Figure 30.

“Knobs into holes” packing analysis of the helix–helix interfaces of TolC. (A) The structure of TolC (PDB ID: 1EK9) is visualized as a ribbon, with residues forming canonical coiled-coils (yellow and orange spheres) and residues forming noncanonical coiled coils (red and blue spheres). (B and C) A closer look into the knobs-into-holes packing patterns at the interfaces between α-helices, which are also depicted in “ladder” representation. Helical IDs are listed at the top, and amino acid residues are specified by the one-letter code. Heavy lines and bold helix identification numbers correspond to α-helices viewed from the exterior, while dotted lines and light identification correspond to α-helices viewed from the interior. (B) The layout of the four interfaces between α-helices participating in the construction of the 12-helix tube forming the α-cylinder. (C) The layout of the two interfaces between α-helices in the construction of the four-helix bundle forming the canonical coiled-coil restricting the periplasmic extremity of the TolC channel.