ConSurfDB vs. ConSurf: Difference between revisions
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* <span style="background-color:#ec6d96;color:white;padding:0.2em 0.4em 0.1em 0.4em;">Level 8:</span> | * <span style="background-color:#ec6d96;color:white;padding:0.2em 0.4em 0.1em 0.4em;">Level 8:</span> | ||
**Tyr84: hydrogen bonds to the peptide C-terminus. | **Tyr84: hydrogen bonds to the peptide C-terminus. | ||
**Thr143: hydrogen bonds to the peptide C-terminus. | **Thr143: hydrogen bonds to the peptide C-terminus. (Buried, hard to see.) | ||
(Tyr159 was level 6. CD8 binding site Trp274 remains level 9.) | (Tyr159 was level 6. CD8 binding site Trp274 remains level 9.) | ||
Here are all the polar residues contacting the peptide. (This scene is easily obtained in [http://firstglance.jmol.org FirstGlance]: Tools tab, click Contacts, check Label Contacts, and [[How to Insert a ConSurf Result Into a Proteopedia Green Link|made into a Green Link]]. | |||
Another custom ConSurf Server job<ref name="apd0.30">Custom ConSurf Server settings for APD 0.30: UniRef90 database, excluding sequences with > 95% or < 35% identity with the query, MSA has '''250''' sequences '''closest''' to the query.</ref> gave an '''APD of 0.30''', but levels for the above 4 groove residues were 7-8. These lower levels can be accounted for by the highest expectation value<ref name="evalue" /> in the MSA, which was 10 to the power -141. In contrast, for the job with APD 0.31, the highest expectation value was 10 to the power -84. | Another custom ConSurf Server job<ref name="apd0.30">Custom ConSurf Server settings for APD 0.30: UniRef90 database, excluding sequences with > 95% or < 35% identity with the query, MSA has '''250''' sequences '''closest''' to the query.</ref> gave an '''APD of 0.30''', but levels for the above 4 groove residues were 7-8. These lower levels can be accounted for by the highest expectation value<ref name="evalue" /> in the MSA, which was 10 to the power -141. In contrast, for the job with APD 0.31, the highest expectation value was 10 to the power -84. | ||
