Dear all,
I am trying to calculate the contribution to protein-protein aggregation from hydrophobic interactions but quickly get confused.
My initial attempt was to follow the V P Chuprina, 1993, 10.1006/jmbi.1993.1598 paper, where the hydrophobic interaction is defined for each C−C pair with distance of < 4.5 Å.
Naturally, multiple hydrophobic interactions would be identified between Leu and Phe and their partners as the %occupied bewteen each C atom.
For example, by running the ptraj command, the following entries, corresponding to interactions between Leu76 and Phe212, were obtained.
The approach by the V P Chuprina, 1993, 10.1006/jmbi.1993.1598 Show in Citavi paper relates the strength of hydrophobic interaction to their %occupied,
and truncates the list by showing only the interactions with total %occupied > 100%.
Furthermore, the hydrophobic interactions per residue-pair are represented by the sum of the %occupied of interactions between individual atom-pairs.
The problem for me is then three folds :
(1) is there some de facto way to analyze hydrophobic interactions in AmberTools. I did not find any after reading the manual.
(2) is the way to calculate the hydrophobic interaction per residue-pair correct and accuracy.
(3) based on visual inspection, I would think the hydrophobic interactions between Leu76 and Phe212 are important for protein-protein aggregation.
However, the interactions between them have the %occupied more than 100%, if we count all of C−C pair with distance of < 4.5 Åbewteen.
Nevertheless, should we chooes the top %occupied of one C−C pair bewteen Leu76 and Phe212 to mean the hydrophobic interactions.
Many thanks for your efforts to help !
atom# res.atom atom# res.atom atom# res.atom %occupied distance angle lifetime maxocc
| 1248 76.CD2 | 3411 212.HD2 3410 212.CD2 | 88.36 3.818 ( 0.31) 90.04 (14.21) 12.0 ( 22.4) 202
| 994 61.CB | 2791 174.HD21 2790 174.CD2 | 84.51 4.073 ( 0.21) 103.30 (40.61) 8.5 ( 13.6) 198
| 1248 76.CD2 | 3403 212.HD1 3401
212.CG | 80.45 4.049 ( 0.26) 135.87 (10.40) 6.1 ( 9.8) 201
| 1244 76.CD1 | 3403 212.HD1 3401
212.CG | 75.84 3.844 ( 0.27) 116.71 ( 9.88) 19.8 ( 46.6) 410
| 1244 76.CD1 | 3405 212.HE1 3402 212.CD1 | 73.50 3.924 ( 0.28) 125.19 ( 7.33) 13.8 ( 23.2) 189
| 1248 76.CD2 | 3399 212.HB2 3398 212.CB | 69.59 4.132 ( 0.23) 57.82 (14.84) 3.7 ( 4.9) 134
| 997 61.CG | 2785 174.HG 2784
174.CG | 69.06 4.218 ( 0.18) 40.70 (12.87) 4.1 ( 5.4) 80
| 1244 76.CD1 | 3411 212.HD2 3410 212.CD2 | 68.80 3.978 ( 0.28) 116.34 (10.54) 7.6 ( 13.4) 156
| 994 61.CB | 2785 174.HG 2784
