A novel tool/method for visualization of orientations of side chains relative to the protein's main chain

A novel visualization tool (method) is developed in order to achieve more efficient insight into protein structure and relative orientations of protein's side chains. Using arrows as vectors, which start (for all amino acid residues in a protein) from the C-alpha atom and end at the most distant non-hydrogen atom in the side chain belonging to the same amino acid residue, this method visualizes orientations of side chains relative to protein's main chain (defined by positions of C-alpha atoms). The orientation of vector for each amino acid residue is from C-alpha atom to the end of its side chain. The only one exception is in the case of glycine, where the residue will be represented by sphere (because the side chain of glycine consists of a single hydrogen atom). In all cases coloring is made using Kyte-Doolittle hydrophobic scale. By such a method one can obtain better insight into the orientation of protein's side chains relative to its interior or its outer surface area.