In addition to noncovalent interactions, the cation-π interaction (Dougherty, 1996) is recognized as an important noncovalent binding interaction relevant to structural biology. It is formed by the interaction of the positively charged residues, Lys and Arg, with the aromatic residues, Phe, Trp, and Tyr. Gallivan and Dougherty (1999) identified and evaluated cation-π interactions in protein structures. They reported that cation-π interactions are commonly occurring in protein structures in such a way that when a cationic side chain (Lys or Arg) is near to an aromatic side chain (Phe, Tyr, or Trp), the geometry is biased toward one that would experience a favorable cation-π interaction.
阳离子-π相互作用（Dougherty，1996）被认为是与结构生物学相关的重要的非共价结合相互作用。它由带正电的残基Lys和Arg与芳香族残基Phe，Trp和Tyr相互作用而形成。 Gallivan和Dougherty（1999）发现和评估了蛋白质结构中的阳离子-π相互作用。他们报道，阳离子-π相互作用通常以这样的方式发生在蛋白质结构中，当阳离子侧链（Lys或Arg）靠近芳香侧链（Phe，Tyr或Trp）时，几何结构偏向于阳离子-π相互作用。
Cation-π interactions in protein structures have been identified with distance and energy criteria, (i) distance between the cationic group (the ammonium nitrogen (NZ) in Lys or the guanidinium carbon [CZ] in Arg) and the centers of all aromatic rings and (ii) the interaction energy between the positive charged and aromatic residues using OPLS (optimized potentials for liquid simulations) force field. This interaction is between Lys408 and Trp356 in a sulfite reductase (PDB code: 1AOP), and it is one of the strongest interactions with the energy of −9.4 kcal/mol. The total cation-π interaction energy (Ecat−π ) has been divided into electrostatic (Ees) and van der Waals energies (Evdw). The electrostatic energy (Ees) is calculated using the equation,
Ees=qiqj/rij,
已经用距离和能量标准鉴定了蛋白质结构中的阳离子-π相互作用，（i）阳离子基团（Lys中的铵态氮（NZ）或Arg中的胍基碳[CZ]）与所有芳族环（ii）带正电荷和芳香族残基之间的相互作用使用OPLS（用于液体模拟的优化电位）力场。这种相互作用是在亚硫酸还原酶（PDB编码：1AOP）中的Lys408和Trp356之间，并且是-9.4kcal / mol的能量最强的相互作用之一。总的阳离子-π相互作用能（Ecat-π）被分成静电（Ees）和范德华能（Evdw）。静电能量（Ees）用公式计算，
where qi and qj are, respectively, the effective partial charges for the atoms i and j,and rij is the distance between them. The van der Waals energy between a pair of atoms i and j is given by
其中qi和qj分别是原子i和j的有效部分电荷，rij是它们之间的距离。