Conformation Energy Contour Plots

As discussed earlier, the (φ, ψ) conformation map of the polypeptide chain can be produced in three different ways:

  1. Steric plot as originally proposed, based on various distance criteria, yielding allowed (no steric overlaps) and disallowed (overlaps) boundaries in the map.
  2. Statistical probability-based conformational map, using quality data from PDB.
  3. Energy contour map describing the energy landscape of the (φ, ψ) conformations.

The information obtained from a steric plot (by using simple criteria of allowed/disallowed atomic overlaps) is not quite enough. For instance, the question may arise as to how many contacts are bad in a disallowed region and how bad they are (Ramachandran & Sasisekharan, 1968, p.347). It is also possible they might be accommodated in the structure by compensating with favorable conformation (Kumar & Rathore, 2024).

Such plots can be generated by a coordinate scan algorithm, in which both the coordinates (φ, ψ) are scanned (usually by 1–10°), and for each conformation, the potential energy of the molecule is calculated and minimized. The energy may be evaluated either by using molecular mechanics-based force fields or computationally demanding QM methods (such as semi-empirical, DFT, ab initio, or QM/MM methods). Finally, the (φ, ψ) plot is generated with energy contours drawn on 2D or energy values represented on the third z-axis in a 3D energy map.

Conformation Illustration
Cite: Kumar, Mayank & Rathore, R. S. (2025). RamPlot: A webserver to draw 2D, 3D, and assorted Ramachandran (φ, ψ) maps. Journal of Applied Crystallography, 58(3), 630-636. DOI :10.1107/S1600576725001669