Table 2.
Tilt angle and the centers of mass relative to the membrane normal
| PDB ID | HDGBv3 | HDGBvdW | OPM | PDBTM | MD Simulations | ||||
|---|---|---|---|---|---|---|---|---|---|
| Tilt (˚) | Z (Å) | Tilt (˚) | Z (Å) | Tilt (˚) | Z (Å) | Tilt (˚) | Z (Å) | Tilt (˚) | |
| 1hxx | 22.3 | −4.0 | 22.9 | −5.0 | 28.8 | −6.6 | 28.8 | −5.7 | - |
| 1fep | 17.0 | 12.9 | 17.0 | 12.9 | 12.8 | 12.8 | 15.1 | 9.7 | - |
| 1nqe | 42.1 | 8.7 | 40.7 | 8.8 | 39.5 | 9.8 | 36.5 | 8.1 | - |
| 1qj8 | 15.1 | −6.8 | 27.6 | −5.7 | 19.8 | −7.3 | 7.4 | −3.4 | - |
| 1qfg | 14.5 | −10.8 | 14.5 | −11.8 | 20.1 | −12.4 | 10.8 | −8.9 | - |
| 1qd6 | 27.9 | −1.6 | 27.8 | −4.6 | 25.6 | −5.2 | 25.6 | −3.5 | 20–2567 |
| 1qjp | 15.3 | −5.9 | 6.7 | −5.9 | 13.4 | −3.8 | 8.4 | −5.4 | 5–1065 |
| 1m0l | 7.3 | −1.1 | 6.3 | −1.1 | 11.9 | −1.7 | 11.9 | 0.3 | - |
| 1gzm | 13.0 | 1.3 | 13.0 | 1.3 | 13.0 | −0.4 | 7.2 | −4.8 | 8–1666 |
| 1rzh | 18.5 | 8.0 | 18.8 | 8.0 | 27.4 | 8.6 | 31.9 | 7.4 | - |
| 1v55 | 11.2 | 4.0 | 21.4 | 3.0 | 9.5 | 2.5 | 9.2 | 2.7 | - |
| 1r3j | 2.0 | 2.1 | 2.0 | 3.1 | 0.0 | 2.1 | 0.0 | 2.4 | - |
| 2oar | 4.1 | 4.8 | 4.0 | 4.8 | 1.4 | 9.5 | 0.0 | 11.9 | - |
| 1yce | 1.4 | −1.3 | 1.4 | −1.3 | 0.0 | −4.2 | 0.8 | 5.6 | - |
| 2cfp | 3.1 | −4.1 | 2.0 | −4.1 | 9.3 | −4.4 | 9.0 | −2.1 | - |
| 1p4t | 19.8 | 6.0 | 19.8 | 6.0 | 19.5 | 6.5 | 5.6 | −1.5 | - |
| 2qom | 4.4 | 6.0 | 22.0 | 3.9 | 18.0 | 7.7 | 18.7 | 4.1 | - |
| 2x9k | 11.2 | −3.7 | 11.2 | −5.7 | 9.1 | −7.6 | 6.4 | −1.4 | - |
| 3aeh | 5.0 | −5.8 | 8.2 | −7.8 | 10.5 | −7.6 | 4.9 | −4.8 | - |
| 3dzm | 16.4 | 9.2 | 17.4 | 8.3 | 7.6 | 11.4 | 9.7 | 12.7 | - |
| 3syb | 42.0 | −5.7 | 42.0 | −5.7 | 44.3 | −6.8 | 39.6 | −2.0 | - |
| 4afk | 13.0 | 5.9 | 13.0 | 5.9 | 7.1 | 7.0 | 8.5 | 5.3 | - |
| 4d5b | 5.7 | 9.2 | 5.0 | 9.2 | 8.3 | 10.6 | 1.4 | 3.5 | - |
| 4fqe | 19.0 | 5.8 | 19.0 | 3.8 | 13.7 | 3.3 | 25.0 | −1.4 | - |
| 4rl8 | 18.8 | −3.4 | 16.4 | −3.4 | 9.4 | −6.2 | 16.4 | −1.5 | - |
| 1okc | 16.0 | −3.0 | 16.0 | −3.0 | 20.1 | −4.4 | 8.8 | −7.2 | - |
| 3wbn | 9.2 | −2.0 | 7.6 | −1.0 | 16.7 | −0.7 | 17.3 | 0.1 | - |
| 3wfd | 13.9 | 1.8 | 13.9 | 0.8 | 11.6 | −0.4 | 7.6 | 1.7 | - |
| 3wxv | 23.2 | −2.1 | 23.2 | −4.1 | 25.1 | −2.0 | 5.6 | −2.6 | - |
| 4hyj | 6.4 | −1.2 | 5.8 | −0.2 | 16.9 | −1.5 | 8.8 | 1.3 | - |
| 4m48 | 43.2 | 0.7 | 16.5 | 1.7 | 33.1 | 1.9 | 21.5 | 0.4 | - |
| 4n6h | 11.2 | −5.6 | 15.2 | −4.7 | 30.0 | −9.1 | 10.7 | −7.3 | - |
| 4uc2 | 13.0 | 3.9 | 12.1 | 3.9 | 9.8 | 4.6 | 8.9 | 3.1 | - |
| 4x5n | 8.2 | 6.0 | 9.5 | 6.0 | 1.4 | 0.8 | 3.7 | 1.9 | - |
| 4yl3 | 2.0 | −4.0 | 2.0 | −4.0 | 0.0 | −3.9 | 0.0 | −5.1 | - |
| avg. | 14.8 | 0.69 | 14.9 | 0.35 | 15.6 | 0.08 | 12.3 | 0.39 | - |
| R2 | 0.66 | 0.97 | - | - | 0.63 | 0.92 | 0.57 | 0.66 | |
| slope | 0.89 | 0.97 | - | - | 0.88 | 1.11 | 0.79 | 0.76 | |
| 95% CIa | 0.22 | 0.06 | - | - | 0.23 | 0.11 | 0.23 | 0.19 | |
| pb | 3·10−9 | ~0 | - | - | 1·10−8 | ~0 | 1·10−7 | 3·10−9 | |
| MRc | −0.16 | 0.34 | - | - | 0.65 | −0.27 | −2.6 | 0.04 | |
| MSEd | 40.01 | 1.15 | - | - | 44.57 | 4.1 | 54.8 | 11.4 | |
Tilt angles were calculated as the angle between the principal axis of the protein and the z-axis. For 1qd6, the average tilt angle of the two monomers was calculated to be able to compare with the MD simulation data. OPM and PDBTM structures were downloaded from the corresponding databases. For 1hxx, 1m0l and 1v55, chain A was used for the calculations since the monomer structures were used for these proteins in this work. For the calculated positions of the center of mass, the HDGB-based models were taken as the reference. In some cases, OPM and/or PDBTM models had to be flipped with respect to the membrane bilayer to compare equivalent orientations. Statistical analyses were applied to the pairs between HDGBvdW and each of the other models, HDGBv3, OPM and PDBTM. The F-test was applied to determine the probability that the results from two models are correlated via a linear relationship.
confidence interval for slope;
p-value from the F-test for significance of a linear fit;
mean residuals;
mean squared error between predicted and experimental values.