Introduction - This script shows some details of DNA-protein interactions. Scroll down until the text corresponding to the view is visible. (Based on 1d66.pdb, R. Marmorstein et al., Nature 356 408 (1992)).
Here is a DNA duplex.
Here is the dimeric transcription factor GAL4.
Here is the complex between GAL4 and DNA.
One type of protein-DNA interaction is illustrated by this hydrogen bond between an Arg (on the left) and a guanine.
Here is another hydrogen bond between a Lys (on left) and a cytosine that is mediated by water (GREEN).
Here is a hydrophobic interaction between Val (on the left) and the methyl group of thymine.
Here is a salt bridge between and Arg (on the left) and a phosphate of the backbone.