background white
select all
cartoon off
trace off
cpk 20
wireframe 20
color lightgrey

define ribose_polar dna and *.O?*
define ribose_nonpolar dna and *.C?*
define phosphate_polar *.OP? and dna
define phosphate_nonpolar *.P? and dna
define large_polar (DC.N4) or (DT.O4) or (DA.N6, DA.N7) or (DG.O6, DG.N7)  
define large_nonpolar (DA.C6, DA.C5, DA.C5) or (DG.C6, DG.C5, DG.C8) or (DC.C6, DC.C5, DC.C4) or (DT.C6, DT.C5, DT.C4, DT.C7) or (DA.C6, DA.C5, DA.C5)
define small_polar (DA.N3, DA.N9) or (DG.N2, DG.N3, DG.N9) or (DC.O2, DC.N1) or (DT.O2, DT.N1)
define small_nonpolar (DA.C2, DA.C4) or (DG.C2, DG.C4) or (DC.C2) or (DT.C2, DT.C6)
define protein_polar (oxygen or nitrogen) and protein
define protein_nonpolar protein and NOT protein_polar
pause

select within (3.5, ribose_polar) and protein_polar
color yellow
cpk 200

select within (3.5, phosphate_polar) and protein_polar
color red
cpk 200

select within (3.5, large_polar) and protein_polar
color green
cpk 200

select within (3.5, small_polar) and protein_polar
color blue
cpk 200
pause

select all
color lightgrey
cpk 20

select within (4.5, ribose_nonpolar) and protein_nonpolar
color yellow
cpk 200

select within (4.5, phosphate_nonpolar) and protein_nonpolar
color red
cpk 200

select within (4.5, large_nonpolar) and protein_nonpolar
color green
cpk 200

select within (4.5, small_nonpolar) and protein_nonpolar
color blue
cpk 200