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To identify these determinants, we used computational methods to generate models of complexes that hAID and its N51A mutant form with C and 5 mC.
In addition, we calculated the structural models of complexes of PTP-Bas PDZ1 and the C-terminal peptides of TAPP1/2 (referred to as TAPP1p/2p).
The first analysis, involving the four above-described models of complexes formed by wt hAID/N51A mutant and C/5 mC bismonophosphates, showed that the number of intermolecular interactions was the highest (24) in the wt hAID C complex (20 vdW interactions and 4 H-bonds) and the lowest (17) in the N51A C complex (14 vdW interactions and 3 H-bonds).
The models of complexes of nSCARB2 (A), aSCARB2 (C) and one icosahedral asymmetric unit of EV71 (PDB code: 3VBH).
Determining the three-dimensional models of complexes from the predicted contacts was successful in many of the tested instances.
When 3D models of complexes were available, information about the interacting amino acid residues on different peptide chains (defined as amino acids that were within a distance <4.0 Å of each other) were also added to the IR data.
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