ConSurfDB vs. ConSurf: Difference between revisions
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===Case #1: MHC=== | ===Case #1: MHC=== | ||
The alpha chain of [https://www.youtube.com/watch?v=2ZakngfbHSo Major Histocompatibility Complex (MHC)] 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)] 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, ConSurf colors are applied only to the alpha chain (chain A), while the beta chain (chain B) and the peptide (chain P) are shown as gray backbone traces. See also [[Help:How to Insert a ConSurf Result Into a Proteopedia Green Link|How to Insert a ConSurf Result Into a Proteopedia Green Link]]. | |||
'''ConSurfDB''' has a result with an APD of 1.63. 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 Leu5 (level 8), part of a hydrophobic pocket that binds a peptide "anchor residue". Only a handful of surface residues are highly conserved (level 8), including Trp274 involved in binding CD8. | |||
Examples of conserved patches on other proteins, revealed by ConSurf, will be found in the articles on | Examples of conserved patches on other proteins, revealed by ConSurf, will be found in the articles on | ||
