Hi Geoff,
Thanks, I do know what a Venn diagram represents! Also the page I linked to does show multiple properties for amino acids. 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). >From a Google search on amino acid properties, these pages class T as not >hydrophobic: http://www.sigmaaldrich.com/life-science/metabolomics/learning-center/amino-acid-reference-chart.html http://p53.iarc.fr/AAProperties.aspx https://www.mcb.ucdavis.edu/courses/bis102/aaprop.html https://www.thermofisher.com/uk/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/amino-acid-physical-properties.html# http://www.proteinstructures.com/Structure/Structure/amino-acids.html https://en.wikipedia.org/wiki/Amino_acid#Physicochemical_properties_of_amino_acids http://www.biology.arizona.edu/biochemistry/problem_sets/aa/Threonine.html These class T as hydrophobic: http://www.russelllab.org/aas/ https://www.ncbi.nlm.nih.gov/Class/Structure/aa/aa_explorer.cgi Question remains, which is it (for Jalview conservation purposes at least)? thanks mungo 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 Geoff Barton <[email protected]> Sent: 01 November 2016 17:38:40 To: Jalview Development List Subject: Re: [Jalview-dev] Is Threonine hydrophobic? Hi Mungo, The point of the Venn Diagram is that it shows amino acids to have multiple properties. Threonine sits in the middle of the diagram and has the properties: Polar, Hydrophobic, Small. Simple classifications like the one you link to do not capture the fact that amino acids exhibit multiple physico-chemical properties. Rob Russell developed the definitive online resource for amino acid properties: See http://www.russelllab.org/aas/ Geoff. On 01/11/2016 12:43, Mungo Carstairs (Staff) wrote: The Venn Diagram (included in Jalview Help as Amino Acid Properties) says that it is. Jalview code, and other reference sources, say it is hydrophilic. e.g. http://p53.iarc.fr/AAProperties.aspx Does the diagram need an update? Thanks, mungo 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/> The University of Dundee is a registered Scottish Charity, No: SC015096 _______________________________________________ Jalview-dev mailing list [email protected]<mailto:[email protected]> http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev -- Geoff Barton | Professor of Bioinformatics | Head of Division of Computational Biology School of Life Sciences | University of Dundee, Scotland, UK | [email protected]<mailto:[email protected]> Tel: +44 1382 385860 | www.compbio.dundee.ac.uk<http://www.compbio.dundee.ac.uk> | twitter: @gjbarton The University of Dundee is registered Scottish charity: No.SC015096 The University of Dundee is a registered Scottish Charity, No: SC015096 The University of Dundee is a registered Scottish Charity, No: SC015096
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