HydrophilicityTable: Residue Atom Type Hydrophilicity Values

In vanddraabe: Identification and Statistical Analysis of Conserved Waters Near Proteins

Description

Atomic hydrophilicity values for the 20 naturally occurring amino acids and water.

Details

The Hydrophilicity Table is based on the work of Esposito (see reference below) in vanddraabe package. The hydrophilicity values are based on information from a 1995 analysis of published PDB structures and indicate how likely the individual atoms of the amino acid residues are to have a water molecule within 4.0 angstroms.

The data contained within the Hydrophilicity Table is based on ~7900 experimentally determined crystallographic protein structures with resolution values less than or equal to x.x Angstroms, a R-factor less than or equal to 0.26, and 20 or more bound waters each. The protein structures are from the Top8000 ("a database of about 8000 high-resolution, quality-filtered protein chains"; reference below) high quality protein dataset from the Kinemage laboratory at Duke University. The included structures had a range of B-values and occupancy values.

These values are based on the methods and protocols of Kuhn et al.

The Hydrophilicity Table contains:

• residueAtomName: Contracted residue type and atom name to aid looking up hydrophilicity values.

• residue: Three-letter residue name.

• atomName: Atom name indicating the atom type and its position in the amino acid residue.

• surfaceOccurrences: Number of times each atom has a defined solvent exposed surface area.

• hydratOccurrences: Proportion of the solvent exposed residue-specific atom type with a water molecule closely bound (within 4.0 Angstroms).

Author(s)

Emilio Xavier Esposito [e-mail]

References

Leslie A Kuhn, Craig A Swanson, Michael E Pique, John A Tainer, and Elizabeth D Getzof. Atomic and Residue Hydrophilicity in the Context of Folded Protein Structures. PROTEINS: Structure, Function, and Genetics, 1995, 23 (4), pp 536-547. DOI: 10.1002/prot.340230408 PMID: 8749849

Bradley J Hintze, Steven M Lewis, Jane S Richardson, and David C Richardson. Molprobity's ultimate rotamer-library distributions for model validation. Proteins: Structure, Function, and Bioinformatics, 2016, 84 (9), pp 1177-1189. DOI: 10.1002/prot.25039 Top8000 webpage

vanddraabe documentation built on June 8, 2019, 1:03 a.m.