**Direct Readout Energy**

Protein residues and DNA bases show a variety of interactions. Some
interactions such as Asn-A and Lys-G are frequently observed in the
complex structures. The spatial distributions of side chains around
base pair indicate a possibility that the distribution may be converted
to energy potential, in a similar manner to the contact potential
between amino acids in protein structures, and it can be used for the
target prediction In order to derive the statistical potential of
interactions between bases and amino acids, we defined a coordinate
system by taking an origin N9 atom for A and G and N1 atom for T and C.
We considered the amino acids within a given box, and the box was
divided into grids. Then we transformed the distributions of C atom of
amino acid into statistical potentials defined by the following
equations,

where *m*_{ab}_{ }is
the number of pairs,* a* and *b* observed, *w* is the
weight given to each observation, *f(s)*
is the relative frequency of occurrence of any amino acids at grid point *s*,
and *g*^{ab}(s) is the equivalent relative frequency of
occurrence of amino acid *a* against base *b*. *R* and *T*
are gas constant and absolute temperature, respectively. Here, we used a
box of |x| = |y| =13.5Å and |z| = 6 Å and a grid interval
of 3Å, which was determined by examining various intervals. In
order to quantify the specificity, we evaluated Z-score by calculating
energy against 50,000 random DNA sequences. Z-score is defined by (*X* - *m*)/s in the histogram, where *X*
is sum of contact potential in a complex form, *m* is mean energy
over 50,000 combinations and s is standard deviation of the
energy. For example, Z-score of -3.0 means that
there are potentially two DNA sequences that are better fit to the
framework among 1,000 random sequences.