zap
load 1hdd.pdb
define myDNA (:A or :B)
define prot_polar protein and (oxygen or nitrogen)
define prot_nopolar protein and not prot_polar
define d_polar myDNA and (oxygen or nitrogen)
define d_nopolar myDNA and not d_polar
define cont_prot_polar prot_polar and within(3.5, d_polar)
define cont_prot_nopolar prot_nopolar and within(4.5, d_nopolar)
define cont_d_polar d_polar and within(3.5, prot_polar)
define cont_d_nopolar d_nopolar and within(4.5, prot_nopolar)
define big_channel_a DA and (*.C5 or *.C6 or *.C8 or *.N6 or *.N7)
define big_channel_g DG and (*.C5 or *.C6 or *.C8 or *.O6 or *.N7)
define big_channel_c DC and (*.C4 or *.C5 or *.C6 or *.N4)
define big_channel_t DT and (*.C4 or *.C5 or *.C6 or *.C7 or *.O4)
define big_channel big_channel_a or big_channel_g or big_channel_c or big_channel_t
define small_channel_a DA and (*.C2 or *.C4 or *.N3 or *.N9)
define small_channel_g DG and (*.C2 or *.C4 or *.N2 or *.N3 or *.N9)
define small_channel_c DC and (*.C2 or *.O2 or *.N1)
define small_channel_t DT and (*.C2 or *.C6 or *.N1 or *.O2)
define small_channel small_channel_a or small_channel_g or small_channel_c or small_channel_t

select all
wireframe 30
pause
select cont_prot_polar or cont_prot_nopolar
spacefill 80
select DA21.N7
label Protein atoms, possible to contact
pause
select cont_d_polar or cont_d_nopolar
spacefill 120
select DA21.N7
label DNA atoms, possible to contact
pause

select cont_prot_polar or cont_prot_nopolar
spacefill 10
select cont_d_polar or cont_d_nopolar
spacefill 10
select cont_d_polar and (*.O3' or *.O4' or *.O5')
spacefill 200
select cont_prot_polar and within(3.5, (*.O3' or *.O4' or *.O5') and myDNA)
spacefill 200
select DA21.N7
label Polar contacts with sugar
pause

select cont_d_polar and (*.O3' or *.O4' or *.O5')
spacefill 10
select cont_prot_polar and within(3.5, (*.O3' or *.O4' or *.O5') and myDNA)
spacefill 10
select cont_d_nopolar and *.C?'
spacefill 200
select cont_prot_nopolar and within(4.5, *.C?' and myDNA)
spacefill 200
select DA21.N7
label Non-polar contacts with sugar
pause

select cont_d_nopolar and *.C?'
spacefill 10
select cont_prot_nopolar and within(4.5, *.C?' and myDNA)
spacefill 10
select cont_d_polar and *.OP?
spacefill 200
select cont_prot_polar and within(3.5, *.OP? and myDNA)
spacefill 200
select DA21.N7
label Polar contacts with posphate
pause

select cont_d_polar and *.OP?
spacefill 10
select cont_prot_polar and within(3.5, *.OP? and myDNA)
spacefill 10
select cont_d_nopolar and *.P
spacefill 200
select cont_prot_nopolar and within(4.5, *.P and myDNA)
spacefill 200
select DA21.N7
label Non-polar contacts with posphate
pause

select cont_d_nopolar and *.P
spacefill 10
select cont_prot_nopolar and within(4.5, *.P and myDNA)
spacefill 10
select cont_d_polar and big_channel
spacefill 200
select cont_prot_polar and within(3.5, big_channel and myDNA)
spacefill 200
select DA21.N7
label Polar contacts with big channel atoms
pause

select cont_d_polar and big_channel
spacefill 10
select cont_prot_polar and within(3.5, big_channel and myDNA)
spacefill 10
select cont_d_nopolar and big_channel
spacefill 200
select cont_prot_nopolar and within(4.5, big_channel and myDNA)
spacefill 200
select DA21.N7
label Non-polar contacts with big channel atoms
pause

select cont_d_nopolar and big_channel
spacefill 10
select cont_prot_nopolar and within(4.5, big_channel and myDNA)
spacefill 10
select cont_d_polar and small_channel
spacefill 200
select cont_prot_polar and within(3.5, small_channel and myDNA)
spacefill 200
select DA21.N7
label Polar contacts with small channel atoms
pause

select cont_d_polar and small_channel
spacefill 10
select cont_prot_polar and within(3.5, small_channel and myDNA)
spacefill 10
select cont_d_nopolar and small_channel
spacefill 200
select cont_prot_nopolar and within(4.5, small_channel and myDNA)
spacefill 200
select DA21.N7
label Non-polar contacts with small channel atoms
pause