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Atom Depth as a Descriptor of the Protein Interior

Alessandro Pintar^*, Oliviero Carugo^*, and Sándor Pongor^*

^* Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, AREA Science Park, Padriciano 99, 34012 Trieste, Italy; and Department of General Chemistry, University of Pavia, 27100 Pavia, Italy

Correspondence: Address reprint requests to Alessandro Pintar, Protein Structure and Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, AREA Science Park, Padriciano 99, 34012 Trieste, Italy. Tel.: 39-040-3757354; Fax: 39-040-226555; E-mail: pintar{at}icgeb.org.

Atom depth, defined as the distance (dpx, Å) 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.

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