load =1DDN
delete HOH
delete Ni
delete *:A.*
define prot_polar  :c.O?? or :c.N?? or :b.O?? or :b.N?? or :d.O?? or :d.N??
define prot_npolar  protein and (not prot_polar)
define bgr_polar ((DA.N6 or DA.N7) or (DG.O6 or DG.N7)  or (DC.N4) or (DT.O4)) and DNA
define bgr_npolar (DA.C5 or DA.C6) or (DG.C5 or DG.C6 or DG.C8) or (DC.C4 or DC.C5 or DC.C6) or (DT.C4 or DT.C5 or DT.C6 or DT.C7)
define sgr_polar (DA.N3 or DA.N9) or (DG.N2 or DG.N3 or DG.N9) or (DC.O2 or DC.N1) or (DT.O2 or DT.N1)
define sgr_npolar (DA.C2 or DA.C4) or (DG.C2 or DG.C4) or (DC.C2) or (DT.C2 or DT.C6)
define sugar_polar :e.O?' or :f.O?'
define sugar_npolar :e.C?' or :f.C?'
define PA_polar :e.OP? or :f.OP?
define PA_npolar :e.P or :f.P
select all
cpk off
select prot_polar and within (4.5, sugar_polar)
cpk 150
select sugar_polar and within (4.5, prot_polar)
cpk 150
pause
resume
select all
cpk off
select prot_polar and within (4.5, PA_polar)
cpk 150
select PA_polar and within (4.5, prot_polar)
cpk 150
pause
resume
select all
cpk off
select prot_polar and within (4.5, bgr_polar)
cpk 150
select bgr_polar and within (4.5, prot_polar)
cpk 150
pause
resume
select all
cpk off
select prot_polar and within (4.5, sgr_polar)
cpk 150
select sgr_polar and within (4.5, prot_polar)
cpk 150
pause
resume
select all
cpk off
select prot_npolar and within (4.5, sugar_npolar)
cpk 150
select sugar_npolar and within (4.5, prot_npolar)
cpk 150
pause
resume
select all
cpk off
select prot_npolar and within (4.5, PA_npolar)
cpk 150
select PA_npolar and within (4.5, prot_npolar)
cpk 150
pause
resume
select all
cpk off
select prot_npolar and within (4.5, bgr_npolar)
cpk 150
select bgr_npolar and within (4.5, prot_npolar)
cpk 150
pause
resume
select all
cpk off
select prot_npolar and within (4.5, sgr_npolar)
cpk 150
select sgr_npolar and within (4.5, prot_npolar)
cpk 150