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G-protein coupled receptor sequence numbering system
3 "generic numbering systems" in use that allow comparison of equivalent positions in the GPCR family (Gether (2000) review):
System 1. "Ballesteros Weinstein System"
originally described in Ballesteros and Weinstein (1995) Methods Neurosci 25, 366-428:
aa residues in the TM domain are assigned two numbers (N1,N2)
N1 = TM number
N2 = number relative to the most conserved residue in this TM, which is assigned 50, numbers decreasing towards N-terminus and increasing towards C-terminus
P267 in TM6 of rhodopsin:
P6.50 or P6.50(267)
E134/R135 in D/E R Y sequence in rhodopsin:
Helix I Helix II Helix III Helix IV Helix V Helix VI Helix VI
Rhodopsin 135 267
System based on Baldwin (1993) EMBO J. 12, 1693-1703. Also described in BaldwinJMB1997.
helix symbol from I to VII
the most conserved residue in each helix is given a number describing their predicted relative position in a standard helix of 26 residues
number based on 26 residue segment with position :13 and :14 expected to be in the center of the bilayer, see Table 3
Second system by Schwartz et al (1995) Curr. Pharm. Design 1, 325-342.
same as system 2, but the most conserved residues are different except for helix I