Table 3.
Interface Behavior Relative to Deposited Model for each of four Different Simulations
| Interface | X | Y | Z | XY | XZ | YZ | Total | |
|---|---|---|---|---|---|---|---|---|
| Avg. Δdist of monomer COM across interface | ff14SB | 0.01 | −0.1 | −0.08 | 0.01 | 0 | −0.13 | 0.33 |
| ff14ipq | 0.01 | −0.14 | −0.16 | 0.01 | 0 | −0.33 | 0.65 | |
| C36 | 0.01 | −0.03 | −0.06 | 0.01 | 0 | −0.16 | 0.27 | |
| ff99SB | 0.01 | −0.09 | −0.10 | 0.01 | 0.01 | −0.19 | 0.41 | |
| Avg. no. contacts | Exp | 9 | 15 | 14 | 11 | 5 | 4 | 58 |
| ff14SB | 10.69 | 14.45 | 15.69 | 11.14 | 7.54 | 5.10 | 64.61 | |
| ff14ipq | 11.87 | 18.39 | 13.76 | 12.33 | 6.01 | 4.61 | 66.97 | |
| C36 | 11.02 | 16.13 | 13.43 | 12.31 | 6.54 | 4.57 | 64.00 | |
| ff99SB | 11.69 | 14.74 | 13.90 | 11.51 | 7.69 | 4.79 | 64.32 | |
| Crystal contacts maintained (strong/weak) | ff14SB | 7 (6/1) | 9(4/5) | 11(5/6) | 10(7/3) | 5(3/2) | 4(4/0) | 46 |
| ff14ipq | 8(7/1) | 14(7/7) | 8(3/5) | 9(8/1) | 2(1/1) | 3(2/1) | 44 | |
| C36 | 9(4/5) | 9(6/3) | 7(3/4) | 8(6/2) | 3(2/1) | 3(2/1) | 39 | |
| ff99SB | 9(4/5) | 10(5/5) | 11(4/7) | 9(8/1) | 5(3/2) | 4(2/2) | 48 | |
| Crystal contacts lost | ff14SB | 2 | 6 | 3 | 1 | 0 | 0 | 12 |
| ff14ipq | 1 | 1 | 6 | 2 | 3 | 1 | 14 | |
| C36 | 0 | 6 | 7 | 3 | 2 | 1 | 19 | |
| ff99SB | 0 | 5 | 3 | 2 | 0 | 0 | 10 | |
| New contacts | ff14SB | 1 | 4 | 3 | 0 | 3 | 1 | 12 |
| ff14ipq | 4 | 7 | 4 | 0 | 3 | 1 | 19 | |
| C36 | 2 | 7 | 4 | 3 | 2 | 1 | 19 | |
| ff99SB | 2 | 2 | 1 | 0 | 1 | 1 | 7 | |
| Interface area | Exp | 268 | 394 | 379 | 239 | 168 | 113 | |
| ff14SB | 319 | 347 | 348 | 252 | 248 | 112 | ||
| ff14ipq | 326 | 396 | 298 | 277 | 196 | 109 | ||
| C36 | 314 | 399 | 337 | 266 | 227 | 112 | ||
| ff99SB | 303 | 374 | 323 | 264 | 243 | 109 | ||
| Avg. no. H‐bonds (crystal/newly formed) | Exp | 5 | 2 | 3 | 2 | 1 | 0 | 13 |
| ff14SB | 2.14/0.81 | 0.14/0.91 | 0.74/1.65 | 1.03/0 | 0.61/0 | 0 | 4.66/3.37 | |
| ff14ipq | 2.34/1.71 | 0.29/1.85 | 0.34/2.68 | 1.02/0 | 0.14/0.25 | 0 | 4.13/6.49 | |
| C36 | 1.77/0 | 0.63/1.35 | 0.70/1.99 | 0.84/0 | 0.36/0.16 | 0 | 4.30/3.50 | |
| ff99SB | 2.40/0.88 | 0.78/0.69 | 0.73/0.93 | 1.08/0 | 0.47/0.15 | 0 | 5.46/2.65 |
Six columns correspond to each of the six unique crystal interfaces in the model. Each simulation contained 12 independent copies of each interface. The top block shows the relative change in distance between the centers of mass of the interfacing residues. The second block shows the average number of contacts made between unique residues across interface. The third block shows the number of residue contacts from the experimental models that were maintained in each simulation. This number is further subdivided (in parentheses) into strong contacts (on average found in 10 or more unit cells at a time) and weak contacts (on average found in more than 6 but less than 10 unit cells at a time). The fourth block shows the number of residue contacts from the experimental model that were lost in each simulation (found in less than six unit cells at a time). The fifth block shows the number of new interface residue contacts formed in each simulation that were not present in the experimental model (“formed” means that they were present on average in more than seven unit cells at a time). The sixth block shows the average surface area in each simulation. The last block shows the average number of hydrogen bonds across each interface. The first number corresponds to hydrogen bonds that exist also in the experimental model and the second number to new hydrogens bond formed in the simulation.