.
• It is significant to note that Ramachandran plot for
many amino acid residues are generally very similar
having only three region with favourable conformation.
• However for instance where the side chain is branched
near alpha-C atom as in the case of threonine , it
occupies more space close to the peptide backbone and
restricts the approach of atoms in the neighbouring
peptide groups.
• As a result allowed conformations are more restricted
for polypeptides of branched amino acids.
RAMACHANDARN PLOT
• When Psi(Ψ) is
fixed at 165°,most
Phi(Φ) angles
produce clashes.
RAMACHANDRAN PLOT
RAMACHANDRAN PLOT
STRUCTURE PHI(Φ) PSI(Ψ)
TYPE
β Strand - 150° to -100° + 120° to +160°
α helix - 70° to - 60° -50° to - 40°
310 helix - 70° to - 60° -30° to - 10°
RAMACHANDRAN PLOT
REFERENCE
PRINCIPLES OF BIOCHEMISTRY
LEHNINGER
BIOCHEMISTRY
VOET AND VOET
THANK YOU
