FirstGlance/Visualizing Conservation: Difference between revisions
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To further explore the pattern of conservation, we need to change from the ''ConSurf View'' to the ''FirstGlance Control Panel''. Click the link indicated by the red arrow in the above snapshot. | To further explore the pattern of conservation, we need to change from the ''ConSurf View'' to the ''FirstGlance Control Panel''. Click the link indicated by the red arrow in the above snapshot. | ||
The ''FirstGlance Control Panel'' has 5 tabs (see snapshot | The ''FirstGlance Control Panel'' has 5 tabs (see snapshot at right). The ''Molecule Information Tab'' and the ''Views'' tab each provide a wealth of information. | ||
Notice that you can move freely back and forth between the ''ConSurf Controls'' and the ''FirstGlance Controls'' using the link '''ConSurf Controls''' in the middle of the left side of FirstGlance. | Notice that you can move freely back and forth between the ''ConSurf Controls'' and the ''FirstGlance Controls'' using the link '''ConSurf Controls''' in the middle of the left side of FirstGlance. | ||
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===Color by Conservation=== | ===Color by Conservation=== | ||
To see how well the salt-bridged residues are conserved, click the checkbox ''ConSurf Colors'' (red arrow below). Declutter the view by unchecking ''Show Backbones'' (green arrow below). | To see how well the salt-bridged residues are conserved, click the checkbox ''ConSurf Colors'' (red arrow below). Declutter the view by unchecking ''Show Backbones'' (green arrow below). Scroll down in the lower left panel and click {{Yelspan|List All}} to get a spreadsheet-ready list that includes conservation values for each pair of salt-bridged atoms. | ||
<br> | <br> | ||
<table class="wikitable"><tr><td> | <table class="wikitable"><tr><td> | ||
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FirstGlance provides an easy and powerful tool to explore residues contacting any specified portion of the model. For this example, we'll use [[acetylcholinesterase]] complexed to the [https://en.wikipedia.org/wiki/VX_(nerve_agent) inhibitor VX], crystal structure [[6cqz]]. | FirstGlance provides an easy and powerful tool to explore residues contacting any specified portion of the model. For this example, we'll use [[acetylcholinesterase]] complexed to the [https://en.wikipedia.org/wiki/VX_(nerve_agent) inhibitor VX], crystal structure [[6cqz]]. | ||
:[http://firstglance.jmol.org/fg.htm?mol=6cqz_consurf1641072297_pipe.pdb Display 6CQZ ConSurf Result in | :[http://firstglance.jmol.org/fg.htm?mol=6cqz_consurf1641072297_pipe.pdb Display 6CQZ ConSurf Result in FirstGlance] | ||
We'll look at the conservation of the residues that contact the ligand/inhibitor VX. From the ''ConSurf View'', go to the FirstGlance Control Panel. | We'll look at the conservation of the residues that contact the ligand/inhibitor VX. From the ''ConSurf View'', go to the FirstGlance Control Panel. | ||
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and Astrid Walrant. ''Crystals'', 2021, '''11'''(9), 1032; [https://doi.org/10.3390/cryst11091032 doi.org/10.3390/cryst11091032].</ref>. Let's see which Trps are conserved in the potassium channel [[1bl8]] (a [[Nobel_Prizes_for_3D_Molecular_Structure#2000-2009|Nobel Prize-winning structure]]!). | and Astrid Walrant. ''Crystals'', 2021, '''11'''(9), 1032; [https://doi.org/10.3390/cryst11091032 doi.org/10.3390/cryst11091032].</ref>. Let's see which Trps are conserved in the potassium channel [[1bl8]] (a [[Nobel_Prizes_for_3D_Molecular_Structure#2000-2009|Nobel Prize-winning structure]]!). | ||
:[http://firstglance.jmol.org/fg.htm?mol=1bl8_consurf1640894833_pipe.pdb Display 1BL8 ConSurf Result | :[http://firstglance.jmol.org/fg.htm?mol=1bl8_consurf1640894833_pipe.pdb Display 1BL8 ConSurf Result FirstGlance] | ||
<table class="wikitable"><tr><td colspan=3><center> | <table class="wikitable"><tr><td colspan=3><center> | ||
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An example is isopeptide bond-linked chains of ubiquitin. [[7cap]] is an isopeptide-linked trimer of ubiquitin. The carboxy-terminal Gly76 forms an isopeptide bond with Lys48. Here is one ConSurf result (300 sequences in the multiple sequence alignment (MSA), sampled from 10,122 unique similar sequences. The MSA had an [[Interpreting_ConSurf_Results#Average_Pairwise_Distance|average pairwise distance]] of 1.15): | An example is isopeptide bond-linked chains of ubiquitin. [[7cap]] is an isopeptide-linked trimer of ubiquitin. The carboxy-terminal Gly76 forms an isopeptide bond with Lys48. Here is one ConSurf result (300 sequences in the multiple sequence alignment (MSA), sampled from 10,122 unique similar sequences. The MSA had an [[Interpreting_ConSurf_Results#Average_Pairwise_Distance|average pairwise distance]] of 1.15): | ||
:[http://firstglance.jmol.org/fg.htm?mol=7cap_consurf1639680092_pipe.pdb 7CAP Conservation in | :[http://firstglance.jmol.org/fg.htm?mol=7cap_consurf1639680092_pipe.pdb 7CAP Conservation in FirstGlance] | ||
First, follow the [[FirstGlance/Evaluating_Protein_Crosslinks#Instructions_for_an_Isopeptide_Bond|instructions for getting a list of the isopeptide crosslinks]]. | First, follow the [[FirstGlance/Evaluating_Protein_Crosslinks#Instructions_for_an_Isopeptide_Bond|instructions for getting a list of the isopeptide crosslinks]]. | ||
