Results for 5a63

PDB: 5a63 Gene name: APH1A UniProt: APH1A_HUMAN EMD: emd_3061.gz
EMD-3061

Membrane mimetics: amphipol; A8-35 Note: More manual adjustment needed because of the noise level


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

* end0 around -30 5
* end1 around 30 5

Boundary values (averages for MemBlob)


Z (PDBTM) Z (MemBlob) Z - 8
End1 12.25 30.33 22.33
End0 -12.25 -34.06 -26.06

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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