FIG. 6.

(A to C) Influence of entropy (A), fraction of forbidden amino acids (AA) (B), and proteasomal cleavage scores (C) on the frequency of recognition of OLPs. Entropy and the fraction of forbidden amino acids correlate inversely (P < 0.0001) and cleavage scores correlate positively (P = 0.0003) with the frequency of recognition. (D) Favorable conditions for high recognition are defined as low entropy, few forbidden amino acids, and high cleavage scores; scores are divided into high and low categories at the median. Stepwise multiple-regression analyses indicated that each of the three variables contributed significantly to the model, that there were no second-order effects based on combinations of the variables, and that there was no benefit in using a quadratic model rather than a linear model to fit the data.