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Clustering snapshots from the 1 μs MD trajectory of the P22/DNA complex. (A) Manhattan distance matrix for all protein–NA base contacts involving each monomer. The vertical scale shows increasing distances (black → yellow). (B) Alternative orientations observed for glutamine 37 (Q37): positioned in the major groove (left), bound to the backbone (right). (C) summary of the position of the Q37 residues in each cluster.
