Mean bound water environment summary per percent conservation
Logical indicator to plot results for waters passing
The title for the plot
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.
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
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