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Chlorine in PDB 4g3j: Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)]

Enzymatic activity of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)]

All present enzymatic activity of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)]:
1.14.13.70;

Protein crystallography data

The structure of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)], PDB code: 4g3j was solved by T.Y.Hargrove, Z.Wawrzak, M.R.Waterman, G.I.Lepesheva, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.93 / 1.83
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 60.013, 79.480, 116.353, 74.59, 79.28, 68.48
R / Rfree (%) 16.9 / 22

Other elements in 4g3j:

The structure of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)] also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)] (pdb code 4g3j). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)], PDB code: 4g3j:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4g3j

Go back to Chlorine Binding Sites List in 4g3j
Chlorine binding site 1 out of 8 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:24.2
occ:1.00
CLC A:VNT502 0.0 24.2 1.0
CBA A:VNT502 1.7 22.0 1.0
CAQ A:VNT502 2.6 21.5 1.0
CBE A:VNT502 2.7 21.5 1.0
CBH A:VNT502 3.0 21.6 1.0
CD1 A:PHE290 3.4 26.8 1.0
N A:ALA291 3.5 23.6 1.0
CA A:ALA291 3.6 24.4 1.0
CB A:ALA291 3.7 24.2 1.0
O A:ALA287 3.8 23.2 1.0
CAZ A:VNT502 3.9 22.0 1.0
CE A:MET106 3.9 23.4 1.0
NAW A:VNT502 3.9 21.7 1.0
CB A:PHE290 3.9 24.1 1.0
CAN A:VNT502 3.9 21.9 1.0
CG A:PHE290 3.9 28.2 1.0
CZ A:PHE110 4.0 23.3 1.0
C A:PHE290 4.1 27.5 1.0
CE1 A:PHE290 4.2 26.5 1.0
CE1 A:PHE110 4.2 22.8 1.0
CAR A:VNT502 4.2 22.2 1.0
OAA A:VNT502 4.3 22.8 1.0
O A:HOH780 4.4 37.1 1.0
CAI A:VNT502 4.4 21.8 1.0
NBI A:VNT502 4.5 22.4 1.0
CAY A:VNT502 4.5 21.9 1.0
NAT A:VNT502 4.6 22.8 1.0
C A:ALA287 4.7 20.3 1.0
CA A:PHE290 4.7 22.4 1.0
CA A:ALA287 4.7 19.2 1.0
O A:PHE290 4.8 23.9 1.0
SD A:MET106 5.0 26.7 1.0

Chlorine binding site 2 out of 8 in 4g3j

Go back to Chlorine Binding Sites List in 4g3j
Chlorine binding site 2 out of 8 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)] within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:24.5
occ:1.00
CLB A:VNT502 0.0 24.5 1.0
CAZ A:VNT502 1.7 22.0 1.0
CAQ A:VNT502 2.7 21.5 1.0
CAI A:VNT502 2.7 21.8 1.0
CMD A:HEM501 3.6 22.6 1.0
OH A:TYR116 3.7 27.0 1.0
CE2 A:TYR116 3.8 29.9 1.0
CB A:ALA287 3.9 21.7 1.0
CBA A:VNT502 4.0 22.0 1.0
CAN A:VNT502 4.0 21.9 1.0
CZ A:TYR116 4.1 30.8 1.0
CD2 A:LEU127 4.1 30.6 1.0
CAD A:HEM501 4.2 23.4 1.0
C2D A:HEM501 4.2 19.9 1.0
CZ A:PHE110 4.4 23.3 1.0
C3D A:HEM501 4.4 20.0 1.0
CE2 A:PHE110 4.5 25.7 1.0
CBE A:VNT502 4.5 21.5 1.0
CB A:ALA115 4.7 22.7 1.0
CD2 A:TYR116 4.8 26.9 1.0
CA A:ALA287 4.9 19.2 1.0

Chlorine binding site 3 out of 8 in 4g3j

Go back to Chlorine Binding Sites List in 4g3j
Chlorine binding site 3 out of 8 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:24.4
occ:1.00
CLC B:VNT502 0.0 24.4 1.0
CBA B:VNT502 1.7 20.8 1.0
CAQ B:VNT502 2.6 20.9 1.0
CBE B:VNT502 2.6 20.9 1.0
CBH B:VNT502 2.9 22.1 1.0
CB B:PHE290 3.4 28.9 1.0
N B:ALA291 3.6 19.7 1.0
NAW B:VNT502 3.6 21.8 1.0
CA B:ALA291 3.7 21.8 1.0
CZ B:PHE110 3.8 31.8 1.0
CAZ B:VNT502 3.9 20.7 1.0
CAN B:VNT502 3.9 21.7 1.0
C B:PHE290 3.9 26.6 1.0
CB B:ALA291 3.9 18.0 1.0
OAA B:VNT502 4.0 23.3 1.0
O B:ALA287 4.1 21.7 1.0
CAY B:VNT502 4.1 22.5 1.0
CE B:MET106 4.1 32.7 1.0
CAR B:VNT502 4.3 22.4 1.0
CA B:PHE290 4.3 24.3 1.0
CD2 B:PHE290 4.4 39.7 1.0
CAI B:VNT502 4.4 22.2 1.0
CG B:PHE290 4.4 29.5 1.0
CE1 B:PHE110 4.5 28.9 1.0
O B:PHE290 4.5 30.8 1.0
NBI B:VNT502 4.6 21.7 1.0
NAT B:VNT502 4.7 21.4 1.0
SD B:MET106 4.8 33.7 1.0
CE2 B:PHE110 4.9 28.9 1.0
O B:HOH805 4.9 34.0 1.0

