vanddraabe (version 1.1.1)

BoundWaterEnvironment.interact: Bound Water Environment (interactions)

Description

Various enviroment counts for bound waters.

Usage

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

Arguments

distances

Matrix of atomic pairwise distances

set.oi.idc

Indices of protein atoms; can also HETATMs if those are of interest

names.atoms

Atom names from the PDB file in the PDB atomic naming convention.

names.res.atoms

Atom names of the form "RES AT"; created by combining the residue and atom name while separating the two by a space. These do not need to be unique because these names will be used to lookup hydrophilicity 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

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.quality, BoundWaterEnvironment, 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 =" ")
  BoundWaterEnvironment.interact(distances,
                                 set.oi.idc,
                                 names.atoms,
                                 names.res.atoms,
                                 radius = 3.6)
  # $adn
  # [1] 9
  #
  # $ahp.sum
  # [1] 2.001
  #
  # $ahp.mu
  # [1] 0.2223
  #
  # $ahp.sd
  # [1] 0.2229
  #
  # $hbonds
  # [1] 4
  
# }
# NOT RUN {
# }