Amino Acid Pairs in Proteins Figure 5. The relevance of warp plots. A) Warp plot merging information about the absolute number of pairs observed in Figure 4B with information about the ratio information displayed in Figure 4F, showing the statistical relevance of each peak. B) Warp plot showing the statistically relevant pairwise interactions that Lys residues make with other amino acids residues and at which spatial distances those interactions occur. The intensity map is color coded, dark blue coding for low statistic relevance and red for the highest statistic relevance. doi:10.1371/journal.pone.0025638.g005 present in beta strands can be involved in multiple salt bridge network involving 7 titratable residues (Lys and Arg residues) present in six adjacent b-strands and 6 phosphate groups. The pair in question is Arg403-Arg436 (3.4 A˚ apart, colored yellow and blue) present in 2P1M.pdb, an outer membrane protein involved in lipid deacylation. The closest distances (2.9–4.1 A˚) to the functional groups of other Lys and Arg residues (displayed in purple) are displayed. In Figures 10D and 10E are displayed typical protein motifs involving Asp-Asp pairs that are in close proximity (2.3–3.3 A˚) in protein shells with 0,SA#10%. These were the characteristics of the unexpected peak displayed in Figure 7B. Such Asp-Asp pairs (displayed in blue and yellow) are involved in Mg2+ and Ca2+ binding involving 2 additional Asp residues (displayed in brown). The pair Asp28-Asp39 displayed in Figure 10D belongs to 1WDC.pdb, a myosin regulatory domain of a muscle protein. The residues are located in two nearby a-helices while the two additional Asp residues are located in loop regions. The distances between the charged functional groups of each Asp residue to Mg2+ are displayed in Figure 10D. The pair Asp16-Asp27 PLoS ONE | www.plosone.org 10 December 2011 | Volume 6 | Issue 12 | e25638