vanddraabe (version 1.1.1)

BoundWaterEnvironment: Bound Water Environment

Description

Various enviroment counts for bound waters.

Usage

BoundWaterEnvironment(distances, set.oi.idc, names.atoms, names.res.atoms,
  structure, radius = 3.6)

Arguments

distances

Matrix of atomic pairwise distances

set.oi.idc

Indices of atoms of interest; can be protein, water, or HETATMs if those are of interest

names.atoms

Atom names for the atoms of interest. Valid atom names are provided in the names.backbone.atoms() and names.sidechain.atoms() functions; e.g.; "C", "O", "CB", "OG1", "CG2", "N"

names.res.atoms

Residue and atom names of interest. Valid residue-atom names are provided in the names.res.AtomTypes() function; e.g.; "THR C", "THR O", "THR CB", "THR OG1"

structure

The protein structure of interest with its residue and atom names; X, Y, and Z coordinates; residue and atom numbers; and B-value, Normalized B-value, Occupancy, and Mobility values.

radius

Distance in Angstroms between the atoms of interest; default: 3.6 Angstroms

Value

A list of the bound water environment values for nearby heavy atoms.

• adn: num of nearby heavy atoms

• ahp.sum: sum of hydrodrophilicy values

• ahp.mu: mean of hydrodrophilicy values

• ahp.sd: standard deviation of hydrodrophilicy values

• hbonds: number of possible hydrogen bonds

• o.sum: sum of occupancy values

• o.mu: mean of occupancy values

• o.sd: standard deviation of occupancy values

• b.exp.sum: sum of experimental B-values

• b.exp.mu: mean of experimental B-values

• b.exp.sd: standard deviation of experimental B-values

• mobility.sum: sum of mobility values

• mobility.mu: mean of mobility values

• mobility.sd: standard deviation of mobility values

• nBvalue.sum: sum of normalized Bvalues

• nBvalue.mu: mean of normalized Bvalues

• nBvalue.sd: standard deviation of normalized Bvalues

Details

For the heavy atoms near each water molecule (oxygen atom) the bound water environment is calculated. These values are defined in the Return section. The default radius distance is 3.6 Angstroms. While it is possible to define the radius to a value other than 3.6 this value is hardcoded into the ConservedWaters() function. This might change in future versions.

NOTE: This function is designed to work with ConservedWaters() via the base::apply() function processing rows (the MARGIN = 1 option). For this reason it is NOT a public function. The Nearby() is specifically designed to work with this function.

References

Paul C Sanschagrin and Leslie A Kuhn. Cluster analysis of consensus water sites in thrombin and trypsin shows conservation between serine proteases and contributions to ligand specificity. Protein Science, 1998, 7 (10), pp 2054-2064. DOI: 10.1002/pro.5560071002 PMID: 9792092 WatCH webpage

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, 2 (4), pp 536-547. DOI: 10.1002/prot.340230408 PMID: 8749849

See Also

Other "Bound Water Environment": BoundWaterEnvironment.interact, BoundWaterEnvironment.quality, Mobility, NormalizedBvalue, calcBvalue, calcNearbyHydrationFraction, calcNumHydrogenBonds

Examples

# NOT RUN {
  
# }
# NOT RUN {
  distances <- PDB.1hai.h2o.prot.dists[3, ]
  set.oi.idc <- prot.idc
  names.atoms <- PDB.1hai.aoi.clean$elety[prot.idc]
  names.res.atoms <- paste(PDB.1hai.aoi.clean$resid[prot.idc], names.atoms, sep =" ")
  structure <- PDB.1hai.aoi.clean
  BoundWaterEnvironment(distances,
                        set.oi.idc,
                        names.atoms,
                        names.res.atoms,
                        structure,
                        radius = 3.6)
  
# }
# NOT RUN {
# }