Atom depth in protein structure and function.

Alessandro Pintar; Oliviero Carugo; Sándor Pongor

doi:10.1016/j.tibs.2003.09.004

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Atom depth in protein structure and function.

Alessandro Pintar·Oliviero Carugo·Sándor Pongor

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Abstract

Atom depth, originally defined as the distance between a protein atom and the nearest water molecule surrounding a protein, is a simple but valuable geometrical descriptor of the protein interior. It can be easily computed from the 3D structure of a protein, thus complementing the information provided by the calculation of the solvent accessible surface area and buried surface area. Depth has been found to be correlated with several molecular, residue and atomic properties, such as average protein domain size, protein stability, free energy of formation of protein complexes, amino acid type hydrophobicity, residue conservation and hydrogen/deuterium amide proton exchange rates.

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Algorithms Amino Acids Computer Simulation Humans Interferon alpha-2 Interferon-alpha Models, Molecular Protein Conformation Protein Subunits Proteins Recombinant Proteins Solvents Journal Article Review

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Alessandro Pintar, Oliviero Carugo, Sándor Pongor. 2003. Atom depth in protein structure and function.. https://doi.org/10.1016/j.tibs.2003.09.004

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