These chemical groups are available for contact through H-bonds. Residues such as Ser, Cys, and Thr have a hydroxyl or sulphydryl group which can be used simultaneously as a donor and as acceptor, and they can therefore contact any base. The main target for hydrophobic interaction in the major groove of DNA is the single methyl group of the T base. Hydrophobic residues such as Ala, Val, Ile, Leu, Met, Phe, Tyr, Trp and Thr can recognize thee methyl on T. The two ring CH groups of the C base are also possible targets for recognition by hydrophobic residues. However, interaction with the hydrogen atoms of C will not be as strong as with the methyl group of the thymine.
Ala appears to be insufficiently hydrophobic to contact the C base.
Some residues can recognize two chemical groups on the same DNA base and such interactions would be stronger than single contacts. Thus, only one of the two groups seems likely to be available for base recognition at any one time making a bidentate contact difficult. Ionic effects on contacts. Theoretically, Arg and Lys can bind to any of the bases, other than C, by H-bond. However, these two residues almost always bind to G even through a single contact.