Table 3.
Analysis of the position of the most conserved contacts between helices (summarized by a series of heat maps in Figure 5 and Figures S1–S3).
| Residue involved in contact | Helix–Helix | Description |
|---|---|---|
| STNQ | 1–2 | Keeps periplasmic end of helices in contact regardless of state |
| STNQ | 2–11 | Keeps periplasmic end of helices in contact regardless of state |
| STNQ | 5–8 | In the center of the TM region, and state dependent |
| STNQ | 7–11 | In the center of the TM region, and state dependent |
| Small hydrophobic | 1–5 | Contacts are at a pivot point in the helices, with each conformation having a different tilt to bilayer normal |
| Small hydrophobic | 1–6 | The contact is in the middle of the helix and TMH 1 has different tilts for each state |
| Small hydrophobic | 2–4 | The contact is in the middle of the helices and small changes in tilt |
| Small hydrophobic | 2–11 | The contact is along length of helices in occluded and inward structure but only at cytoplasmic end in outward structure |
| Small hydrophobic | 3–4 | Mediates packing |
| Small hydrophobic | 3–6 | Mediates packing |
| Small hydrophobic | 5–8 | The contacts are in the center of TM region |
| Small hydrophobic | 7–11 | In cytoplasmic half of the helices, outward state TMH 7 bends away from TMH 11 at periplasmic end to occluded and inward |
| Small hydrophobic | 8–10 | The contacts are along the helices—mediates packing |
| Small hydrophobic | 9–10 | The contacts are along the helices—mediates packing |
| Small hydrophobic | 9–12 | The contacts are along the helices—mediates packing, all three states have straight helices |
| Large hydrophobic | 2–4 | The position of the contact is in the center of the TM region, and the helices rock around that central point |
| Large hydrophobic | 3–6 | At the periplasmic end of the TM region. Inward structure has a further contact at cytoplasmic end of the TM region |
| Large hydrophobic | 8–10 | The contacts are in the center of the TM region, with a small difference in TMH 10 tilt between the conformations |
| Glycine | 1–5 | The contact is in the center of the helices, and is a pivot point for the helices which have different tilts in each state |
| Glycine | 2–4 | The contact is in the center of the helices, not much difference in tilt implying a packing motif |
| Glycine | 9–10 | The contacts are along the length of the helices, indicating packing mediators |
The analysis depicts either static contact points (green) that do not change between different conformational states; contacts that move according to conformational state (blue), and contacts that constitute distinct pivot points (purple) around which the rest of the protein moves.