load=1xbr
cpk off
wireframe 30
rotate -x 90
rotate -y 90

define nb_small ((dt and (*.N1 or *.C2 or *.O2 or *.N3)) or (da and (*.N1 or *.C2 or *.C4 or *.N3 or *.N9)) or (dc and (*.N3 or *.O2 or *.C2 or *.N1)) or (dg and (*.N9 or *.C4 or *.N3 or *.C2 or *.N2 or *.N1))) and dna
define nb_large ((dt and (*.C5 or *.C6 or *.C7 or *.C4 or *.O4)) or (da and (*.C5 or *.C6 or *.N7 or *.C8 or *.N6)) or (dc and (*.N4 or *.C4 or *.C5 or *.C6)) or (dg and (*.C8 or *.N7 or *.C5 or *.O6 or *.C6))) and dna
define deoxyribose (*.O3' or *.O4' or *.O5') and dna
define deoxyribose_carb *.C?' and dna
define phosphate_oxygen (*.OP1 or *.OP2) and dna
define phosphate *.P and dna
define prot_polar protein and (*.O?? or *.N??)
define prot_nonpolar protein and (*.C?? or *.S??)

select nb_small
cpk 100
echo "minor groove"
pause

cpk off
select nb_large
cpk 100
echo "major groove"
pause

cpk off
select deoxyribose or deoxyribose_carb
cpk 100
echo "deoxyribose"
pause

cpk off
select phosphate or phosphate_oxygen
cpk 100
echo "phosphate"
pause

cpk off
select prot_polar
cpk 100
echo "polar atoms of protein"
pause

cpk off
select prot_nonpolar
cpk 100
echo "nonpolar atoms of protein"
pause

cpk off
select all
measure RANGE 1.0 3.5 ALL (nb_small and *.N??) (prot_polar)
echo "polar contacts with minor groove nucleobases"
pause

measure off
measure RANGE 1.0 3.5 ALL (nb_large and *.N??) (prot_polar) 
echo "polar contacts with major groove nucleobases"
pause

measure off
measure RANGE 1.0 3.5 ALL (deoxyribose) (prot_polar) 
echo "polar contacts with deoxyribose"
pause

measure off
measure RANGE 1.0 3.5 ALL (phosphate_oxygen) (prot_polar) 
echo "polar contacts with phosphate"
pause

measure off
measure RANGE 1.0 4.5 ALL (phosphate) (prot_nonpolar) 
echo "nonpolar contacts with phosphate"
pause

measure off
measure RANGE 1.0 4.5 ALL (deoxyribose_carb) (prot_nonpolar) 
echo "nonpolar contacts with deoxyribose"
pause

measure off
measure RANGE 1.0 4.5 ALL (nb_small and *.C??) (prot_nonpolar) 
echo "nonpolar contacts with minor groove nucleobases"
pause

measure off
measure RANGE 1.0 4.5 ALL (nb_large and *.C??) (prot_nonpolar) 
echo "nonpolar contacts with major groove nucleobases"
pause