zap
load 1D5Y_mod.pdb
restrict none

define rib_pol *.O?* and dna
define rib_nonpol *.C?* and dna
define phosph_pol *.O?P and dna
define phosph_nonpol *.P and dna
define major_pol (DA.N6, DA.N7) or DT.O4 or (DG.N7, DG.O6) or DC.N4
define major_nonpol (DA.C5, DA.C6, DA.C8) or (DT.C4, DT.C5, DT.C6, DT.C7) or (DG.C5, DG.C6, DG.C8) or (DC.C4, DC.C5, DC.C6)
define minor_pol (DA.N3, DA.N9) or (DT.N1, DT.O2) OR (DG.N2, DG.N3, DG.N9) OR (DC.N1, DC.O2)
define minor_nonpol (DA.C2, DA.C4) OR (DT.C2) OR (DG.C2, DG.C4) OR(DC.C2)

restrict none
select dna
wireframe 30
zoom 150
center selected
echo 1. dna
pause


select within (3.5, rib_pol) and (*.O?? or *.N??) and protein
spacefill 300
color cpk
echo 2. polar contacts with ribose
pause 

spacefill off
select within (4.5, rib_nonpol) and (*.C?? or *.P?? or *.S??) and protein
spacefill 300
color cpk
echo 3. nonpolar contacts with ribose
pause 

spacefill off
select within (3.5, phosph_pol) and (*.O?? or *.N??) and protein
spacefill 300
color cpk
echo 4. polar contacts with phosphate
pause

spacefill off
select within (4.5, phosph_nonpol) and (*.C?? or *.P?? or *.S??) and protein
spacefill 300
color cpk
echo 5. nonpolar contacts with phosphate
pause

spacefill off
select within (3.5, major_pol) and (*.O?? or *.N??) and protein
spacefill 300
color cpk
echo 6. polar contacts with major groove
pause

spacefill off
select within (4.5, major_nonpol) and (*.C?? or *.P?? or *.S??) and protein
spacefill 300
color cpk
echo 7. nonpolar contacts with major groove
pause

spacefill off
select within (3.5, minor_pol) and (*.O?? or *.N??) and protein
spacefill 300
color cpk
echo 8. polar contacts with minor groove
pause

spacefill off
select within (4.5, minor_nonpol) and (*.C?? or *.P?? or *.S??) and protein
spacefill 300
color cpk
echo 9. nonpolar contacts with minor groove
pause