Figure 6.

A sample PDAgram for 1A02. (A) Two protein complexes, NFAT, and Fos-Jun, bind to different sites on the double-stranded DNA of protein-DNA complex structure 1A02. PDA identifies and separates the protein-DNA binding units as in (B) the NFAT-DNA complex and (C) the Fos-Jun-DNA complex. Protein chain N, F, and J are for NFAT, Fos, and Jun, respectively. A dot (.) represents a canonical base pair. An uppercase-case letter in a DNA sequence represents the base is in contact with the protein while a lower-case letter is not. 'M', 'm', or 'A' above or below a DNA chain indicates that the interaction between the protein and the base is in the major, minor, or both major and minor grooves. '*' above or below a DNA base means more than one protein chain is in contact with the DNA base.

Kim and Guo BMC Genomics 2009 10(Suppl 1):S13   doi:10.1186/1471-2164-10-S1-S13