Hydropathy score

Fig. 2. Conditional probability plot for Sweet and Eisenberg s (1983) hydropathy scale. The black line is the probability ( axis) that a residue is ordered given the hydropathy score indicated on the x-axis. The dashed line is the probability of disorder. Negative values for hydropathy indicate hydrophilicity, positive values indicate hydrophobicity. The area between the two curves is divided by the total area of the graph to obtain the area ratio.

The hydropathy scores from Kyte and Doolittle (K-D index) (30) are presented. 

The SPLIT algorithm was optimized for predicting transmembrane a-helices by using the Kyte-Doolittle hydropathy scale to create profile of a-helix preferences. The digital version of prediction for transmembrane a-helices is designated as the TMH predictor. Predicted profile of P-strand preferences can be used to find sequence location of potential membrane-embedded or surface-attached P-strands. The score for potential membrane-attached P-strand... 

Figure 3 Score profiles for cxlbjarde (Figure 3A) and for cox3 parde (Figure 3B) of cytochrome oxidase from Paracoccus denitrificans [14] are obtained by substraction of turn preferences from a-helix preferences (full line). Digital predictions, as outcome of the best training procedure for the SPLIT algorithm with Kyte-Doolittle hydropathy scale (Methods), are shown as bold horizontal bars at the score level 0.5. Observed location of TMH segments are shown as bold horizontal bars at the score level 0.2.

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