Model of putative helix from pufX protein, color-coded to show the hydropathy profile (Rainbow scale*). The coordinates of the model were generated using the Ribosome function of PSAAM. The model is seen as a stereo-pair (for crossed-eye viewing) displayed by PDVWIN (Protein Data Viewer for Windows).
*Rainbow scale, RedOrgYelGrnCyaBluVioGray with red indicating high values
The PufX helix model shown in the Render window of PDVWIN. The residues are color-coded according to the side-chain volume moment (Rainbow scale). Notice the patch of red-yellow residues showing a span in which the helix is lob-sided, with a cavity of small side-chains on one side among a patch of large side chains. We have suggested that the PufX protein sits in the ring of LH1 light-harvesting complexes surrounding the reaction center; a dimer would make a hole through which ubiquinone could diffuse between the volume inside the ring (to which the Qb-site of the reaction center has access), and the volume outside the ring (to which the bc-complex has access).
SEQRES 1 266 MET ALA THR ALA SER ALA ILE GLN SER SER SER LEU ALA SEQRES 2 266 GLY GLN THR LEU LEU ARG PRO GLN GLN ASN GLU LEU VAL SEQRES 3 266 LYS LYS VAL GLY THR ALA GLN ALA ARG ILE THR MET ARG SEQRES 4 266 ARG THR VAL ARG SER ALA PRO GLU SER ILE TRP TYR GLY SEQRES 5 266 PRO ASP ARG PRO LYS TYR LEU GLY PRO PHE SER GLU GLY SEQRES 6 266 THR PRO SER TYR LEU THR GLY GLU PHE PRO GLY ASP TYR SEQRES 7 266 GLY TRP ASP THR ALA GLY LEU SER ALA ASP PRO GLU THR SEQRES 8 266 PHE ALA LYS ASN ARG GLU LEU GLU VAL ILE HIS CYS ARG SEQRES 9 266 TRP ALA MET LEU GLY ALA LEU GLY CYS LEU PHE PRO GLU SEQRES 10 266 LEU LEU ALA LYS ASN GLY VAL LYS PHE GLY GLU ALA VAL SEQRES 11 266 TRP PHE LYS ALA GLY ALA GLN ILE PHE SER GLU GLY GLY SEQRES 12 266 LEU ASP TYR LEU GLY ASN PRO ASN LEU ILE HIS ALA GLN SEQRES 13 266 SER ILE LEU ALA ILE TRP ALA CYS GLN VAL VAL LEU MET SEQRES 14 266 GLY LEU ILE GLU GLY TYR ARG VAL GLY GLY GLY PRO LEU SEQRES 15 266 GLY GLU GLY LEU ASP PRO LEU TYR PRO GLY GLY ALA PHE SEQRES 16 266 ASP PRO LEU GLY LEU ALA ASP ASP PRO GLU ALA PHE ALA SEQRES 17 266 GLU LEU LYS VAL LYS GLU ILE LYS ASN GLY ARG LEU ALA SEQRES 18 266 MET PHE SER MET PHE GLY PHE PHE VAL GLN ALA ILE VAL SEQRES 19 266 THR GLY LYS GLY PRO ILE GLU ASN LEU TYR ASP HIS LEU SEQRES 20 266 ALA ASP PRO VAL ALA ASN ASN ALA TRP ALA TYR ALA THR SEQRES 21 266 ASN PHE VAL PRO GLY LYS HET CHL 1 HET CHL 2 HET CHL 3 HET CHL 4 HET CHL 5 HET CHL 6 HET CHL 7 HET CHL 8 HET CHL 9 HET CHL 10 HET CHL 11 HET CHL 12 HET CHL 13 HELIX 1 PRO 89 ALA 120 HELIX 2 LEU 152 GLU 173 HELIX 3 GLU 205 THR 235 HELIX 4 ILE 240 ASN 254 TURN 1 PRO 75 TYR 78 TURN 2 LYS 121 VAL 124 TURN 3 GLY 148 ASN 151 TURN 4 GLY 178 PRO 181 TURN 5 PRO 191 ALA 194 TURN 6 ALA 201 PRO 204 TURN 7 GLY 236 PRO 239 ATOM 734 N PRO 89 0.000 0.000 0.000 ATOM 735 CA PRO 89 0.000 -1.325 0.765 ATOM 736 C PRO 89 -1.118 -2.166 0.313 ATOM 737 O PRO 89 -0.953 -3.389 0.189 ATOM 738 CB PRO 89 -0.027 -1.144 2.294 ATOM 739 CG PRO 89 0.002 0.359 2.618 ATOM 740 CD PRO 89 0.046 1.149 1.301 ATOM 741 N PRO 89 0.000 0.000 0.000 ATOM 742 N GLU 90 -2.261 -1.558 0.059 . . .
Sequence.....Side-chain volume moment.....Amphipathy.....Hydropathy
Model color-code using Rainbow scale.
Sequence is -89PETFAKNRELGVIHCRWAMLGALGCLFPELLA-