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| Conserved surface patches identify functional regions of proteins. Less commonly, patches of high variability may also be functional. (Can you think of situations where high variability would be advantageous?<ref>Advantageous variability will be seen in these cases: [[5hmg]], [[2vaa]], [[3hi6]].</ref>) | | Conserved surface patches identify functional regions of proteins. Less commonly, patches of high variability may also be functional. (Can you think of situations where high variability would be advantageous?<ref>Advantageous variability will be seen in these cases: [[5hmg]], [[2vaa]], [[3hi6]].</ref>) |
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| ==Conservation in Proteopedia==
| | For instructions on how to identify conserved regions of a molecule of interest, please see [[How to see conserved regions]]. |
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| Most molecules in Proteopedia, on pages titled with a [[PDB code]], have an ''Evolutionary Conservation'' line below the molecule. Clicking on '''<nowiki>[show]</nowiki>''' in this line will color the molecule by evolutionary conservation, as calculated by [[ConSurfDB_vs._ConSurf|ConSurfDB]].
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| If the molecule of interest lacks the ''Evolutionary Conservation'' line below the molecule, you can calculate it yourself at the ConSurf Server. [[ConSurfDB_vs._ConSurf#Limiting_ConSurf_Analysis_to_Proteins_of_a_Single_Function|Here are instructions.]] When you get the result, there will be a link for showing that result in [[FirstGlance in Jmol]].
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| You can also [[Help:How to Insert a ConSurf Result Into a Proteopedia Green Link|show ConSurf-colored molecules with green links in Proteopedia]].
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| ==Conservation in FirstGlance==
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| You might wish to explore a conservation-colored molecule in [[FirstGlance in Jmol|FirstGlance]] so you can hide portions of it, locate sequence numbers of interest, or examine the conservation of the amino acids that bind a ligand, or for other reasons.
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| #Enter the [[PDB code]] in the search slot in Proteopedia.
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| #At the page title with the PDB code, click on '''<nowiki>[show]</nowiki>''' in the line labeled ''Evolutionary Conservation'' beneath the molecule. (If there is no such line, see below.)
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| #The ''Evolutionary Conservation'' section is now expanded. Click on the link ''Complete Results at ConSurfDB''.
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| #At ConSurfDB, click on the button for the chain of interest under ''View 3D structure colored by conservation in FirstGlance in Jmol''. (You can only see one chain at a time at ConSurfDB. [[Conservation%2C_Evolutionary#Use_Caution_When_Comparing_Conservation_of_Sequence-Different_Chains|Here is the reason.]])
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| {{Clear}} | | {{Clear}} |
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| ==See Also== | | ==See Also== |
| | *[[How to see conserved regions]] |
| *[[Evolutionary Conservation]] | | *[[Evolutionary Conservation]] |
| *[[ConSurfDB_vs._ConSurf]] | | *[[ConSurfDB_vs._ConSurf]] |
