Table 4. Frequencies of intra-turn hydrogen bond formations.
Atom involved | Full-length ProTαa | 32-mer Neh2a |
mcb i to mc i+2 | 0.196% | |
mc i to mc i+3 | 3.844% | |
mc i to sc i+3 | 27.808% | |
mc i+2 to sc i+3 | 0.284% | 0.204% |
scc i to mc i+2 | 0.396% | 55.368% |
sc i to mc i+3 | 6.696% | 77.524% |
sc i+1 to mc i+2 | 0.428% | |
sc i to sc i+3 | 80.212% | |
sc i+2 to sc i+3 | 7.316% | 0.572% |
Intra-turn total | 14.348% | 98.644% |
Each frame from the last 0.1 µs of the mouse full-length ProTα and 32-mer Neh2 trajectories were used for the hydrogen bond calculations (25,000 structures). A hydrogen bond between a hydrogen donor (D–H) and a hydrogen acceptor (A) was judged to be formed when the DA distance (r) was less than 3.2 Å and the angle between the DA vector and the D–H bond (AD-H angle) was less than 35°.For clarity, only hydrogen bonds occur in more than 0.1% of the structures are listed and intra-residue hydrogen bonds are excluded.
mc – main chain atoms.
sc – side chain atoms.