ConSurfDB vs. ConSurf: Difference between revisions
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The alpha chain of [https://www.youtube.com/watch?v=2ZakngfbHSo Major Histocompatibility Complex (MHC)] Class I protein has a groove that binds a wide range of peptides, and a small loop that binds CD8. Our example is [[2vaa]] (mouse H-2Kb). | The alpha chain of [https://www.youtube.com/watch?v=2ZakngfbHSo Major Histocompatibility Complex (MHC)] Class I protein has a groove that binds a wide range of peptides, and a small loop that binds CD8. Our example is [[2vaa]] (mouse H-2Kb). | ||
<span style="float:right;">{{Template:ColorKey_ConSurf}}</span> | <span style="float:right;">{{Template:ColorKey_ConSurf}}</span> | ||
[[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>) ConSurf colors are applied only to the alpha chain (chain A), while the beta chain (chain B = β-2 microglobulin) and the 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>) 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, as expected (enabling it to bind a wide range of peptide sequences). The only groove residue that is conserved at greater than level 6 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. | 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, as expected (enabling it to bind a wide range of peptide sequences). The only groove residue that is conserved at greater than level 6 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. | ||
