Table 1.

Nucleotide atom subsets used in the definition of AIRs

DNA base	Minor groove atoms	Major groove atoms
Thy	H3, O2, C2′	H3, O4, C4, C5, C6, C7′
Ade	N1, N3, C2, C4′	H61, H62, N1, N7, C5, C6, C8′
Gua	H1, H21, H22, N3, C2, C4′	H1, H21, N7, O6, C5, C6, C8′
Cyt	N3, O2, C2′	H41, H42, N3, C4, C5, C6′
	Non-specific backbone atoms
Sugar–phosphate backbone	C1′, C2′, O3′, O5′, P, O1P, O2P

Subsets are defined for atoms capable of interacting using non-bonded or hydrogen bonded interactions. Individual subsets are defined for those atoms facing the DNA major and minor groove for the four bases and for the sugar–phosphate backbone atoms.