Atom depth as a descriptor of the protein interior.

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