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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

Examples:

P267 in TM6 of rhodopsin:

P6.50 or P6.50(267)

E134/R135 in D/E R Y sequence in rhodopsin:

E3.49(134)/R3.50(135)

                                                                    Helix I    Helix II    Helix III    Helix IV    Helix V    Helix VI    Helix VI

                                                                                                   R.3.50                                         P6.50

Rhodopsin                                                                                  135                                              267

System 2

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

System 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