background [xFFFF99]
var x__id__ = '1by4'; if (x__id__.length != 4) { x__id__ = '1BY4'};x__id__ = prompt('Press enter',x__id__)
if (!x__id__) { quit }; load @{'=' + x__id__}
select dna; wireframe 50; cpk off; color cpk
select protein; wireframe off; cpk off
cartoons on; rotate x 90; rotate z 25; zoom out
define set1 *.o?' and dna
define set2 *.op? and dna
define polar (oxygen or nitrogen) and protein
define nonpolar (sulphur or phosphorus or carbon) and protein
select within (3.5, polar) and set1
select within (3.5, set1) and polar and protein; cpk 300
echo 13 polar protein-desoxiribose contacts
pause; cpk off
select within (4.5, *.c?' and dna) and nonpolar and protein; cpk 300
echo 33 nonpolar protein-desoxiribose contacts
pause; cpk off
select within (3.5, set2) and polar and protein; cpk 300
echo 51 polar DNA phosphate oxygen-protein contacts;
pause; cpk off
select within (4.5, *.p and dna) and nonpolar and protein; cpk 300
echo 45 DNA phosphorus-protein contacts;
pause; cpk off
define pol_b_ind (a, t, c, g) and (c.n4, a.n6, *.o4, *.n7, g.o6)
define carb_b_ind (a, t, c, g) and (*.c6, *.c5, g.c8, c.c4, t.c4)
define pol_s_ind (a, t, c, g) and (*.o2, *.n1, g.n2, *.n3, *.n9)
define carb_s_ind (a, t, c, g) and (*.c2, a.c4, g.c4)
select within (3.5, pol_s_ind) and polar; cpk 300
echo 1 polar minor groove-protein contact;
pause; cpk off
select within (3.5, pol_b_ind) and polar; cpk 300
echo 9 polar major groove-protein contacts;
pause; cpk off
select within (4.5, carb_s_ind) and nonpolar; cpk 300
echo 0 nonpolar minor groove-protein contacts;
pause; cpk off
select within (4.5, carb_b_ind) and nonpolar; cpk 300
echo 13 nonpolar major groove-protein contacts;
pause; cpk off