Results for 5va3

PDB: 5va3 Gene name: KCNH2 UniProt: KCNH2_HUMAN EMD: emd_8652.gz

Membrane mimetics: micelle; POPE:POPC:POPA; POPE:POPC:POPA; loaded into DDM, CHS

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

* end1 around 25 3

Boundary values (averages for MemBlob)

Z (PDBTM) Z (MemBlob) Z - 8
End1 15.50 25.00 17.00
End0 -15.50 -30.22 -22.22

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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