ASBAAC: Automated Salt-Bridge and Aromatic- Aromatic Calculator

Abstract

Biological systems are made of complex networks non-covalent interactions observed among protein-protein, protein-DNA, protein-lipid complexes using hydrogen-bonds, salt-bridges, aromatic-aromatic, van der Waals (vdW), hydrophobic-interactions and several others using distance criteria. Hence, large-scale data analysis is required to understand the principles of biological complex formation. Therefore, it is of interest to analyze non-covalent interaction namely, salt-bridge and aromatic-aromatic contacts in known and modeled protein complex structures. Here, we describe ASBAAC for automatic calculation of salt-bridges and aromatic-aromatic contacts in protein complexes. This software tool is fast, robust and user-friendly for large-scale analysis of inter-chain salt bridges and aromatic-aromatic contact in protein complexes. Availability: ASBAAC is available for free at https://sourceforge.net/projects/asbaac Abbreviation: S-B = Salt-Bridge, A-A = Aromatic-Aromatic Background: Interaction between two or more proteins play a crucial role in maintaining cellular systems through non-covalent interactions such as hydrogen bonds, salt bridges and aromatic-aromatic (A-A) contacts. A particular region where two or more proteins interact with each other is called the interface [1]. Knowledge of amino acids, which are involved in the formation of salt-bridges and A-A contacts with other interacting interfaces between various proteins, is important for the better understanding of protein-protein binding. Salt-bridges most often arise from the anionic amino acids (aspartic acid or glutamic acid) and the cationic amino acids (lysine, arginine or histidine) [2]. The interaction with these functional groups plays an important role in the formation of the structure and function of proteins. Formation of Salt Bridge between two residues occurs at a distance of 4A° [3]. There are numerous salt-bridge interaction strategies such as simple or complex, isolated or networked [4], intra-helical, coiled, strand or inter-helical, coiled and strand [5].