Chlorine binding site 4 out of 8 in 4g3j

Go back to Chlorine Binding Sites List in 4g3j
Chlorine binding site 4 out of 8 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)] within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:25.1
occ:1.00
CLB B:VNT502 0.0 25.1 1.0
CAZ B:VNT502 1.7 20.7 1.0
CAQ B:VNT502 2.7 20.9 1.0
CAI B:VNT502 2.7 22.2 1.0
CBA B:VNT502 4.0 20.8 1.0
CAN B:VNT502 4.0 21.7 1.0
CMD B:HEM501 4.0 26.8 1.0
CB B:ALA287 4.1 20.6 1.0
CE2 B:TYR116 4.2 37.7 1.0
CD2 B:LEU127 4.3 45.3 1.0
CE2 B:PHE110 4.3 28.9 1.0
OH B:TYR116 4.3 35.2 1.0
CZ B:TYR116 4.4 35.3 1.0
CB B:ALA115 4.4 27.5 1.0
CBE B:VNT502 4.5 20.9 1.0
CZ B:PHE110 4.5 31.8 1.0
C2D B:HEM501 4.7 23.7 1.0
CAD B:HEM501 4.8 21.9 1.0
CD2 B:TYR116 4.8 36.4 1.0
CD2 B:PHE110 4.9 28.1 1.0
C3D B:HEM501 5.0 22.4 1.0

Chlorine binding site 5 out of 8 in 4g3j

Go back to Chlorine Binding Sites List in 4g3j
Chlorine binding site 5 out of 8 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)] within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl502

b:25.0
occ:1.00
CLC C:VNT502 0.0 25.0 1.0
CBA C:VNT502 1.6 22.3 1.0
CAQ C:VNT502 2.6 22.3 1.0
CBE C:VNT502 2.6 22.6 1.0
CBH C:VNT502 3.0 22.2 1.0
O C:HOH723 3.5 40.2 1.0
NAW C:VNT502 3.6 22.1 1.0
CB C:PHE290 3.6 26.5 1.0
N C:ALA291 3.7 24.5 1.0
CZ C:PHE110 3.8 32.7 1.0
C C:PHE290 3.8 31.9 1.0
CE C:MET106 3.9 28.5 1.0
CAZ C:VNT502 3.9 22.9 1.0
CAN C:VNT502 3.9 24.2 1.0
OAA C:VNT502 3.9 24.7 1.0
CA C:ALA291 4.0 24.6 1.0
CAY C:VNT502 4.0 22.2 1.0
O C:PHE290 4.1 31.4 1.0
SD C:MET106 4.3 31.1 1.0
CB C:ALA291 4.3 25.9 1.0
CAR C:VNT502 4.3 23.0 1.0
CE1 C:PHE110 4.4 30.6 1.0
CA C:PHE290 4.4 27.4 1.0
O C:ALA287 4.4 23.7 1.0
CAI C:VNT502 4.4 23.2 1.0
CG C:PHE290 4.7 28.7 1.0
NAT C:VNT502 4.7 22.7 1.0
NBI C:VNT502 4.7 21.9 1.0
CD2 C:PHE290 4.8 33.6 1.0
CE2 C:TYR103 4.8 30.0 1.0
O C:HOH719 4.9 35.2 1.0
CE2 C:PHE110 4.9 36.3 1.0

Chlorine binding site 6 out of 8 in 4g3j

Go back to Chlorine Binding Sites List in 4g3j
Chlorine binding site 6 out of 8 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)] within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl502

b:27.5
occ:1.00
CLB C:VNT502 0.0 27.5 1.0
CAZ C:VNT502 1.7 22.9 1.0
CAQ C:VNT502 2.7 22.3 1.0
CAI C:VNT502 2.7 23.2 1.0
CMD C:HEM501 3.7 35.9 1.0
CB C:ALA287 3.9 28.1 1.0
CE2 C:TYR116 4.0 44.5 1.0
CBA C:VNT502 4.0 22.3 1.0
CAN C:VNT502 4.0 24.2 1.0
CD2 C:LEU127 4.2 57.2 1.0
C2D C:HEM501 4.5 30.3 1.0
CB C:ALA115 4.5 36.5 1.0
CBE C:VNT502 4.5 22.6 1.0
CZ C:PHE110 4.6 32.7 1.0
OH C:TYR116 4.6 41.3 1.0
CZ C:TYR116 4.6 47.4 1.0
CE2 C:PHE110 4.6 36.3 1.0
CD2 C:TYR116 4.6 49.1 1.0
CA C:ALA287 4.9 27.2 1.0
O C:ALA287 5.0 23.7 1.0

