PDBsum entry 1vaf

Tunnel analysis for: 1vaf calculated with

MOLE 2.0

PDB id

1vaf

Tunnels calculated on whole structure

Tunnels calculated excluding ligands

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MOLEonline 2.0 manipulation
and
visualization
with HETATM:

without HETATM:

2 tunnels, coloured by tunnel radius

13 tunnels, coloured by tunnel radius

13 tunnels, coloured as in
list below

Tunnels are interior spaces connected with the protein surrounding. Only channels longer than 15 Å are shown.

Tunnels

Free R

Length

HPathy

HPhob

Polar

Rel Mut

Residue..type

Ligands

Radius

1

1.76

2.97

19.5

0.17

0.60

2.1

63

0

0

1

4

4

0

1

HEM 900 A ARR 902 A

2

1.68

2.91

31.5

0.57

0.49

9.1

67

1

1

0

5

4

0

1

HEM 900 A H4B 901 A ARR 902 A

3

1.66

2.91

33.5

-0.09

0.30

8.5

74

1

1

5

5

5

0

1

HEM 900 A ARR 902 A

4

1.36

3.80

15.9

-0.43

0.08

9.8

70

1

1

1

3

2

1

1

5

1.36

3.78

18.2

0.22

0.17

6.7

67

1

1

1

3

1

1

2

ZN 950 B

6

1.38

1.36

28.9

-0.04

0.42

8.2

76

2

0

4

6

5

1

1

HEM 900 B ARR 903 B

7

1.39

1.38

34.6

0.10

0.41

10.5

75

2

1

1

8

4

1

1

HEM 900 B ARR 903 B H4B 1901 B

8

1.41

1.39

35.4

0.46

0.28

6.2

71

1

1

3

7

6

1

1

HEM 900 B ARR 903 B

9

2.05

2.76

15.8

-0.62

0.34

1.9

74

0

0

1

3

3

2

0

10

1.86

2.09

17.3

-1.20

-0.12

5.1

73

1

0

2

1

3

1

0

11

2.12

2.20

17.5

-0.64

0.25

3.7

76

1

0

3

2

3

1

0

12

1.61

1.69

25.5

-0.75

0.17

4.0

75

2

0

2

2

3

2

0

13

1.42

1.44

15.6

-0.90

-0.08

20.0

80

2

1

2

2

0

0

0

Residue-type_colouring

Positive	Negative	Neutral	Aliphatic	Aromatic	Pro & Gly	Cysteine
H,K,R	D,E	S,T,N,Q	A,V,L,I,M	F,Y,W	P,G	C

Acknowledgement

Tunnels were calculated by

MOLE 2.0 program version 2.5.13.11.08 and visualized using Pymol 0.97rc.