Figure 1. Pore-lining helix bundle, modelled as consisting of ideal helices obeying rotational symmetry.

(a) Top view of KcsA (Protein Data Bank entry 1BL8), with the pore-lining helix bundle highlighted in green. (b) Side view of an idealized helix bundle. The rotational symmetry axis, pointing towards the N termini of the helices, is defined as the z axis; the centres of the protomers lie on the xy plane, with the y axis pointing from the centre of the first protomer (shown in yellow) to the z axis. The helical axis of the first protomer crosses the xy plane at the point (0, −r, 0) and has polar angle θ and azimuthal angle φ. (c) Top view of the idealized bundle. (d) The contact distance d, defined as the closest distance between backbone N, C_α, C and O atoms of two neighbouring helices.