Figure 6. Generalized nucleotide scale constraints and real nucleotide property scales.

Real nucleotide scales rescaled between 0 and 1 and overlaid with 2D histograms of summed PUR and PYR weights obtained from calculations of R (w_G, w_A, w_C, w_U) for mRNA sequence properties and 152 different hydrophobicity scales that give |R|>0.75. Positions of summed PUR/PYR values for different real scales are shown with blue crosses and reflect various physicochemical properties of nucleotides (see Methods for full annotation): size/SASA (scales 1–3), knowledge-based contact statistics (scales 4–7), knowledge-based preference of unpaired conformation (scales 8–9) and hydrophobicity-related scores (scales 10–25). The heat map is coloured according to the colour legend given below.