getResidueData: Number of Residues and Solvent Accessible/Exposed Residues

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

Description

Calculate the number of residues and solvent exposed residues.

Usage

getResidueData(atoms.oi.prot, SurExp.res.atoms.tf)

Arguments

atoms.oi.prot	The protein data.frame with the SASA and SASA lost values for each protein atom.
SurExp.res.atoms.tf	TRUE/FALSE vector indicating if an atom is solvent exposed/accessible

Details

This function is called within HydrophilicityEvaluation() to provide general solvent accessibility data for the protein structure of interest.

Value

This function returns:

• num.res: number of residues within the structure

• num.res.buried: number of residues with NO solvent accessible surface area

• num.res.SurExp: number of residues with solvent accessible surface area

• pct.res.SurExp: percentage of residues with solvent accessible surface area

• SASA.total: total protein solvent accessible surface area; Angstroms^2^

• SASA.lost: total protein solvent accessible surface area lost due to bound waters; Angstroms^2^

• pct.SASA.exposed: percentage protein solvent accessible surface area (SASA.total - SASA.lost) / SASA.total

These values are returned in df.residue.hydro of the results of HydrophilicityEvaluation()

Author(s)

Emilio Xavier Esposito [e-mail]

See Also

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

Examples

  ## Not run: 
  getResidueData(atoms.oi.prot = PDB.1hai.aoi.clean.SASA.prot,
        SurExp.res.atoms.tf = PDB.1hai.SurExp.res.atoms.tf)
  
## End(Not run)

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