HydrophilicityTable: Residue Atom Type Hydrophilicity Values

Description Details Author(s) References


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


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:


Emilio Xavier Esposito emilio@exeResearch.com


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.