Residue interactions within interfaces
Notations representing different interactions.
Refering the PDBsum database and using PyMol, the interactions between interfacing residues, as well as the number of interactions are demonstrated in the diagrams below. The nature of these interactions helps gain deeper insights about binding affinity, entropy and surface complementarity.
Interactions of interfacing residues in CTF3 and MCM16
Interactions of interfacing residues in CTF3 and IML3
Interactions of interfacing residues in CTF3 and MCM22
Interactions of interfacing residues in CTF3 and CTF19
Usually in the interface between CTF3 and CTF19, Arg433 (green) and Asp99 (deepteal) are supposed to have a salt-bridge as their interaction. However in this case, the interaction between them is VDW interaction. Using PyMol it is explained that because of the excessive distance of 5.3Å between the side chains, only VDW interaction is formed between Arg433 and Asp99.
Number of amino acids in CTF3 interface
Frequency distribution of hydrophobic and hydrophilic amino acids in the CTF3 interfaces. The relative degree of hydrophobicity is shown with a scale bar as reference.