ConSurfDB vs. ConSurf: Difference between revisions

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====ConSurf Server Default APD 1.1====

[[2vaa]] contains three chains. Here, (<scene name='39/399854/2vaa_consurf_halos_w274_y159/4'>restore initial scene, ConSurf Server default settings, APD 1.1</scene>)<ref name="~~consurfdefault~~">Default ConSurf Server settings: UniRef90 database, excluding sequences with > 95% or < 35% identity with the query, MSA has 150 sequences sampled evenly from all unique sequence hits.</ref> ConSurf colors are applied only to the alpha chain (chain A), while the beta chain (chain B = β-2 microglobulin) and the 8 amino acid peptide (chain P) are shown as gray backbone traces.

[[2vaa]] contains three chains. Here, (<scene name='39/399854/2vaa_consurf_halos_w274_y159/4'>restore initial scene, ConSurf Server default settings, APD 1.1</scene>)<ref name="consurfdefaults">Default ConSurf Server settings: UniRef90 database, excluding sequences with > 95% or < 35% identity with the query, MSA has 150 sequences sampled evenly from all unique sequence hits.</ref> ConSurf colors are applied only to the alpha chain (chain A), while the beta chain (chain B = β-2 microglobulin) and the 8 amino acid peptide (chain P) are shown as gray backbone traces.

Conservation of important residues in the groove is obscured by inclusion in the MSA of proteins with different functions ([[#Example With Multiple Functions|see analysis above]]). The sides of the groove are variable due to many alleles that enable it to bind a wide range of peptide sequences. The only groove residue that is conserved at greater than level 7 is '''Tyr159''' (level 8), whose sidechain hydrogen bonds the main-chain oxygen of the amino-terminal peptide residue. Only a handful of surface residues are highly conserved (level 9), including '''Trp274''' involved in binding CD8.

ConSurfDB vs. ConSurf: Difference between revisions

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@@ Line 132: / Line 132: @@
 ====ConSurf Server Default APD 1.1====
-[[2vaa]] contains three chains. Here, (<scene name='39/399854/2vaa_consurf_halos_w274_y159/4'>restore initial scene, ConSurf Server default settings, APD 1.1</scene>)<ref name="consurfdefault">Default ConSurf Server settings: UniRef90 database, excluding sequences with > 95% or < 35% identity with the query, MSA has 150 sequences sampled evenly from all unique sequence hits.</ref> ConSurf colors are applied only to the alpha chain (chain A), while the beta chain (chain B = &beta;-2 microglobulin) and the 8 amino acid peptide (chain P) are shown as gray backbone traces.
+[[2vaa]] contains three chains. Here, (<scene name='39/399854/2vaa_consurf_halos_w274_y159/4'>restore initial scene, ConSurf Server default settings, APD 1.1</scene>)<ref name="consurfdefaults">Default ConSurf Server settings: UniRef90 database, excluding sequences with > 95% or < 35% identity with the query, MSA has 150 sequences sampled evenly from all unique sequence hits.</ref> ConSurf colors are applied only to the alpha chain (chain A), while the beta chain (chain B = &beta;-2 microglobulin) and the 8 amino acid peptide (chain P) are shown as gray backbone traces.
 Conservation of important residues in the groove is obscured by inclusion in the MSA of proteins with different functions ([[#Example With Multiple Functions|see analysis above]]). The sides of the groove are variable due to many alleles that enable it to bind a wide range of peptide sequences. The only groove residue that is conserved at greater than level 7 is '''Tyr159''' (level 8), whose sidechain hydrogen bonds the main-chain oxygen of the amino-terminal peptide residue. Only a handful of surface residues are highly conserved (level 9), including '''Trp274''' involved in binding CD8.