Figure 5. Determining the H-bond network in the active site of the single cysteine peroxiredoxin, AhpE.

(a) The current established H-bond determination methods³,⁶,⁷,²⁵ compare the distance between the hydrogen and acceptor atom (R) with a user-defined maximum length. (b) The adapted equation uses the minimum van der Waals distance (R_min) between the donor and acceptor atom to establish the maximum length for a H-bond based on the nature of the atoms. A fixed value of 1.1 Å is subtracted from R_min. This value was computed by subtracting the distances of the H-bonds found by the NCI index method²¹ from R_min for the different pairs of donor and acceptor atoms. The lowest value for R_min – R_NCI was determined to be 1.1 Å.