Table 1:
Summaries of epistasis models for binding (A) and folding (B). The leftmost column (column one) contains features. Any categorical abstractions are listed directly below the category with right justification. Column two gives the specific number of mutation pairs for a given category, where applicable. For complex type specifically, the number of complexes of that type are indicated in parentheses. Column three is the change in R2 (ΔR2), i.e., how much poorer the model fits the data after removing this feature. In the case of the full model, column three is the R2. Removal of a feature also removes all subcategories and any interaction terms involving the feature. Column four lists coefficients for the feature/interaction term in the full model. The rightmost column contains p-values for the features, and features within a given category.
| 1A: Binding Model | ||||
|---|---|---|---|---|
| Feature | CategoricalBreakdown | Removal (ΔR2) | Coefficient | P-value |
| Full Model | 572 | 0.2991 | ||
| Intercept | 0.6994 | 0.0000 | ||
| Complex Type | 0.1275 | |||
| AB/AG | 66 (8) | −0.8401 | 0.0120 | |
| Cyto/Cyto | 69 (4) | 0.4677 | 0.3738 | |
| GTPase/other | 85 (7) | −0.4134 | 0.3153 | |
| TCR/pMHC | 58 (9) | −1.0090 | 0.0071 | |
| Pr/PI | 294 (30) | 0.0000 | 0.0000 | |
| Charge | 0.0778 | |||
| 0 | 450 | 0.0000 | 0.0000 | |
| 0A | 69 | 1.0195 | 0.0041 | |
| 0R | 53 | −0.7424 | 0.0131 | |
| Separation | 0.0522 | −0.0025 | 0.8074 | |
| Interaction Side | 0.0464 | 0.5889 | 0.0055 | |
| 1 | 399 | |||
| 0 | 173 | |||
| Sizenet | 0.0427 | 0.0022 | 0.1345 | |
| SASAabs | 0.0327 | −0.0060 | 0.0002 | |
| Secondary Structure | 0.0162 | 0.5837 | 0.0014 | |
| 1 | 315 | |||
| 0 | 257 | |||
| Binding Model Interaction Terms | ||||
| Feature1:Feature2 | Coefficient | P-value | ||
| Separation:Secondary Structure | −0.0331 | 0.0246 | ||
| Sizenet:Interaction Side | −0.0052 | 0.0081 | ||
| Separation:Charae | ||||
| 0A | −0.0882 | 0.0001 | ||
| 0R | 0.0454 | 0.0401 | ||
| SASAabs:Complex Type | ||||
| AB/AG | −0.0140 | 0.0207 | ||
| Cyto/Cyto | 0.0072 | 0.2340 | ||
| GTPase/other | 0.0072 | 0.0789 | ||
| TCR/pMHC | 0.0062 | 0.1631 | ||
| Sizenet:Complex Type | ||||
| AB/AG | 0.0130 | 0.0000 | ||
| Cyto/Cyto | 0.0023 | 0.4650 | ||
| GTPase/other | 0.0008 | 0.7843 | ||
| TCR/pMHC | 0.0060 | 0.0754 | ||
| Interaction Side:Charge | ||||
| 0A | 0.7289 | 0.0089 | ||
| 0R | 0.1460 | 0.5625 | ||
| Interaction Side: Complex Type | ||||
| AB/AG | 0.1376 | 0.6577 | ||
| Cyto/Cyto | −1.4297 | 0.0004 | ||
| GTPase/other | −0.3189 | 0.3331 | ||
| TCR/pMHC | 0.0062 | 0.9824 | ||
| 1B: Folding Model | ||||
| Feature | Categorical Breakdown | Removal (ΔR2) | Coefficient | P-value |
| Full Model | 204 | 0.2578 | ||
| Intercept | −0.0607 | 0.8513 | ||
| HP | 0.1506 | 0.0746 | 0.0018 | |
| 0 | 133 | |||
| 1 | 71 | |||
| Sizenet | 0.0765 | 0.0120 | 0.0000 | |
| Charge | 0.0695 | |||
| 0 | 174 | 0.0000 | 0.0000 | |
| 0A | 13 | 1.8631 | 0.0015 | |
| 0R | 17 | −0.7356 | 0.0133 | |
| Separation | 0.0446 | −0.0416 | 0.0054 | |
| SASArel | 0.0383 | 0.3269 | 0.8546 | |
| Folding Model Interaction Terms | ||||
| Feature1:Feature2 | Coefficient | P-val | ||
| SASArel:Sizenet | −0.0437 | 0.0174 | ||
| SASArel:Separation | 0.1577 | 0.1324 | ||
| Sizenet:HP | −0.0103 | 0.0085 | ||
| SASArel:HP | 2.7022 | 0.0459 | ||
| HP:Charge | ||||
| 0A | −2.0467 | 0.0016 | ||
| 0R | 0.8380 | 0.0391 | ||