Probabilistic Chemical Shift Assignment of the Sidechain

 

 

Currently ADAPT-NMR supports sidechain assignment if the user provides sidechain peak lists as described in “setting the parameter”. We are planning to include adaptive collection and assignment of sidechain data in the next release of ADAPT-NMR.

ADAPT-NMR produces a probabilistic assignment for every atom in each residue.  This means that it is possible for some atoms to have more than one candidate chemical shift assignment.   In these cases, an associated probability is assigned to each candidate assigned to an atom.  The sum of all probabilities always adds to one.  See the sample output shown in the table below.

The probabilities are one column ahead of the assignments. A chemical shift assignment of 999.00 and its probability indicates the probability that no assignment is found for that particular atom in the peak lists. The table shows portions of the backbone assignment with computed probabilities.

 

1

1

MET

CA

1

54.4

0

54.7

0

54.8

0

54.9

0

55

0

55.1

0

55.2

0

55.3

0

999

0

55.4

2

1

MET

CB

1

33

0

30.6

0

31

0

999

0

31.1

0

31.2

0

30.9

0

31.3

0

31.4

0

31.5

3

1

MET

CG

1

30.8

0

31.1

0

31.2

0

31.3

0

31.4

0

31.5

0

31.6

0

999

0

16.9

0

17

4

1

MET

HA

1

4.18

0

2.03

0

2.02

0

2.01

0

1.96

0

2

0

1.97

0

1.98

0

1.99

0

999

5

1

MET

HB2

1

2.05

0

1.93

0

1.92

0

1.9

0

1.89

0

1.88

0

1.86

0

1.85

0

999

0

3.16

6

1

MET

HB3

1

2.05

0

1.92

0

2

0

2.5

0

2.49

0

1.96

0

1.99

0

1.97

0

1.98

0

999

7

1

MET

HG2

0.505

2.5

0.495

1.92

0

1.96

0

2.07

0

2.08

0

2.03

0

1.97

0

2.06

0

2.05

0

999

8

1

MET

HG3

0.985

2.5

0.015

1.92

0

2.07

0

1.96

0

2.08

0

2.03

0

2.06

0

1.97

0

2.05

0

999

9

2

GLN

CA

0.799

55.7

0.183

55.4

0.017

53.9

0

54.1

0

54.2

0

57

0

54.3

0

55.1

0

54.4

0

999

10

2

GLN

CB

1

29.5

0

27.7

0

35.2

0

999

0

25.6

0

26.1

0

25.7

0

25.8

0

25.9

0

26

11

2

GLN

CG

1

29.2

0

35.2

0

999

0

31.3

0

25.6

0

25.7

0

25.8

0

25.9

0

26

0

26.1

12

2

GLN

HA

1

4.59

0

3.06

0

3.04

0

3.03

0

3.14

0

3.15

0

3.12

0

3.13

0

4.39

0

999

13

2

GLN

HB2

0.997

3.08

0.003

3.02

0

2.99

0

2.98

0

2.96

0

2.97

0

999

0

2.95

0

2.94

0

2.93

14

2

GLN

HB3

1

3.11

0

3.06

0

3.07

0

3.08

0

3.05

0

3.02

0

2.98

0

2.96

0

999

0

1.01

15

2

GLN

HG2

1

3.14

0

3.1

0

3.09

0

3.06

0

