Contact formation probabilities in the unfolded state and contact folding rates for both the entangled RD1 protein and the non-entangled SH3 domain.

The parameters p_U, the contact formation probability in the unfolded state U, and k, the characteristic rate at which this probability increases from p_U to its final value in the folded ensemble F, are shown for each native contact. p_U and its standard deviation are computed from 1500 unfolded configurations sampled with the same procedure used to select the initial configurations for refolding simulations (see Ensemble definition and pathway classification section for details). Contact folding rates k are obtained through exponential fits of the contact formation probabilities as a function of time, averaged over different refolding trajectories (see Fig 7 for specific examples of such fits). When not shown, standard deviations are smaller than the marker size for both observables (see Exponential fit of contact formation curves section for details). The colour scale refers for each contact to the |G′| of the corresponding loop. The darker the color the more entangled the loop. (a) RD1 protein. Only the 52 trajectories achieving refolding through the fast channel are considered in the average. The “trap-avoiding” and the “first-entangling” contacts identified in Fig 6 are framed in red and magenta, respectively. The position in the plot of the latter set is marked by the magenta arrow. (b) SH3 domain. All 100 refolding trajectories are included in the average.