At right is a fragment of a
In the center is a single complete alanine residue.
Check Alanine to identify its atoms1. The other atoms are fragments of adjacent
Drag with your mouse to rotate the model.
The Alanine is covalently bonded to other amino acids through
Peptide Bonds to locate them.
The double bonds between
main chain (backbone)C
delocalize, making the peptide bonds also have partial double bonds
This prevents the peptide bond from rotating. Each peptide bond holds three atoms on each end
in a plane. Check Planes to see them.
in the center of each amino acid
is held in the main chain by two rotatable bonds. The
dihedral (torsion) angles
of these bonds are called3Phi
(in Greek letters,
Use the radio buttons (top of right panel) to identify the rotatable main-chain bonds,
and click the -20° and +20° buttons to see them rotate.
Click the Reset button.
The balls shown are much smaller than the atoms they represent.
Check van der Waals to see the real sizes of the atoms4.
In fact, most
angles are impossible because two atoms cannot occupy the same space.
Check Show Clashes to see where non-bonded atoms are overlapping, and thus
in physically impossible positions.
(This simulation allows two atoms to overlap, unlike real atoms.)
Now, uncheck van der Waals to simplify the view, but keep
Show Clashes checked. Rotate
to find angles where there are no clashes.
In the early 1960’s,
G. N. Ramachandran
(University of Madras, India) and coworkers
computationally determined the phi and psi angles that avoid steric collisions,
initially treating the atoms simply as rigid spheres5, 6.
They showed that the physically allowed angles (avoiding clashes) correspond largely
to the secondary structures observed in proteins:
alpha helices, beta strands/sheets, and turns.
Ramachandran and team also showed that the major effect of sidechains on the allowed phi and psi
angles is due to Cβ2.
Sidechains larger than that of alanine affect the allowed
angles by only a few percent 7, 8.
The Ramachandran Plot below shows the phi and psi angles actually observed in
At right is a Ramachandran Plot9, 10 with 100,000 data points taken from
crystal structures11. Each data point represents the
phi and psi angles
for a single
amino acid. Residues in an alpha-helical conformation are marked
and those in a beta strand conformation, β.
The cluster of data in the upper right quadrant represents mostly turns.
This plot excludes glycine (whose sidechain is a single hydrogen), proline
(whose sidechain is covalently linked back to the main chain), and amino acids that precede
proline. These special cases have
different distributions on Ramachandran plots.
The outlines of the black dots that identify the atoms in Alanine are smaller than
the actual (van der Waals) sizes of those atoms. Check van der Waals to see the actual
Each amino acid contributes 3 atoms directly to the
main chain (backbone)
of covalent bonds:
The model here includes -C-C-N-C-C-N-C-.
Cα has alanine's sidechain, -CH3.
Alanine's sidechain carbon is termed Cβ.
Edsall JT, Flory PJ, Kendrew JC, Liquori AM, Nemethy G, Ramachandran GN, Scheraga HA.
A proposal of standard conventions and nomenclature for the description of
polypeptide conformation. J Biol Chem. 1966 Feb 25;241(4):1004-8.
Actually, the van der Waals checkbox shows the atoms at 88% of their true van der Waals
radii. In the above simulation, clashes are reported when 88% of the true radii overlap.
This is in accord with the observations of
Ramachandran and Sasisekharan6, who found that allowed interatomic distances
for non-bonded atoms are ~0.4 Å less than their van der Waals radii10.
The van der Waals radius of carbon is 1.7 Å. Thus, the van der Waals distance between
the centers of two non-bonded carbon atoms is 3.4 Å. However the minimum allowed distance
is about 0.4 Å less, which is 12% less. Thus 88% of the true van der Waals radii was
used in the above simulation for detection of "clashes".
Ramachandran, G. N., Ramakrishnan, C., Sasisekharan, V.
Stereochemistry of polypeptide chain configurations.
J Mol Biol. 1963 Jul;7:95-9.
Ramachandran, G. N., Sasisekharan V. Conformation of polypeptides and proteins.
Adv Protein Chem. 1968;23:283-438.
Ramakrishnan, C., Ramachandran, G. N.
Stereochemical criteria for polypeptide and protein chain conformations. II.
Allowed conformations for a pair of peptide units. Biophys J. 1965 Nov;5(6):909-33.
Chakrabarti P, Pal D. The interrelationships of side-chain and main-chain conformations in
proteins. Prog Biophys Mol Biol. 2001;76(1-2):1-102.
Ramachandran and Sasisekharan6 determined inter-atomic distances of
closest approach of non-bonded atoms from crystal structures. For each pair of elements
(their Table VI), they determined an allowed distance, and a partially allowed distance.
Distances less than the partially allowed values are “very unlikely” to occur due to
steric repulsion. The allowed distances are 0.3 to 0.5 Å less than the van der Waals radii
(their page 327).
The partially allowed distances are usually 0.1 Å, sometimes 0.2 Å,
less than the allowed distances.
Lovell SC, Davis IW, Arendall WB 3rd, de Bakker PI, Word JM, Prisant MG,
Richardson JS, Richardson DC.
Structure validation by C-alpha geometry: phi,psi and C-beta deviation.
Proteins. 2003 Feb 15;50(3):437-50.