Abstract
Given recent emphasis on non-local or large-scale effects (e.g. DNA flexibility, the role of water and ions, the biophysics of the major and minor grooves, etc), it is of interest to ask to what extent the (relatively small) local interactions (e.g. individual hydrogen bonds) contribute to the overall stability of the complex. These specific interactions were visualized and analyzed through molecular surfaces using protein-DNA interactions of the lac repressor headpiece assessed from PDB codes 1L1M, 2BJC, and 1CJG in the program Flare.
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