"Smooth surfaces for protein side chains"

A component of a new backbone-dependent rotamer library is shown. The probability of the trans rotamer of valine is plotted as a function of the backbone dihedrals φ and ψ. The residues in the alpha-helix, parallel beta-sheet and left-handed helix regions are depicted as a snowboarder, a skier and a luger respectively. Their heads are the side-chain C_β atoms. The arms have the same trans-rotamer side-chain conformation while their legs have different backbone conformations in accordance with the residue locations on the Ramachandran map. The heights of the hills are proportional to the backbone-dependent probability of the <trans> rotamer, relative to the <g+> and <g-> rotamers.

back to top

Shapovalov, M.S., and Dunbrack, R.L., Jr. (2011). A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions. Structure, 19, 844-858.

back to top