The document summarizes Ramachandran plots, which visualize backbone dihedral angles ψ against φ of amino acid residues in protein structures. Ramachandran plots show sterically allowed and disallowed conformations based on calculations using van der Waals radii and bond angles. Specific regions of the plot correspond to different secondary structures like alpha helices and beta sheets. The plots can also be used to validate protein structures by comparing observed dihedral angles to expected allowed regions.

1. Ramachandran plot
By
Krunal Chodvadiya
10MBT001

2. Ramachandran plot
 A Ramachandran plot (also known as a Ramachandran
diagram or a [φ,ψ] plot), originally developed in 1963 by G. N.
Ramachandran, C. Ramakrishnan and V. Sasisekharan, is a
way to visualize backbone dihedral angles ψ against φ
of amino acid residues in protein structure.
 Plot of φ vs. ψ
 The conformations of peptides are defined by the values of φ
and ψ.

3.  Each peptide bond has partial double-bond character due to
resonance and cannot rotate.
 Three bonds separate sequential C in a polypeptide chain.
The N-C and C – C bonds can rotate, with bond angles
designated φ and ψ respectively. The peptide C-N bond is not
free to rotate.
 Other single bonds in the backbone may also be rotationally
hindered, depending on the size and charge of the side chain
R groups.

4. Both φ and ψ increases as the carbonyl and amide nitrogen
(respectively) rotate clockwise.

5. • By convention, both φ and ψ are defined as 00 when the two
peptide bonds flanking that C carbon are in the same plane.
• In a protein, this conformation is prohibited by steric overlap
between an carbonyl oxygen and an amino hydrogen atom.

6. Ramachandran plot for L-Ala residues.
• Conformations deemed possible are those that involve
little or no steric interference, based on calculations using
known van der Waals radii and bond angles.

7. • The areas shaded dark blue reflect conformations that
involve no steric overlap and thus are fully allowed.
• Medium blue indicates conformations allowed at the
extreme limits for unfavorable atomic contacts.
• lightest blue area reflects conformations that are
permissible if a little flexibility is allowed in the bond
angles.
• Unshaded portion indicates sterically disallowed
conformations

8. values of φ and ψ for various allowed 20 structures
Every type of secondary structure can be completely described by the
bond angles φ and ψ at each residue.

9. The structure of cytochrome C shows many segments of helix
and the Ramachandran plot shows a tight grouping of φ = -60 and
psi = -45 to -50.
-helix cytochrome C
Ramachandran plot

10. Similarly, repetitive values in the region of φ = -110 to -140 and ψ =
+110 to +135 give beta sheets. The structure of plastocyanin is
composed mostly of beta sheets; the Ramachandran plot shows
values in the –110, +130 region:
beta-sheet plastocyanin
Ramachandran plot

11. Glycine Ramachandran Plot
Because its side chain, a single hydrogen atom, is small, a Gly residue
can take part in many conformations that are sterically forbidden for
other amino acids.

12. Proline Ramachandran Plot
The range for Pro residues is greatly restricted because φ is limited by
the cyclic side chain to the range of -35 to -85.

13. Significance
 A Ramachandran plot can be used in 2 somewhat different ways.
i. One is to show in theory which values, or conformations, of the ψ and φ
angles are possible for an amino-acid residue in a protein.
ii. A second is to show the empirical distribution of datapoints observed in
a single structure in usage for structure validation, or else in a database
of many structures.

14. Thank you