define set1 *.C2' and dna
define set2 *.OP?, *.P? and dna
define polar oxygen, nitrogen
define nonpolar carbon, phosphorus, sulfur
define major_groove ([DA] and *.C6, *.N6, *.C5, *.N7), ([DC] and *.C6, *.C5, *.C4, *.N4), ([DT] and *.C6, *.C5, *.C4, *.O4, *.C7), ([DG] and *.C6, *.O6, *.C5, *.N7, *.C8)
define minor_groove ([DA] and *.C2, *.N3, *.C4, *.N9), ([DG] and *.C2, *.N2, *.N3, *.C4, *.N9), ([DC] and *.O2, *.N1, *.C2), ([DT] *.O2, *.C2, *.N1, *.C6)

select protein and within(3.5, set1) and polar
select protein and within(4.5, set2) and nonpolar

select protein and within(3.5, set2) and polar
select protein and within(4.5, set2) and nonpolar

select protein and within(3.5, major_groove) and polar
select protein and within(4.5, major_groove) and nonpolar

select protein and within(3.5, minor_groove) and polar
select protein and within(4.5, minor_groove) and nonpolar