Ramachandran Plot Explained — What Phi and Psi Angles Tell You

What is a Ramachandran plot?

A Ramachandran plot (named after G.N. Ramachandran who first described it in 1963) is a scatter plot of the backbone dihedral angles phi (φ) and psi (ψ) for every residue in a protein. It's one of the most important tools for validating protein structure quality — a good structure has most of its residues in the "allowed" regions of the plot.

Understanding phi and psi angles

Every amino acid residue in a protein backbone has two rotatable bonds: the N-Cα bond (rotation around this is the phi angle) and the Cα-C bond (rotation around this is the psi angle). The peptide bond itself (C-N) is planar and doesn't rotate. These two angles, phi and psi, completely define the backbone conformation at each residue. Both angles range from -180° to +180°.

The allowed regions

Not all combinations of phi and psi are physically possible. Many would cause atoms to clash (come too close together). The Ramachandran plot shows which combinations are sterically allowed. There are typically three main populated regions:

The beta-sheet region (upper left quadrant, phi ≈ -120° to -60°, psi ≈ +100° to +180°) corresponds to the extended conformations found in beta strands. The alpha-helix region (middle left, phi ≈ -90° to -40°, psi ≈ -60° to -20°) corresponds to the right-handed alpha helix. The left-handed helix region (upper right, phi ≈ +40° to +100°) is sparsely populated since left-handed helices are energetically unfavorable for L-amino acids.

Glycine is special

Glycine, the smallest amino acid (its side chain is just a hydrogen atom), has much more conformational freedom than other residues. It can occupy regions of the Ramachandran plot that are forbidden for other amino acids. This is why glycine is often found in tight turns and loops.

Proline is restricted

Proline, whose side chain cyclizes back to the backbone nitrogen, is highly restricted. Its phi angle is locked at approximately -65°, so it appears as a narrow vertical strip on the plot.

Using the plot for validation

A high-quality experimental structure should have at least 90% of its residues in the favored regions. Outliers (residues outside allowed regions) may indicate errors in the structure, or they may be functionally important — active site residues sometimes adopt strained conformations to perform catalysis.

Try generating a Ramachandran plot for any protein using our free Ramachandran plot generator.