vanddraabe (version 1.1.1)

BoundWaterEnvSummaryPlot: Bound Water Environment Summary Plot

Description

Mean bound water environment summary per percent conservation

Usage

BoundWaterEnvSummaryPlot(data, passed.waters = TRUE,
  title = "Bound Water Environment per Conservation")

Arguments

data

The h2o.clusters.summary data.frame from the ClusterWaters function containing the nBvalue.mu information. This data.frame is found within the h2o.cluster.passed and h2o.cluster.all

passed.waters

Logical indicator to plot results for waters passing Mobility() and NormalizedBvalue() OR using all waters within the PDB files.

title

The title for the plot

Details

Constructs a line plot with the bound water environment measures for the nearby protein and water atoms. The protein atomic density (ADN), hydrophilicity, mobility, normalized B-values, and potential hydrogen bonds are summarized for protein heavy atoms with 3.6 Angstroms along with the mobility, normalized B-values, and hydrogen bonds are summarized for the waters within 3.6 Angstroms of the protein and water atoms of interest, respectively. The raw values are scaled to values between 0 and 1 and plotted for each of the percent conservation available. Thus if there are ten structures being analyzed the percent conservation can range from 10 to 100% in 10% increments. The protein related values are shown as solid lines and the water related values are shown as dotted lines.

Interpreting the plot

• dark green: protein atom density

• medium green: protein atom hydrophilicity

• green: protein mobility

• pale green: protein nBvalue

• light green: protein hydrogen bonds

• dark blue: water mobility

• medium blue: water nBvalue

• blue: water hydrogen bonds

This plot is based on Figure 3 of Sanschagrin and Kuhn (1998). Please note the B-value have been replaced with normalized B-values and hydrophilicity has been removed. Hydrophilicity was removed because the range between average hydrophilicity values for the percent conservations would likely be narrow. Due to the way scaling works, the lowest value is scaled to zero and the greatest value is scaled to one. Scaling the mean hydrophilicity values works against our goal of showing an overall tread and instead creates confusion about the values.

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

See Also

Other plots: BoundWaterEnvPlots, BvalueBarplot.summ, BvalueBarplot, ClusterSummaryPlots, MobNormBvalEvalPlots, MobilityBarplot.summ, MobilityBarplot, OccupancyBarplot.summ, OccupancyBarplot, nBvalueBarplot, normBvalueBarplot.summ

Examples

# NOT RUN {
  
# }
# NOT RUN {
  bwe.summary.plot <- BoundWaterEnvSummaryPlot(data=thrombin10.conservedWaters,
                                               passed.waters=TRUE,
                                               title="Bound Water Environment per Conservation")
 
# }
# NOT RUN {
# }