Contacts in Puzzle 1227

Case number:699969-2002432
Topic:General
Opened by:jeff101
Status:Open
Type:Bug
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!

(Sat, 05/07/2016 - 23:24  |  2 comments)


Joined: 06/06/2013
Groups: Gargleblasters

Per chat and other comments, we have not had a complete contact map in over a year. Some of us had just started to master them and they went away to incomplete puzzles or non-existent.
My team encourages novices to join, and we work with them to learn folding skills. We need some training puzzles that would include complete map, parallel and antiparallel sheets, and perhaps helices on both sides of sheet plane. We don't really need points, just a tool we can open together and easily share. I've been using 1138 right now from expired list per Susume, and it does work well to line up the two sheets. I had to download from the Foldit site, instruct my team mate to do the same, and then share pictures back and forth on chat. A shared puzzle would be much easier
I can't tell if 1127 has errors on map, if I have to bend or cut my SS into pieces, or all of the above. I know all contacts have some play in them, but don't know how much.
Feedback would be appreciated. Training puzzles really really appreciated
Thanks

jeff101's picture
User offline. Last seen 9 hours 37 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

I think that if the black dot contacts on the Contact Map are determined by distances between alpha or beta-carbons, wiggle sidechains and shake should not affect them. This makes sense for alpha-carbons, because alpha-carbons are part of the protein backbone while wiggle sidechains and shake only affect the sidechains. Is it also true for beta-carbons?

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