define mjg  c.n4,a.n6,t.o4,g.o6,g.n7,a.n7,t.c5m,c.c5,g.c8,a.c8,t.c6,c.c6,g.c5,a.c5
define mig  c.o2,t.o2,g.n3,g.n2,a.n3,a.c2
define tocompl t.o4,t.n3,c.n4,c.n3,c.o2,g.o6,g.n1,g.n2,a.n6,a.n1
define basen c.c2,c.c4,c.n1,t.c4,t.c2,t.c5,t.n1,g.c2,g.c4,g.n9,g.c6,a.c4,a.n9,a.c6
define base  mjg,mig,tocompl,basen  
define phosph *.O?P
define sugar (*.O5*,*.C5*,*.C4*,*.O4*,*.C3*,*.O3*,*.C2*,*.C1*) and not protein                                          
# polar contact with dna 
restrict none
select within(3.5, sugar)  and polar
cpk 100
color blue
select *.O?* and within(3.5, selected)
cpk 100
color red
echo polar contact with dna 
pause
# hydrophobic contacts
restrict none
select within(3.5, sugar) and hydrophobic
cpk 100
color blue
select *.C?*
cpk 100
echo no hydrophobic contacts
pause
# polar contacts with phosphor acid
restrict none
select polar and within(3.5, phosph)
cpk 100
color blue
select phosph and within(3.5, selected)
cpk 100
color red
echo polar contacts with phosphor acid
pause
# not polar contacts with phosphoacid
restrict none
select hydrophobic and within(3.5, phosph)
cpk 100
color blue
select phosph and within(3.5, selected)
cpk 100
color red
echo not polar contacts with phosphoacid
pause
# polar contact with mjg
restrict none
define mjg_pol (oxygen,nitrogen) and mjg
select polar and within (3.5, mjg_pol)
cpk 100
color blue
select mjg_pol and within(3.5, selected)
cpk 100
color red
echo polar contact with mjg
pause
# not polar contact with mjg
restrict none 
define mjg_npol carbon and mjg
select hydrophobic and within(3.5, mjg_npol)
cpk 100
color blue
select mjg_npol and within(3.5, selected)
cpk 100
color red
echo not polar contact with mjg
pause
# polar contact with mig
restrict none
define mig_pol   (oxygen,nitrogen) and mig
select polar and within (3.5, mig_pol)
cpk 100
color blue
select mig_pol and within(3.5, selected)
cpk 100
color red
echo polar contact with mig
pause
# not polar contact with mig
restrict none 
define mig_npol carbon and mig
select hydrophobic and within(3.5, mig_npol)
cpk 100
color blue
select mig_npol and within(3.5, selected)
cpk 100
color red
echo not polar contact with mig
pause