174.CG | 63.45 4.153 ( 0.19) 50.53 ( 8.11) 6.8 ( 12.7) 174
| 1244 76.CD1 | 3399 212.HB2 3398 212.CB | 58.27 4.075 ( 0.24) 82.97 (10.93) 5.0 ( 9.6) 166
| 1248 76.CD2 | 3410 212.CD2 3408 212.CE2 | 58.00 4.079 ( 0.26) 82.52 ( 8.99) 3.3 ( 4.5) 54
| 1244 76.CD1 | 3407 212.HZ 3404 212.CE1 | 57.78 4.106 ( 0.24) 125.41 ( 6.89) 4.6 ( 6.8) 123
| 2576 161.CB | 4674 290.HD2 4673
290.CD | 56.86 4.178 ( 0.20) 49.34 ( 9.82) 3.0 ( 3.5) 38
| 1248 76.CD2 | 3436 214.HE2 3433
214.CZ | 56.31 4.006 ( 0.29) 117.56 (17.73) 3.5 ( 6.1) 94
| 2570 161.CD | 4674 290.HD2 4673
290.CD | 54.98 4.214 ( 0.19) 37.92 (13.63) 2.5 ( 2.4) 37
| 1244 76.CD1 | 3410 212.CD2 3408 212.CE2 | 51.44 4.148 ( 0.23) 89.41 ( 8.44) 3.3 ( 4.4) 69
| 997 61.CG | 2791 174.HD21 2790 174.CD2 | 44.49 4.164 ( 0.26) 107.07 (40.48) 2.8 ( 10.5) 247
| 1244 76.CD1 | 3409 212.HE2 3406
212.CZ | 42.82 4.203 ( 0.21) 116.77 ( 8.01) 2.6 ( 3.4) 69
| 1001 61.CE | 2787 174.HD11 2786 174.CD1 | 33.71 4.132 ( 0.26) 100.71 (40.38) 2.0 ( 1.8) 17
| 1242 76.CG | 3411 212.HD2 3410 212.CD2 | 33.23 4.295 ( 0.18) 97.81 ( 9.47) 1.9 ( 3.8) 148
| 1244 76.CD1 | 2787 174.HD11 2786 174.CD1 | 30.98 4.247 ( 0.19) 87.08 (34.89) 1.7 ( 1.2) 13
| 2570 161.CD | 4678 290.HG3 4676
290.CG | 30.54 4.263 ( 0.17) 125.86 (10.11) 1.6 ( 1.0) 11
| 2573 161.CG | 4674 290.HD2 4673
290.CD | 29.74 4.216 ( 0.20) 49.81 (11.83) 1.8 ( 1.3) 14
| 1248 76.CD2 | 3437 214.CD2 3435 214.CE2 | 28.14 4.127 ( 0.25) 147.43 (10.14) 2.5 ( 3.4) 40
| 1001 61.CE | 2785 174.HG 2784
174.CG | 26.04 4.204 ( 0.20) 49.51 (13.80) 2.3 ( 2.7) 29
| 1242 76.CG | 3403 212.HD1 3401
212.CG | 24.45 4.322 ( 0.19) 125.01 ( 7.34) 1.7 ( 5.9) 222
| 997 61.CG | 2787 174.HD11 2786 174.CD1 | 22.85 4.305 ( 0.17) 109.64 (41.18) 1.7 ( 1.3) 15
| 1239 76.CB | 2787 174.HD11 2786 174.CD1 | 21.95 4.311 ( 0.16) 90.09 (44.40) 1.5 ( 1.1) 26
| 1248 76.CD2 | 3434 214.HZ 3431 214.CE1 | 21.80 4.189 ( 0.24) 86.89 (17.41) 1.7 ( 2.4) 66
| 1248 76.CD2 | 3405 212.HE1 3402 212.CD1 | 20.75 4.159 ( 0.28) 132.12 ( 6.69) 1.9 ( 4.4) 80
| 994 61.CB | 2787 174.HD11 2786 174.CD1 | 14.83 4.256 ( 0.19) 105.62 (38.86) 2.0 ( 2.7) 48
| 1239 76.CB | 2791 174.HD21 2790 174.CD2 | 14.40 4.332 ( 0.13) 89.98 (48.18) 1.4 ( 0.9) 9
| 1242 76.CG | 3399 212.HB2 3398 212.CB | 12.76 4.304 ( 0.19) 63.31 (11.03) 1.7 ( 3.1) 39
| 1248 76.CD2 | 3409 212.HE2 3406
212.CZ | 12.34 4.289 ( 0.17) 100.14 (12.73) 1.4 ( 1.1) 15
| 1001 61.CE | 2782 174.HB2 2781 174.CB | 10.42 4.225 ( 0.19) 155.26 (10.79) 2.9 ( 2.8) 24
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Received on Thu May 13 2021 - 06:30:02 PDT
