Atom depth as a descriptor of the protein interior

From: Biophysical Journal | Date: April 1, 2003| Author: | Copyright information

ABSTRACT Atom 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 ...

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