In cases like this I use PISA for the first analysis - it will give buried surface area - h bonds, salt bridges etc, then work up from there. Eleanor
On 28 August 2018 at 14:43, Anastassis Perrakis <[email protected]> wrote: > 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 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
