Contact analysis for LIN and STE in CG simulations. (A) Histogram of total interaction time of each residue in KCNQ1 for LIN. The gray highlighted boxes in the background indicate the position of the transmembrane helices. The total interaction times reported cover the simulation period of 5–50 µs, since convergence of the number of LIN molecules within 6 Å of the channel is achieved after 5 µs into the simulation. The total interaction time for each residue has been averaged across the four channel subunits to account for the fourfold symmetry of the channel. (B) Box plots showing the total interaction time for the residues, with those that fall above Q3 + 1.5 interquartile range in the total interaction time (i.e., high-contact residues) labeled. (C) Heat maps of total interaction times in the 3-D structure of the channel shown both from a top and a side view. The unit for the color scale is in microseconds. (D–F) Same as in A–C but for longest lifetime of each residue. As with the total interaction time calculations, the longest lifetime measurements are based on the last 45 µs of the simulation and are averaged across the four channel subunits. (G–L) Same as in A–F but for STE. The only common high-contact residue between the two FAs in the total interaction time analysis was R218 in S4 at site I (H). However, instead of the other residues that formed site I for LIN, high-contact residues for STE included W148 in S2 and I201 and C204 in S3 (H). While site I was rarely occupied in the STE simulations, STE at site II could not be identified in the total interaction time analysis (G–I). When comparing the longest lifetime residues for the two FAs, similarly to LIN, residues R218, G219, and F222 in the S3–S4 loop and Y268 in S5 form site I for STE. However, in contrast to LIN, for STE, F269 and L272 did not contribute to site I and I314 and T317 in S6 and I128 in S1 did not contribute to site II. For STE, only the upper S6 residue W313 and S1 residue Y138 form interaction site II.