Determinants of protein side‐chain packing

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Abstract
The problem of protein side‐chain packing for a given backbone trace is investigated using 3 different prediction models. The first requires an exhaustive search of all possible combinations of side‐chain conformers, using the dead‐end elimination theorem. The second considers only side‐chain‐backbone interactions, whereas the third neglects side‐chain‐backbone interactions and instead keeps side‐chain‐side‐chain interactions. Predictions of side‐chain conformations for 11 proteins using all 3 models show that removal of side‐chain‐side‐chain interactions does not cause a large decrease in the prediction accuracy, whereas the model having only side‐chain‐side‐chain interactions still retains a significant level of accuracy. These results suggest that the 2 classes of interactions, side‐chain‐backbone and side‐chain‐side‐chain, are consistent with each other and work concurrently to stabilize the native conformations. This is confirmed by analyses of energy spectra of the side‐chain conformations derived from the fourth prediction model, the Independent model, which gives almost the same quality of the prediction as the dead‐end elimination. The analyses indicate that the 2 classes of interactions simultaneously increase the energy difference between the native and nonnative conformations.