The DNA nucleotide sequence of A, T, G, and C determines the precise arrangement of these hydrogen bonds and hydrophobic patches. Since the major groove provides a more distinctive array of interactions than the minor groove, most proteins bind to the major groove. The binding of a protein to DNA often requires that the DNA bend along the surface of the protein. Too long - The more contacts the higher the affinity. Typical site sizes range from 6-10 bp, with some as high as 20 or more.
Sites are often inverted repeats .
Binding sites don't need to be exact. However, the more exact it is the better the binding. The cell can use this for regulatory purposes. A low affinity site requires a higher activator concentration to achieve binding. In eukaryotes, this domain is mostly associated with transcriptional regulator sof genes involved in development.