▁hydro ph ob ic ▁interactions , ▁as ▁well ▁as ▁indirect ▁interactions ▁via ▁water ▁mole cules , ▁which ▁occur ▁between ▁specific ▁side ▁ch ains ▁and ▁the ▁exposed ▁bases ▁within ▁the ▁major ▁gro ove ▁of ▁the ▁DNA . ▁ ▁Home od om ain ▁prote ins ▁are ▁found ▁in ▁e uk ary otes . ▁Through ▁the ▁HT H ▁mot if , ▁they ▁share ▁limited ▁sequence ▁similarity ▁and ▁struct ural ▁similarity ▁to ▁ ▁pro k ary otic ▁trans cription ▁factors , ▁such ▁as ▁lambda ▁ph age ▁prote ins ▁that ▁alter ▁the ▁expression ▁of ▁gen es ▁in ▁pro k ary otes . ▁The ▁HT H ▁mot if ▁shows ▁some ▁sequence ▁similarity ▁but ▁a ▁similar ▁structure ▁in ▁a ▁wide ▁range ▁of ▁DNA - binding ▁prote ins ▁( e . g ., ▁cro ▁and ▁repr essor ▁prote ins , ▁home od om ain ▁prote ins , ▁etc .). ▁One ▁of ▁the ▁principal ▁differences ▁between ▁HT H ▁mot ifs ▁in ▁these ▁different ▁prote ins ▁ar ises ▁from ▁the ▁s tere och em ical ▁requirement ▁for ▁g ly c ine ▁in ▁the ▁turn ▁which ▁is ▁needed ▁to ▁avoid ▁ster ic ▁inter ference ▁of ▁the ▁beta - car bon ▁with ▁the ▁main ▁chain : ▁for ▁cro ▁and ▁repr essor ▁prote ins ▁the ▁g ly c ine ▁appears ▁to ▁be ▁mand atory , ▁whereas ▁for ▁many ▁of ▁the ▁home otic ▁and ▁other ▁DNA - binding ▁prote ins ▁the ▁requirement ▁is ▁relax ed . ▁ ▁Se quence ▁specific ity ▁ ▁Home od om ains ▁can ▁bind ▁both ▁specifically ▁and ▁n ons pec ific ally ▁to