At right is a fragment of a polypeptide chain. In the center is a single complete alanine residue. Check Alanine to identify its atoms1. The other atoms are fragments of adjacent amino acids2. Drag with your mouse to rotate the model.
The Alanine is covalently bonded to other amino acids through peptide bonds. Check Peptide Bonds to locate them.
The double bonds between main chain (backbone) C and O delocalize, making the peptide bonds also have partial double bonds (half-dotted bonds). This prevents the peptide bond from rotating.
Each peptide bond holds six atoms in a plane. Check Planes to see them.
The alpha carbon (Cα) 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 called3 Phi and Psi (in Greek letters, φ and ψ). 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 Phi and Psi angle combinations 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 model simulation allows two atoms to overlap, unlike real atoms.)
Check White to make clashes easier to see. Rotate Phi and Psi to find angle combinations 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 angle combinations (that avoid clashes) correspond largely to the secondary structures observed in proteins: alpha helices, beta sheets, and turns.
Ramachandran and team also showed that the major effect of sidechains on the allowed phi and psi angles is due to Cβ 2. 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 proteins.
At right is a Ramachandran Plot 9, 10 with 100,000 data points taken from
crystal structures11. Each data point represents the
combination of phi and psi angles
occurring in a single
amino acid. Residues in an
conformation are marked
and those in a
The cluster of data in the upper right quadrant represents mostly
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.
Challenge your understanding with the PRACTICE QUIZ.
This tutorial is available in two locations:
There is also a Slideshow, a YouTube Video, and a Practice Quiz.