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> | ||
====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>) 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>) 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. | 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==== | ====ConSurfDB APD 1.63==== | ||
ConSurfDB has a result (NOT SHOWN) with an '''APD of 1.63''', much higher than the APD 1.1 for the ConSurf Server with default settings. As expected, nothing in the contacts between the peptide and the groove shows high conservation in the ConSurfDB result, but Trp274 (the CD8 binding site) remains highly conserved. | ConSurfDB has a result (NOT SHOWN) with an '''APD of 1.63''', much higher than the APD 1.1 for the ConSurf Server with default settings. As expected, nothing in the contacts between the peptide and the groove shows high conservation in the ConSurfDB result, but Trp274 (the CD8 binding site) remains highly conserved. | ||
====APD 0.31==== | ====ConSurf Server Custom APD 0.31==== | ||
{{Template:ColorKey_ConSurf_NoYellow_NoGray}} | {{Template:ColorKey_ConSurf_NoYellow_NoGray}} | ||
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**Lys146: salt bridges to the carboxy terminus of the peptide. | **Lys146: salt bridges to the carboxy terminus of the peptide. | ||
* <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: | **Tyr84: hydrogen bonds to the peptide C-terminus. | ||
**Thr143: hydrogen bonds to the peptide C-terminus. | |||
<font color="red">UPDATE IN PROGRESS:</FONT> [[User:Eric Martz|Eric Martz]] 15:02, 29 July 2024 (UTC) | <font color="red">UPDATE IN PROGRESS:</FONT> [[User:Eric Martz|Eric Martz]] 15:02, 29 July 2024 (UTC) | ||
