Atom depth as a descriptor of the protein interior

tom depth, defined as the distance (dpx, A
̊
) of a nonhydrogen atom from its closest solvent-accessible protein
neighbor, provides a simple but precise description of the protein interior. Mean residue depths can be easily computed and are
very sensitive to structural features. From the analysis of the average and maximum atom depths of a set of 136 protein
structures, we derive a limit of
;
200 residues for protein and protein domain size. The average and maximum atom depths in
a protein are related to its size but not to the fold type. From the same set of structures, we calculated the mean residue depths
for the 20 amino acid types, and show that they correlate well with hydrophobicity scales. We show that dpx values can be used
to partition atoms in discrete layers according to their depth and to identify atoms that, although buried, are potential targets for
posttranslational modifications like phosphorylation. Finally, we find a correlation between highly conserved residues in
structural neighbors of the same fold type, and their mean residue depth in the reference structure