Various enviroment counts for bound waters.
Matrix of atomic pairwise distances
Indices of atoms of interest; can be protein, water, or HETATMs if those are of interest
Atom names for the atoms of interest. Valid atom names are
provided in the
Residue and atom names of interest. Valid residue-atom
names are provided in the
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.
Distance in Angstroms between the atoms of interest; default: 3.6 Angstroms
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
ConservedWaters() function. This might change in future versions.
NOTE: This function is designed to work with
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.
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
Emilio Xavier Esposito emilio@exeResearch.com
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
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## 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) ## End(Not run)
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