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Hyperdimensional Analysis of Amino Acid Pair Distributions in Proteins

Figure 10

Figures 10A to 10C display typical protein motifs involving Arg-Arg pairs that are in close proximity (3.3–3.8 Å) in protein shells with 10–30%SA.

Arg residues should be within a sequence distance larger than 4 and located in coil elements (Fig. 10A, PO4 is a phosphate group, 2HNH.pdb), in α-helix (Fig. 10B, 202K.pdb, structural water molecules are displayed as red spheres) or in β-strands (Fig. 10C, 2P1M .pdb, HP is a sugar molecular linked to six phosphate group). Figures 10D and 10E displayed typical protein motifs involving Asp-Asp pairs that are in close proximity (2.3–3.3 Å) in protein shells with 0<SA≤10% (1WDC.pdb and 2SCP.pdb, respectively). Such Asp-Asp pairs (displayed in blue and yellow) are involved in Mg2+ and Ca2+ binding involving 2 additional Asp residues (displayed in brown). Distances between functional groups are shown.

Figure 10

doi: https://doi.org/10.1371/journal.pone.0025638.g010