Conformational energy maps of amino acids with a side chain Cβ atom derived from high-resolution protein structures

Experimental protein energy maps in the (φ, ψ) space for the dipeptides of 20 naturally occurring amino acids using the current collections of high-resolution entries in the protein data bank (PDB) are presented here. Data sets were generated for hydrogen bond distance cut-off values of 2.7 Å and 3.1 Å. Neighborhood effects of proline residues on the (φ, ψ) maps have been examined. The impact of disulphide bridges on these maps has been critically examined. The comparisons of experimental maps with those obtained using various mole­cular mechanics and molecular dynamics methods were published earlier. The comparison metrics are: (i) locations of global and secondary minima, (ii) percentage areas enclosed by isoenergy contours, (iii) energy-based RMSD and (iv) barriers to conformational transitions. The experimental maps for individual amino acid dipeptide motifs show a higher degree of qualitative consistency with theoretical maps derived using molecular mechanics when compared to those from molecular dynamics methods. We also demonstrate that a majority of backbone conformations observed in the structures of small peptides in the Cambridge Crystallographic Database are within the allowed regions of the experimental Ramachandran maps. A few protein models obtained from NMR spectroscopy were evaluated in terms of the amino acid outlier energies using the experimental maps