3.04

0

3.03

0

3.07

0

3

0

2.96

0

999

16

2

GLN

HG3

1

3.14

0

3.1

0

3.09

0

3.06

0

3.04

0

3.03

0

3.07

0

3

0

2.96

0

999

17

3

ILE

CA

1

59.6

0

60.3

0

60.4

0

999

0

60.5

0

57

0

57.1

0

57.3

0

57.4

0

60.6

18

3

ILE

CB

1

42

0

999

0

38.6

0

38.3

0

38.4

0

38.2

0

38.1

0

38.5

0

38

0

38.7

19

3

ILE

CD1

1

14.2

0

17.7

0

17.5

0

9.2

0

999

0

17.1

0

16.3

0

17

0

16.9

0

999

20

3

ILE

CG1

1

24.9

0

25.6

0

25.7

0

25.8

0

25.9

0

999

0

18.9

0

29.2

0

17.5

0

16.3

21

3

ILE

CG2

0.996

17.8

0.003

14.1

0

14.3

0

999

0

18.7

0

16.3

0

19

0

19.2

0

19.1

0

18.9

22

3

ILE

HA

1

4.11

0

4.26

0

4.25

0

4.27

0

4.24

0

4.23

0

4.22

0

999

0

4.31

0

3.58

23

3

ILE

HB

1

1.72

0

0.55

0

0.54

0

0.52

0

0.51

0

0.78

0

0.49

0

0.47

0

0.73

0

999

24

3

ILE

HD1

1

0.54

0

0.6

0

0.62

0

0.63

0

0.78

0

0.77

0

0.75

0

0.73

0

0.74

0

999

25

3

ILE

HG12

1

1

0

0.79

0

0.76

0

0.81

0

0.54

0

0.52

0

0.73

0

1.24

0

999

0

1.23

26

3

ILE

HG13

1

1

0

0.79

0

0.76

0

0.81

0

0.54

0

0.52

0

0.73

0

999

0

1.24

0

1.23

27

3

ILE

HG2

1

0.57

0

0.54

0

0.52

0

1

0

1.01

0

0.78

0

0.77

0

0.73

0

0.74

0

999

28

4

PHE

CA

1

55.1

0

55.4

0

55.5

0

999

0

56.5

0

56.6

0

56.7

0

56.8

0

57

0

57.1

29

4

PHE

CB

1

41.2

0

45.5

0

999

0

40.2

0

40.1

0

39.6

0

39.7

0

39.8

0

39.9

0

40

30

4

PHE

HA

1

5.59

0

2.99

0

3

0

2.98

0

2.97

0

999

0

2.96

0

2.95

0

2.93

0

2.94

31

4

PHE

HB2

0.748

2.83

0.224

3

0.029

2.82

0

3.03

0

3.04

0

3.05

0

999

0

3.06

0

3.07

0

3.08

32

4

PHE

HB3

0.94

2.83

0.031

3

0.029

2.82

0

2.75

0

999

0

2.74

0

2.73

0

2.71

0

2.7

0

2.69

33

5

VAL

CA

1

60.5

0

999

0

62

0

62.2

0

62.3

0

62.4

0

62.5

0

62.1

0

61.9

0

61.8

34

5

VAL

CB

1

34.2

0

27.7

0

999

0

36.4

0

36.3

0

36.2

0

36.1

0

35.8

0

35.9

0

36

35

5

VAL

CG1

0.993

20.8

0.007

22.2

0

17.7

0

17.2

0

17.4

0

1px"> 999

0

17.1

0

17.5

0

17

0

17.6

36

5

VAL

CG2

0.99

22.2

0.01

20.8

0

26.5

0

19

0

18.9

0

999

0

17.5

0

17.7

0

17

0

16.9

37

5

VAL

HA

1

4.72

0

1.86

0

1.88

0

1.85

0

1.89

0

1.9

0

4.54

0

1.91

0

1.92

0

999

38

5

VAL

HB

1

1.86

0

0.68

0

0.67

0

0.66

0

0.69

0

0.64

0

0.63

0

0.62

0

0.6

0

999

39

5

VAL

HG1

0.875

0.68

0.101

0.69

0.019

