Comparison of helices found in CL with idealized α-helices Values compare models of the entire TM region (helical bundle) and individual helices (single helix) with ideal α-helices by recording the RMSD of α-carbon atoms and the angle between the central α-carbon and the α-carbons at either end of the helix. For rhodopsin, the angle of deviation for TM 6 is 37° when it is modelled as part of the helical bundle and 22° when it is modelled as a single helix. Proline is present in helices 4–6.
| Helix | RMSD from Ideal Helix Helical Bundle | Angle of Deviation from Ideal Helix | |
|---|---|---|---|
| Helical Bundle | Single Helix | ||
| nm | |||
| 1 | 0.11 | N.D. | N.D. |
| 2 | 0.10 | N.D. | N.D. |
| 3 | 0.05 | N.D. | N.D. |
| 4 | 0.03 | 3 | 4 |
| 5 | 0.07 | 4 | 9 |
| 6 | 0.28 | 38 | 24 |
| 7 | 0.14 | N.D. | N.D. |
N.D. not determined.