Results for 5u6p

PDB: 5u6p Gene name: HCN1 UniProt: HCN1_HUMAN EMD: emd_8512.gz

Membrane mimetics: micelle; LMNG, CHS, digitonin; extraction buffer contained LMNG, CHS then SEC buffer containing digitonin

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 17.00 31.33 23.33
End0 -17.00 -33.17 -25.17

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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