calcAtomClassHydrophilicity: Atom Class Hydration Fraction

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

Description

Calculates the mean hydration value for atoms within a class.

Usage

calcAtomClassHydrophilicity(df.AtomHydroTEMP)

Arguments

df.AtomHydroTEMP

The newly calculated (determined) atomic hydrophilicity values

Details

This function is called within HydrophilicityEvaluation() to calculate the hydration fraction for the five atom classes listed in the Value section.

(num surface exposures)/(num atom occurrences)

NOTE: This is a non-public function.

Value

This function returns:

• hydratFraction.oxy.neut: Neutral oxygen atoms; enter names.resATs.oxy.neut to see list of residue-atomtypes

• hydratFraction.oxy.neg: Negative oxygen atoms; enter names.resATs.oxy.neg to see list of residue-atomtypes

• hydratFraction.nitro.neut: Neutral nitrogen atoms; enter names.resATs.nitro.neut to see list of residue-atomtypes

• hydratFraction.nitro.pos: Positive nitrogen atoms; enter names.resATs.nitro.pos to see list of residue-atomtypes

• hydratFraction.carb.sulf: Carbon and sulfur atoms; enter names.resATs.carb.sulf to see list of residue-atomtypes

These values are returned in HydrophilicityValues.AtomTypeClasses of the results of HydrophilicityEvaluation()

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

See Also

Other "Hydrophilicity Evaluation" "Bound Water Environment": HydrophilicityEvaluation, calcAtomHydrationEstimate, getProtAtomsNearWater, getResidueData

Examples

 ## Not run: 
  calcAtomClassHydrophilicity(df.AtomHydroTEMP)
 
## End(Not run)

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