Simulation systems used and distribution of contact surface area (CSA) between the H3 tail and DNA in an obtained ensemble.

<p>(A) The system was prepared based on two nucleosome crystal structures, 1KX5 and 1ZBB. The linker DNA was extended by 10 bp from that of 1KX5 using the DNA structure of 1ZBB as a reference. Only atoms immersed within a water sphere centered at the root of the H3 tail (a nitrogen atom in the 40th residue) were considered in the simulations to reduce computational costs. All simulations were performed within the water sphere boundary. H3 histone tail, DNA, and histone core regions are shown in magenta, orange and green, respectively. (B) Distribution of CSA between the H3 tail and DNA is plotted as a function of the scaling factor λ for ALSD. See <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004788#pcbi.1004788.s001" target="_blank">S1 Fig</a> for the K14ac H3 tail.