From chemistry-request %-% at %-% ccl.net Fri Jun 17 13:18:48 2005 Received: from smtp1.Stanford.EDU (smtp1.Stanford.EDU [171.67.16.123]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j5HHIiMp017990 for ; Fri, 17 Jun 2005 13:18:44 -0400 Received: from [171.65.23.152] (B157-PowerBookG4.Stanford.EDU [171.65.23.152]) by smtp1.Stanford.EDU (8.12.11/8.12.11) with ESMTP id j5HHIgah013851 for ; Fri, 17 Jun 2005 10:18:43 -0700 Message-ID: <42B305F2.4040302 %x% stanford.edu> Date: Fri, 17 Jun 2005 10:18:42 -0700 From: Xavier Deupi User-Agent: Mozilla Thunderbird 1.0.2 (Macintosh/20050317) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry %x% ccl.net Subject: Re: CCL:Alpha Helix kink References: <42B28FE5.30205 %x% pharma.u-strasbg.fr> In-Reply-To: <42B28FE5.30205 %x% pharma.u-strasbg.fr> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hi Mireille, You can also use HelAnal (Bansal et al. J Biomol Struct Dyn. 2000 Apr;17(5):811-9) to detect and measure local distortions of the helical structure, in terms of local (i.e. per residue) bend and twist angles. You can see an application to Pro-kinked alpha-helices in Deupi et al., Biophys J. 2004 Jan;86(1 Pt 1):105-15. Hope this helps, xavi Mireille Krier wrote: > Dear CCLers, > > we are looking for a tool that can detect (because not always induced > by proline) > and measure the angle of an kink in an alpha helix. > Any suggestions? > We found in the literature SWINK, (Cordes et al., Sansom Group) > was developed to estimate the kink and swivel angle of TM small alpha, > Greek-helices. > Any ideas, if this is available? > > Many thanks in advance to the community for the any help provided. > > Mireille Krier > -- Xavier Deupi, Ph.D. Department of Molecular and Cellular Physiology Beckman Center for Molecular and Genetic Medicine (B161) 279 Campus Drive, Stanford University School of Medicine Stanford, CA 94305 (USA) E-mail: Xavier.Deupi %x% stanford.edu Phone: +1 (650) 725-6497 Fax : +1 (650) 725-8021