Chlorine binding site 7 out of 8 in 4g3j

Go back to Chlorine Binding Sites List in 4g3j
Chlorine binding site 7 out of 8 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)] within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl502

b:25.6
occ:1.00
CLC D:VNT502 0.0 25.6 1.0
CBA D:VNT502 1.7 22.4 1.0
CAQ D:VNT502 2.6 23.8 1.0
CBE D:VNT502 2.7 22.3 1.0
CBH D:VNT502 3.0 21.9 1.0
CB D:PHE290 3.3 33.9 1.0
N D:ALA291 3.6 25.5 1.0
NAW D:VNT502 3.6 21.7 1.0
CA D:ALA291 3.8 24.9 1.0
OAA D:VNT502 3.8 24.0 1.0
C D:PHE290 3.9 35.7 1.0
CAZ D:VNT502 3.9 22.6 1.0
CAN D:VNT502 3.9 23.3 1.0
CE D:MET106 4.0 38.9 1.0
CAY D:VNT502 4.0 23.1 1.0
CB D:ALA291 4.1 25.6 1.0
CZ D:PHE110 4.2 27.5 1.0
O D:ALA287 4.2 26.4 1.0
CG D:PHE290 4.2 38.5 1.0
CA D:PHE290 4.2 33.5 1.0
CD2 D:PHE290 4.3 39.4 1.0
CAR D:VNT502 4.3 22.4 1.0
CAI D:VNT502 4.4 23.2 1.0
O D:PHE290 4.4 36.5 1.0
NAT D:VNT502 4.5 23.6 1.0
O D:HOH714 4.6 31.9 1.0
SD D:MET106 4.6 34.8 1.0
CE1 D:PHE110 4.6 31.5 1.0
NBI D:VNT502 4.7 22.7 1.0

Chlorine binding site 8 out of 8 in 4g3j

Go back to Chlorine Binding Sites List in 4g3j
Chlorine binding site 8 out of 8 in the Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)]


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Sterol 14-Alpha Demethylase (CYP51) From Trypanosoma Brucei in Complex with the Vni Derivative (R)-N-(1-(2,4-Dichlorophenyl)-2-(1H-1,2,4- Triazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide [R- Vni-Triazole (Vnt)] within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl502

b:27.1
occ:1.00
CLB D:VNT502 0.0 27.1 1.0
CAZ D:VNT502 1.7 22.6 1.0
CAI D:VNT502 2.6 23.2 1.0
CAQ D:VNT502 2.7 23.8 1.0
CB D:ALA287 3.8 21.2 1.0
CAN D:VNT502 3.9 23.3 1.0
CBA D:VNT502 3.9 22.4 1.0
CE2 D:TYR116 4.0 41.2 1.0
CE2 D:PHE110 4.0 28.1 1.0
CZ D:PHE110 4.1 27.5 1.0
CMD D:HEM501 4.2 28.6 1.0
OH D:TYR116 4.4 39.1 1.0
CZ D:TYR116 4.4 37.4 1.0
CBE D:VNT502 4.4 22.3 1.0
CB D:ALA115 4.5 25.4 1.0
CD2 D:LEU127 4.5 32.9 1.0
CD2 D:TYR116 4.7 41.1 1.0
CD2 D:PHE110 4.7 28.9 1.0
CE1 D:PHE110 4.8 31.5 1.0
CA D:ALA287 4.8 23.6 1.0
C2D D:HEM501 4.9 24.9 1.0
CAD D:HEM501 4.9 29.8 1.0

Reference:

G.I.Lepesheva, T.Y.Hargrove, G.Rachakonda, Z.Wawrzak, S.Pomel, S.Cojean, P.N.Nde, W.D.Nes, C.W.Locuson, M.W.Calcutt, M.R.Waterman, J.S.Daniels, P.M.Loiseau, F.Villalta. Vfv As A New Effective CYP51 Structure-Derived Drug Candidate For Chagas Disease and Visceral Leishmaniasis. J Infect Dis V. 212 1439 2015.
ISSN: ISSN 1537-6613
PubMed: 25883390
DOI: 10.1093/INFDIS/JIV228
Page generated: Sat Dec 12 10:38:36 2020

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