# Use this file to assign the attribute in Chimera with the # Define Attribute tool or the command defattr. # # Solvent-excluded surface area (SESA) of amino acid residue X in Gly-X-Gly # tripeptide, from supplementary Table S1 (revised) of: # # Transient protein-protein interface prediction: datasets, features, # algorithms, and the RAD-T predictor. # Bendell CJ, Liu S, Aumentado-Armstrong T, Istrate B, Cernek PT, Khan S, # Picioreanu S, Zhao M, Murgita RA. # BMC Bioinformatics. 2014 Mar 24;15:82. doi: 10.1186/1471-2105-15-82. # http://www.biomedcentral.com/1471-2105/15/82 # # These values may be useful for normalizing areaSES, e.g. # Attribute Calculator formula for new residue attribute relSESA # residue.areaSES/residue.areaSESgxg # # Notes: # - less applicable to terminal residues and residues with missing atoms # - applies only to standard amino acids (not MSE, etc.) # - Dock Prep could be used to repair truncated sidechains, mutate MSE->MET, # but turning off (unchecking) hydrogen addition and other options is # recommended for purposes of surface area calculation # - normalized areas may exceed 1.0 because the areas in the Gly-X-Gly # reference state are not the maximum possible areas # - depending on the definition of the reference state, there may be other # equally valid sets of normalization denominators # attribute: areaSESgxg recipient: residues :gly 47.155 :ala 61.063 :ser 69.073 :cys 78.62 :pro 81.03 :thr 82.92 :asp 86.142 :val 90.264 :asn 90.541 :glu 102.57 :ile 105.307 :leu 105.842 :gln 106.534 :his 110.864 :met 112.01 :lys 120.502 :phe 124.714 :tyr 130.885 :arg 138.595 :trp 148.915