Thanks Jim!
...still waiting for a straight answer though... [:(] Mungo Carstairs Jalview Computational Scientist The Barton Group Division of Computational Biology School of Life Sciences University of Dundee, Dundee, Scotland, UK. www.jalview.org<http://www.jalview.org/> www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk/> ________________________________ From: [email protected] <[email protected]> on behalf of James Procter <[email protected]> Sent: 02 November 2016 10:10:09 To: [email protected] Subject: Re: [Jalview-dev] Is Threonine hydrophobic? Hi. Interesting question Mungo - and perhaps you may not have realised that it doesn't have a clear cut answer. On 02/11/2016 09:11, Mungo Carstairs (Staff) wrote: > The question was whether Threonine should be classed as hydrophobic (in > which case the diagram needs amended) or not (in which case Jalview code > needs amended). Threonine does have some hydrophobic characteristics - but these are context dependent. The sidechain is relatively small, and dominated by polar groups, so whilst it doesn't hydrogen bond terribly well with water, its polarizable nature allows it to mix, so the entropic solvation cost is not huge. The original reference for this diagram is Taylor 1986 'The classification of amino acid conservation', and many people have redrawn it in subsequent publications. Most interpretations of physicochemical properties at that time were based on empirical scales derived from solubility measurements of the monomer, rather than any protein environment based rational (although there were sufficient structures available to support the hydrophobic core theory). As we get more structures, we also get a better idea of amino acid spatial preferences. > Question remains, which is it (for Jalview conservation purposes at least)? What is important for Jalview right now is that the method and reference data used are those that is widely accepted (warts and all). I think it would be posible to offer configuration to support different forms of the matrix in a future release, but only experts will really use that feature - and then, they may prefer to use entirely different forms of physichemical conservation measurement. I've mentioned one key resource for this before: http://www.genome.jp/aaindex/ For further reading I suggest you first take a look at Valdar 2002 : valdarlab.unc.edu/papers/proteins2002.pdf Jim. -- ------------------------------------------------------------------- Dr JB Procter, Jalview Coordinator, The Barton Group Division of Computational Biology, School of Life Sciences University of Dundee, Dundee DD1 5EH, UK. +44 1382 388734 | www.jalview.org<http://www.jalview.org> | www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> _______________________________________________ Jalview-dev mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev The University of Dundee is a registered Scottish Charity, No: SC015096
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