My /acknowledgements/ to all that have replied to my question.
So many interesting inputs and points to software; I will be checking in
the next days.
I will comment upon just some of the observations.
As far as we can, we try to take as "asymmetric unit content" what is
"expected" (or sometimes, with experimental corroboration) to be the
functional oligomer, but of course, generally, the most probable one.
We had previously used pisa, but to compare domain-domain contacts. Now
we will take it again in a helix-helix context. But, together with the
other software indicated.
Yours,
Jorge
On Tue, Aug 28, 2018 at 6:03 AM, Jorge Iulek <jiu...@gmail.com
<mailto:jiu...@gmail.com>> wrote:
Dear all,
I am working currently on a structure that, nicely, presents
two different orientations between its domains when one compares
monomers of the tetramer in the asymmetric unit.
I notice, in this nature gift, that a helix, probably central
(in its role) for the relation (orientation) between the two
domains, assumes different relation to other one (helix, that
belongs to one of the domains) such that they are (significantly)
more or less "coiled-coiled"one to another, once the domains are in
the "close" or "open" conformation. We have already analyzed the
hydrogen bonds and salt bridges that are disrupted (or formed) due
to the different (domain and helix) conformations.
I wonder whether there is a metric (easy to evaluate) to
characterize how much the two helix are "around each other" (id est,
how much "coiled-coiled" they are) and, preferably, a software to
calculate this metric.
Thank you,
Jorge
State University of Ponta Grossa
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