QuickViews: DNA-Protein contact atoms in two clicks.
The QuickViews menus were used (1.) to select Protein, and (2.) to display a Contact surface.

The result shows protein as a surface, while atoms of DNA or water which are within noncovalent bonding distance from protein atoms are shown as ball and stick (in the Element/CPK color scheme). The upper region of the protein is binding phosphates (Phosphorus atoms are orange), while the middle of the protein is binding the sides of bases in the DNA major groove (hence a specific base sequence).

The image is shown in divergent (wall-eyed) stereo. Stereo viewing is not necessary since rotating the image allows depth perception. (When stereo is selected, detailed instructions are shown which are not displayed in this snapshot.)
(The links in the snapshot don't work since this is just a snapshot.)