From owner-biophysics@net.bio.net Thu Mar 24 22:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!EU.net!uknet!lyra.csx.cam.ac.uk!mole.bio.cam.ac.uk!smb18 From: smb18@mole.bio.cam.ac.uk (Simon Brocklehurst (Bioc)) Newsgroups: bionet.molbio.proteins,bionet.biophysics Subject: Re: Equivalent amino acids for similarity searches Date: 25 Mar 1994 16:26:57 GMT Organization: University of Cambridge, England Lines: 20 Message-ID: <2mv3ch$ksn@lyra.csx.cam.ac.uk> References: <2mmfdp$t1n@usenet.INS.CWRU.Edu> <1994Mar23.235848.60877@kuhub.cc.ukans.edu> <94Mar24.144046edt.631@neuron.ai.toronto.edu> NNTP-Posting-Host: mole.bio.cam.ac.uk Xref: biosci bionet.molbio.proteins:1631 bionet.biophysics:139 Notwithstanding all that has preceeded this thread, it is probably worth pointing out that the physico-chemical properties of amino-acids ARE of course reflected in the pattern amino acid substitutions that are observed in divergently evolved families of proteins. When this doesn't happen, it's often because a particular position a fold doesn't have ANY real preference for a type of residue e.g a lot of surface positions fall into this catagory. !----------------------------------------------------------------------- Simon M. Brocklehurst Cambridge Centre for Molecular Recognition Department of Biochemistry University of Cambridge Cambridge UK E-mail: s.m.brocklehurst@bioc.cam.ac.uk .