Ramachandrans Plot

In a polypeptide, the main chain N-C alpha and C alpha-C bonds relatively
are free to rotate. These rotations are represented by the torsion angles, phi
and psi, respectively.
G.N.Ramachandran used computer models of small polypeptides to
systematically vary phi () and psi () with the objective of finding stable
conformations. For each conformation, the structure was examined for
close contacts between atoms. Atoms were treated as hard spheres with
dimensions corresponding to their van der Waals radii. Therefore, phi ()
and psi () angles, which cause spheres to collide, correspond to sterically
disallowed conformations of the polypeptide backbone.

Prediction of Sterically Permissible Structure From the Use of

Ramachandran Plot:
Rotations about the C-N bond are labeled with the phi (), and rotations
about the C-carbonyl carbon are labeled psi (). The peptide bond itself
tends to be planer, with two allowed states: a. the trans, of the peptide
bond joining the C=O and NH groups is nearly always 180 and b. cis,
0 (rarely). The principle that two atoms cannot occupy the same
space, limits the values of conformational angles. The allowed ranges of
and , for =180, fall into defined regions in a graph called
Ramachandran plot.

All possible conformations of a polypeptide chain, therefore can be

described in terms of their , conformational angles, a description
that automatically takes account of the fixed geometric features of the
polypeptide backbone. Thus any polypeptide conformation can be
represented as a point on a plot of versus , where and have values
that range from -180 to +180. By convention, the formation corresponding
to = 0, = 0 is one in which both peptide planes that are connected to a
common C atom lie in the same plane. Positive-variations in
correspond to clockwise rotations of the preceeding peptide about the
C-N bond when viewed from C toward N1. Positive variations in
correspond to clockwise rotations of the succeeding peptide about the C
-C2 bond when viewed from C toward C2.

A: Angle Atoms
B: Angle Positive
is defined as positive for clockwise rotation of
CO-1, when looking along the C1-NH1
Rotation
bond. In this conformation, 180 .

A: Angle Atoms

B: Angle Positive
Rotation

is defined as positive for clockwise rotation of NH+1, when looking along the C1-CO1
bond.
Glysine residue region

Ramachandran plot, showing which atomic collisions (using a hard-sphere

approximation) produce the restrictions of the main-chain angles and . The
cross-hatched regions are allowed for all residues, and each boundary of a prohibited
region is labeled with the atoms that collide in that conformation. Additional shaded
regions are for glycine residues only. Each boundary of a prohibited region is
labeled with the atoms that collide in that conformation.

Experiments with models that approximate the polypeptide atoms are hard
spheres, with appropriate van der Waals radii, quickly reveal that many ,
angular combinations are impossible because of steric interactions or
collisions between atoms along the backbone or between backbone
atoms and the side-chain R groups. For example, it is clear that at any
circumstance the = 0, = 0 conformation is near to impossible. The
reason is that this conformation results in non-covalently bonded interatomic contacts that are considerably less than the sum of the van der
Waals radii of the atoms involved. In fact, of all the possible ,
combinations, only a relatively restricted number of conformations are
sterically allowed.
What do you mean by Steric interactions?
Atoms take up space and cannot occupy the same space at the same
time. Covalent bonds connect them and these bonds cannot be broken.
So the movements that are more concerned involve rotations only.
And it has been seen previously that there are only two angles that
rotate in a given residue, , .
The Ramachandran plot shows explicitly how the accessible regions of
, space are limited by steric interactions among the polypeptide
backbone and side-chain groups, assuming that the atomic groups
behave as rigid spheres having appropriate van der Waals radii. In
reality, the atoms in molecules do not behave as rigid spheres, so real
proteins span a slightly greater range of values than suggested by this plot.
R

The plot is similar to a topographical map,

where energy, instead of altitude, is shown
with the contours. Surrounding phi=0,
psi=0 there is a high energy "plateau"
which drops into valleys of stability with
minima for alpha helices and beta sheet,
noted in the figure. In large proteins, the
large majority of non-glycine residue
possesses phi, psi combinations that reside
in these valleys.

Explanation:
Red area in the figure delimits energetically preferred regions of and ,
while, the yellow area in the figure delimit sterically-disallowed regions.
The conformations of most amino acids fall into either right-handed
alpha-helix or -sheet regions. Glycine has access to additional
conformations. In particular it can form left-handed helix: L. Most
residues fall in or near the allowed regions, although a few are forced by the
folding into energetically less-favourable states. The goal is to identify the
intramolecular interactions that make certain combinations of torsion
angles unfavorable. Such interactions arise whenever two atoms or
functional groups penetrate each other's van der Waals radii.
The allowed regions generate standard conformations. A stretch of
consecutive residues in the conformation (typically 6-20 in native states of
globular proteins) generates an -helix. Repeating the conformation
generates an extended -strand. Two or more -strands can interact laterally
to form -sheets. Helices and sheets are standard or prefabricated
structural pieces that form components of the conformations of most
proteins. They are stabilized by relatively weak interactions, hydrogen
bonds, between mainchain atoms.
Conclusion: Owing to the basic geometric properties of the polypeptide
chain, the sterically allowed conformations are greatly restricted by the
occurrence of unfavourable steric interactions between various atomic
groups. As a result, fibrous proteins with regularly repeating structures can
be defined by single values for the coordinates and . Proteins that have

less regularly repeating structures would require more than a single set
coordinates but nevertheless they would be expected to obey the same set of
limits established by the Ramachandran plot.