Using program
CluD
possible hydrophobic interactions between protein and DNA were analyzed.
There was found only one conserved hydrophobic cluster on the protein-DNA
interface, which could be important in term of DNA recognition and binding.
It includes Met305, Lys309 and Arg312,
all of them being highly conserved (found in 100%, 86.65% and 100% respectively).
At the same time, Met305 makes no other contacts with DNA,
so its participating in this hydrophobic cluster may be considered as the
main reason of its high conservation. Also this cluster often includes
Ala313 (in 4 of 7 proteins for which there are structures containing DNA)
and seldom — some other residues.
From the DNA side the cluster always includes t839.c5m,
t839.c5, t839.c2* and 838.c2*. As far as there are no
other contacts with t839 major groove atoms and it is absolutely
invariant in all EBS sequences, we can conclude that this hydrophobic
interaction is extremely important for DNA recognition and binding.
As it it is shown in the pictures at the bottom of the page, Tyr316 can either be also involved in the main cluster or form it's own cluster together with c837.c5 or t837.c5m. In case it is in the main cluster, the corresponding DNA atom is also in the main cluster. The fact, that neither adenine nor guanine has hydrophobic atom in that position can explain why only cytosine or thymine were found as nucleotide 837 (see DNA alignment).
In the pictures below atoms of Met305, Lys309 and Arg312 are shown in red, atoms t839.c5m, t839.c5, t839.c2* are shown in pink. Tyr316 and c837.c5 are shown in green in the picture,where they form separate cluster.
