Radial Locations of Amino Acid Residues in a Globular Protein: Correlation with the Sequence1

Abstract

The location measure of a residue in a globular protein is defined as the number of C^α atoms surrounding the residue located within a sphere of the radius of 14 Å. This quantity is a measure of the exposure of a residue to solvent, and is related closely to the distance from the center of mass of a protein. In this work, the experimental value for each residue of a protein is obtained from the X-ray crystallographic data, and the quantity is also calculated from the amino acid sequence data by applying an empirical parameter set to it. The correlation between the experimental and computed quantities is as high as 0.50 on the average over 92 proteins of known three-dimensional structure. Therefore, the location measure of every residue in a globular protein is predictable with good accuracy from the sequence.