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Fig. 5 | BMC Biology

Fig. 5

From: Charged residues next to transmembrane regions revisited: “Positive-inside rule” is complemented by the “negative inside depletion/outside enrichment rule”

Fig. 5

There is a difference in the hydrophobic profiles of TMHs from single-pass and multi-pass proteins. (a) The hydrophobicity of single-pass TMHs compared to multi-pass segments from the UniHuman dataset. The Kyte and Doolittle scale of hydrophobicity [52] was used with a window length of 3 to compare TMHs from proteins with different numbers of TMHs. This scale is based on the water-vapour transfer of free energy and the interior-exterior distribution of individual amino acids. The same datasets also had different scales applied (Additional file 2: Figure S2). The vertical axis is the hydrophobicity score, whilst the horizontal axis is the position of the residue relative to the centre of the TMH, with negative values extending into the cytoplasm. In black are the average hydrophobicity values of TMHs belonging to single-pass TMHs, whilst in other colours are the average hydrophobicity values of TMHs belonging to multi-pass proteins containing the same numbers of TMHs per protein. In purple are the TMHs from proteins with more than 15 TMHs per protein that do not share a typical multi-pass profile, perhaps due to their exceptional nature. (b) The Kruskal-Wallis test (H statistic) was used to compare single-pass windowed hydrophobicity values with the average windowed hydrophobicity value of every TMH from multi-pass proteins at the same position. The vertical axis is the logarithmic scale of the resultant P values. We can much more readily reject the hypothesis that hydrophobicity is the same between TMHs from single-pass and multi-pass proteins in the core of the helix and the flanks than the interfacial regions, particularly at the inner leaflet due to leucine asymmetry (Table 4)

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