Three main regions of the protein make important DNA contacts. Most of the contacts occur in the helix III/IV that lies in the major groove. Additional contacts are provided by the N-terminal flexible arm and the loop between helices I and II.
The contacts made by helix III/IV are extensive. The major amino acids are show as spacefilled structures above on the grey protein backbone, and are in contact with the ball and stick DNA duplex. As you can see there are quite a few contacts spread throughout the region. It would be useful to view some of the more important individual amino acids' contributions in detail.
The contacts made by the N terminal arm are shown above. The amino acids (shown as spacefilled structures) that make important contacts in this region are arginines 3 and 5, glutamine 6, and tyrosine 8. The arginines make contacts in the minor groove of the DNA duplex (ball and stick)
The contacts made by the amino acids in or near the loop region between helices I and II are shown above. The amino acids (show as spacefilled structures) that make important contacts in this region are arginines 28 and 31 and tyrosine 25.
Information in this project comes primarily from these references.
This page has been developed Donovan C. Haines as part of a VSNS-PPS course assignment. Email comments or problems to DCHaines@wsuhub.uc.twsu.edu.