Protein Interaction Calculator

1 Introduction

Protein Interaction Calculator is specifically designed to analyze the interactions between residues in protein structures. By calculating the distances between specific functional residues, it can identify and classify different types of interactions. These interactions include, but are not limited to, hydrophobic interactions, hydrogen bonds, ionic interactions, aromatic interactions, and disulfide bridges.

2 Parameter

• PDB File: Input protein structure file.
• Intra_chains: Specify which chains to calculate interactions for, such as ['H', 'L'].
• Interactions：Specify which interactions to calculate, including the following options:
  • Hydrophobic Interactions: Hydrophobic interactions help stabilize the three-dimensional structure of proteins and typically occur between non-polar amino acids.
  • Disulphide Interactions: Disulfide bridges are strong covalent bonds that help maintain protein stability, usually forming between cysteine residues.
  • Cation-Pi Interactions: The interactions between cations and aromatic rings enhance the structural stability of proteins, typically occurring between positively charged amino acids (such as lysine) and aromatic residues.
  • Ionic Interactions: Interactions between two charged residues contribute to protein folding and stability, usually occurring between amino acids with positive and negative charges (such as aspartic acid and lysine).
  • Aromatic-Aromatic Interactions: Interactions between two aromatic residues typically enhance protein stability through π-π stacking interactions.
  • Aromatic-Sulphur Interactions: Interactions between aromatic residues and sulfur-containing residues (such as cysteine) can enhance protein stability through the interaction between the electron cloud of the sulfur atom and the π electron cloud of the aromatic ring.
  • Hydrogen Bonds (MainChain - MainChain): Hydrogen bonds between main chains play a crucial role in the secondary structure of proteins (such as α-helices and β-sheets).
  • Hydrogen Bonds (MainChain - SideChain): Hydrogen bonds between the main chain and side chains contribute to the overall structure and function of proteins.
  • Hydrogen Bonds (SideChain - SideChain): Hydrogen bonds between side chains can influence protein folding and stability.

3 Results Explanation

• Table: Summary table of results, supports CSV format download, containing the following key fields:

4 Reference

[1] protinter