where D 21 means the distance between atom 2 and atom 1 and x 2 , y 2 , z 2 , x 1 , y 1 , z 1 are coordinates of atom 2 and atom 1. When the methods based on Cα or Cβ atom position are used, the default distance threshold is 7.0 angstroms, as it approximates the upper limit for noncovalent interactions in macromolecular structures [23] . When the third method is used, the distance threshold is calculated as