FirstGlance/Visualizing Conservation: Difference between revisions
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FirstGlance automatically detects [[Protein crosslinks|covalent protein crosslinks of six types]], plus disulfide bonds. Tools are provided making it easy to examine each such crosslink in detail. If the PDB file has been processed by [[ConSurf/Index|ConSurf]], it is easy to see the levels of conservation of the crosslinked residues. | FirstGlance automatically detects [[Protein crosslinks|covalent protein crosslinks of six types]], plus disulfide bonds. Tools are provided making it easy to examine each such crosslink in detail. If the PDB file has been processed by [[ConSurf/Index|ConSurf]], it is easy to see the levels of conservation of the crosslinked residues. | ||
An example is isopeptide bond-linked chains of ubiquitin. [[7cap]] is an isopeptide-linked trimer of ubiquitin. Here is one ConSurf result (300 sequences in the MSA with an APD 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 MSA with an APD of 1.15): | ||
:[http://firstglance.jmol.org/fg.htm?mol=7cap_consurf1639680092_pipe.pdb 7CAP Conservation in FirstGlance 3.8beta2] | :[http://firstglance.jmol.org/fg.htm?mol=7cap_consurf1639680092_pipe.pdb 7CAP Conservation in FirstGlance 3.8beta2] | ||
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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]]. | ||
Then, proceed as follows: | |||
<table class="wikitext"><tr><td width="300"> | |||
1. Click on one of the crosslink bonds. | |||
2. Check the box to apply ConSurf Colors. | |||
3. Touch a residue to pop up a tooltip reporting its ConSurf conservation Grade, as shown in the yellow box on Lys48. | |||
</td><td> | |||
[[Image:7cap-isopeptide-conservation.png]] | [[Image:7cap-isopeptide-conservation.png]] | ||
</td></tr></table> | |||
==See Also== | ==See Also== | ||
