In the context of protein secondary structure, do the loops between strand and helix in a beta-alpha-beta motif form into the conformation known as a beta turn?
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1$\begingroup$ Why is this on hold as unclear? Both Beta-Alpha-Beta motifs and beta turns are well defined concepts. This is also quite a frequent source of confusion, as the names are similar enough that many students assume that beta-turns are only associated with BAB units. Of course, it's on the edge of chemistry, and more structural bioinformatics... $\endgroup$– gilleainCommented Jan 8, 2016 at 17:38
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$\begingroup$ I thought I vtc'ed as homework, but I can't remember any more. I will try and edit later to improve the quality of the question. $\endgroup$– orthocresolCommented Jan 9, 2016 at 4:22
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2$\begingroup$ @gilleain It's easy to close this question as off-topic. The explanation you gave should probably be in the body, so that people who are not familiar with proteins would at least have an understanding as from where any confusion is coming from. In its current form the question is only helping people who already know the answer, hence don't need the question. // I downvoted, but I will not dequeue the question. Please edit the question to give some more context. $\endgroup$– Martin - マーチン ♦Commented Jan 9, 2016 at 9:24
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1 Answer
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So a beta-alpha-beta structure will have two loops that could be turns - between the first beta strand and the alpha helix, and the helix and the second strand. They might be beta turns, but they might not.
Although there are different definitions of beta-turns, one common one is the presence of a hydrogen bond between the carbonyl of residue (i) and the amino of residue (i+3). I'm not actually sure how frequent this is, but you can see this from a search on PDBeMotif. There is also Motivated Proteins, which gives nice 2D (and 3D) images of motifs.
However, you could get other conformations of these loops that are not beta-turns, especially if they are quite long.