Table 3 Threshold distances used in this analysis to define open, intermediate, and closed conformations in our simulations

From: Large scale investigation of GPCR molecular dynamics data uncovers allosteric sites and lateral gateways

Class

Residue pair (GPCR generic numbering)

Mean distance in inactive-labelled systems (Å)

Intermediate

minimum threshold (Å)

Open minimum threshold (Å)

Mean distance in G protein-bound systems (Å)

A

2 × 46–6 × 37

12.18

13.6

16.36

17.74

B1

2 × 46–6 × 37

12.31

14.88

20.01

22.56

C

2 × 46–6 × 37

20.33

-

-

20.70

F

2 × 44–6 × 31

14.36

-

-

18.36

  1. Fully active and inactive conformations were obtained from static structures stored in GPCRdb, G protein-bound and inactive-labelled systems respectively. Threshold columns represent the minimum distance at which we consider a GPCR in ‘intermediate’ or ‘open’ conformations’. Class C and F were not included in the conformational study. The distance value distributions of each class and state are shown in Fig. 2a (right).
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