蛋白质内部氨基酸之间的相互作用②pymol

(1) 选中蛋白质的两个相邻的b-sheet，命名为sel1，sel2。

(2) 添加氢原子

h_add CTGF1

(3) 设置氢键的donor和acceptor

select don, (elem n,o and (neighbor hydro))
select acc, (elem o or (elem n and not (neighbor hydro)))

(4) 得到氢键。

dist HBA, (sel1 and acc),(sel2 and don), 3.2
dist HBD, (sel1 and don),(sel2 and acc), 3.2

(5) 计算距离

dist contact, sel1, sel2, 3