Contacts in Puzzle 1227
|Opened on:||Saturday, May 7, 2016 - 23:24|
|Last modified:||Sunday, May 8, 2016 - 00:13|
In Puzzle 1227, what is the rule for determining if 2 residues in our current protein structure are in contact and so should be given a black dot in the Contact Map? Is it that the alpha-carbons are within 8 Angstroms of each other? Is it that the beta-carbons are within 8 Angstroms of each other? Is there some other rule in use?
Also, when we use the Contact Map to make bands in our protein, what atoms should get connected, and what strength and target length should these connecting bands have?
Posts like https://fold.it/portal/node/997623 make me wonder about these things. Have things changed since Puzzle 883? What procedures are in use for Puzzle 1227?
Also, https://en.wikipedia.org/wiki/Protein_contact_map says the following:
Various contact definitions have been proposed: The distance between the Cα-Cα atom with threshold 6-12 Å; distance between Cβ-Cβ atoms with threshold 6-12 Å (Cα is used for Glycine); and distance between the side-chain centers of mass.
Please clarify these things. Thanks!