Optimized positions of the intracellular end of α S0, β1 TM1, and β1 TM2, relative to S1–S6 in the absence and presence of β1. The intracellular emergence of S0–S6, TM1, and TM2 from the plane of the membrane is represented as circles viewed from the cytoplasm. In one subunit of the tetramer, the top extents of disulfide cross-linking are represented as color-coded lines, the thickness of which indicates the average number of residues of the two Cys from the membrane. The inverse of these averages is used as weights for the square differences between the distances inferred from the extents of cross-linking and the distances between the unknown S0(x,y), TM1(x,y), and TM2(x,y), and the known Sn(x,y) taken from the Kv1.2/2.1 structure threaded with the BK α sequence (see Fig. 1 A). The closer the two cross-linked Cys are to the membrane, the more certainty that the extent of their cross-linking reflects the distance between the membrane-embedded helices. In an exception, the distance from S0 to the center of the S4–S5 linker (double line) is treated independently of S4 and S5. L227C at the center of the linker is taken as residue number 1, and the residues on either side of it are taken as residues 2. (A) α alone. The computation of the optimal position of S0 was based on the top extents of cross-linking. (B) The optimal position of S0 and of TM1 and TM2 was based on the top extents of cross-linking.