Fis, factor for inversion stimulation, is a nucleoid-associated protein in E. coli. Here we study the binding of this protein throughout the genome. The binding of Fis is determined in part by the sequence motif, but the shape of the DNA also correlates with its binding. High occupancy Fis sites have different shape features when compared to low occupancy Fis sites despite the similar motif sequence suggesting that shape helps determine Fis binding.