Results for 5h3o

PDB: 5h3o Gene name: tax-4 UniProt: CNG_CAEEL EMD: emd_6656.gz

Membrane mimetics: amphipol; A8-35; A8-35; solubilized with LMNG, soybean lipids then mixed with amphipol Note: In spite the lack of memblob, the membrane region is detected because of densities among helices

Cross-sections at different angles

green: density, gray dots: atoms from the all-atom model, lines: membrane boundaries defined by TMDET

The determined edges at each slice and their comparison to TMDET

dots: edges of the gradient, triangles: outliers,
dashed and solid lines: membrane boundaries defined by TMDET and MemBlob ( mean(Zi) decreased by the thickness of the interface region (8 Å))
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Manual settings applied

0,40-60,130-150,220-240,270,310-330 end0 around -25 5
320 end1 around 20 5

Boundary values (averages for MemBlob)

Z (PDBTM) Z (MemBlob) Z - 8
End1 16.75 15.83 7.83
End0 -16.75 -28.11 -20.11

Mapping the results to the structure

You can move/scale/rotate the structure. Blue: a.a. facing to bulk water; magenta: interface region; green: a.a. interacting with the hydrophobic membrane core; yellow: burried a.a. red: a.a. with an invisible side chain and non-protein molecules, for which DSSP cannot return SASA
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