Protein DNA-binding potential.

<p>A protein's DNA-binding potential is revealed using one of the test moieties. Each test site is represented by a ball, whose color varies blue (favorable) to red (unfavorable). The first three proteins are known to bind DNA, while the last two are not known to bind DNA. For DNA-binding proteins, a graph tracks the potential for each type of moiety along the actual DNA coordinates. The blue curve tracks the 5′ strand of the DNA (tagged with a star), while the green curve tracks the 3′ strand. A point marks each base pair step, and a black horizontal line each 5 base pair steps. Since the 5′ phosphate is absent for both the 5′ and 3′ strands, the base pair step index starts at two. The potential is more favorable as the curve is more to the left. The x axis is scaled to show the relative change along the DNA molecule.