Dear Jorge, The “coiled coil” has a formal definition - not all interacting helices are coiled coils. I would refrain from expressions like "more or less "coiled-coiled"one to another”. I have found the program “socket” very useful for analysing such structures. http://coiledcoils.chm.bris.ac.uk/socket/server.html
I must say that I really do not understand completely the actual question, but a word of caution: The ‘asymmetric unit’ not has little to do with the ‘functional unit’ of the protein but furthermore, what we define as AU especially in the case of multiple copies of the molecule in the AU, is a personal choice. Sometimes, its worth thinking what we call “asymmetric unit contents” and what is a “crystallographic contact” in cases of NCS. I am not sure this applies here as I cannot completely visualise your problem at hand, but keep it in mind. Best regards, Tassos > On Aug 28, 2018, at 15:11, Andrew Lovering <[email protected]> wrote: > > Dear Jorge > > This may not be exactly what you require, but there is a nice example of > analysis in the shift of a coiled coil register herein: > > Elife. 2018 Jun 5;7. pii: e34815. doi: 10.7554/eLife.34815. > Asymmetric activation mechanism of a homodimeric red light-regulated > photoreceptor. > Best, > Andy > > -----Original Message----- > From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > [email protected] > Sent: 28 August 2018 14:04 > To: [email protected] > Subject: [ccp4bb] coiled-coil "degree" > > 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 > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
