Analyzing the aromatic-aromatic interactions in proteins: A2ID 2.0

The Aromatic-Aromatic Interactions Database (A2ID) is a comprehensive repository dedicated to documenting aromatic-aromatic (π-π) networks observed in experimentally determined protein structures. The first version of A2ID was reported in 2011 [Int J Biol Macromol, 2011, 48, 540]. It has undergone a...

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Bibliographic Details
Published in:International journal of biological macromolecules 2023-12, Vol.253, p.127207-127207, Article 127207
Main Authors: Kumar, Y. Bhargav, Kumar, Nandan, Vaikundamani, S., Nagamani, Selvaraman, Mahanta, Hridoy Jyoti, Sastry, G. Madhavi, Sastry, G. Narahari
Format: Article
Language:English
Subjects:
amino acids
Aromatic interactions
Centroid distance
data collection
geometry
Interplanar angle
Proteins
Citations: Items that this one cites
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Summary:The Aromatic-Aromatic Interactions Database (A2ID) is a comprehensive repository dedicated to documenting aromatic-aromatic (π-π) networks observed in experimentally determined protein structures. The first version of A2ID was reported in 2011 [Int J Biol Macromol, 2011, 48, 540]. It has undergone a series of significant updates, leading to its current version, which focuses on the identification and analysis of 3,444,619 π-π networks from proteins. The geometrical parameters such as centroid-centroid distances (r) and interplanar angles (ϕ) were used to identify and characterize π-π networks. It was observed that among the 84,500 proteins with at least one aromatic π-π network, about 92.50 % of the instances are found to be either 2π (77.34 %) or 3π (15.23 %) networks. The analysis of interacting amino acid pairs in 2π networks indicated a dominance of PHE residues followed by TYR. The updated version of A2ID incorporates analysis of π-π networks based on SCOP2 and ECOD classifiers, in addition to the existing SCOP, CATH, and EC classifications. This expanded scope allows researchers to explore the characteristics and functional implications of π-π networks in protein structures from multiple perspectives. The current version of A2ID along with its extensive dataset and detailed geometric information is publicly accessible using https://acds.neist.res.in/a2idv2. •A2ID V2.0 provides a comprehensive update of π-π networks till June 2023.•Classification schemes – SCOP, SCOP2, CATH, EC and ECOD, have been incorporated.•Connectivity patterns are precisely defined and computed.•Illustrative example on alteration of stability upon loosing/gaining π-π interaction
ISSN:0141-8130
1879-0003
DOI:10.1016/j.ijbiomac.2023.127207