0.67

0.002

0.63

0.002

0.66

0

0.73

0

0.74

0

0.33

0

999

0

0.52

40

5

VAL

HG2

0.998

0.66

0.002

0.63

0

0.69

0

0.7

0

0.71

0

0.73

0

0.74

0

0.33

0

0.52

0

999

41

6

LYS

CA

1

54.5

0

999

0

60.4

0

56.2

0

56.1

0

56.3

0

56

0

57.5

0

57.6

0

57.4

42

6

LYS

CB

1

34.4

0

999

0

32.1

0

32.2

0

32.3

0

32.4

0

32.6

0

32.7

0

32.5

0

32.8

43

6

LYS

CD

1

29.2

0

29.3

0

29.1

0

29.4

0

29

0

28.9

0

28.8

0

28.7

0

24.9

0

999

44

6

LYS

CE

0.782

41.9

0.218

42

0

41.8

0

42.1

0

41.7

0

42.2

0

41.6

0

42.3

0

42.4

0

999

45

6

LYS

CG

0.52

24.9

0.444

29.2

0.036

25

0

25.1

0

24.8

0

25.2

0

24.7

0

24.6

0

24.5

0

999

46

6

LYS

HA

1

5.27

0

1.33

0

1.23

0

1.63

0

1.32

0

4.29

0

4.3

0

4.28

0

999

0

4.31

47

6

LYS

HB2

0.977

1.33

0.015

1.63

0.008

1.32

0

1.23

0

1.42

0

1.52

0

1.83

0

1.82

0

999

0

1.81

48

6

LYS

HB3

0.99

1.33

0.008

1.32

0.002

1.63

0

1.23

0

1.42

0

1.52

0

1.84

0

1.83

0

1.88

0

999

49

6

LYS

HD2

1

1.52

0

1.23

0

1.63

0

1.42

0

2.85

0

1.67

0

1.68

0

1.69

0

1.7

0

999

50

6

LYS

HD3

1

1.52

0

1.63

0

1.23

0

1.42

0

1.67

0

1.68

0

1.69

0

1.7

0

1.71

0

999

51

6

LYS

HE2

1

2.85

0

999

0

2.96

0

3.01

0

3.02

0

3

0

3.03

0

2.99

0

2.98

0

2.97

52

6

LYS

HE3

1

2.85

0

999

0

2.96

0

3.01

0

3.02

0

3

0

3.03

0

2.99

0

2.98

0

2.97

53

6

LYS

HG2

0.556

1.52

0.444

1.23

0

1.42

0

1.41

0

1.33

0

1.4

0

1.43

0

2.85

0

1.45

0

999

54

6

LYS

HG3

0.556

1.52

0.444

1.23

0

1.42

0

1.41

0

1.33

0

1.38

0

1.46

0

1.45

0

1.63

0

999

55

7

THR

CA

1

60.5

0

60.8

0

70.5

0

70.4

0

61

0

999

0

61.1

0

61.3

0

61.4

0

61.6

56

7

THR

CB

0.999

70.5

0

60.5

0

60.3

0

60.6

0

60.4

0

60.8

0

61

0

61.1

0

999

0

69.5

57

7

THR

CG2

1

21.4

0

21.1

0

21

0

18.7

0

999

0

20.8

0

20.1

0

20.3

0

20.5

0

20.7

58

7

THR

HA

1

4.87

0

4.76

0

999

0

4.25

0

4.26

0

4.27

0

4.24

0

4.28

0

4.23

0

4.22

59

7

THR

HB

0.998

4.76

0.002

4.87

0

999

0

3.99

0

4.01

0

4.03

0

4.15

0

4.14

0

4.06

0

4.07

60

7

THR

HG2

1

1.13

0

999

0

1.4

0

1.39

0

1.43

0

1.38

0

1.37

0

1.34

0

1.35

0

1.36

61

8

LEU

CA

1

57.5

0

57.8

0

999

0

52.4

0

52.5

0

52.6

0

52.7

0

54.4

0

54.1

0

54.3

62

8

LEU

CB

1

41.9

0

27

0

999

0

25.6

0

27.2

0

25.7

0

25.8

0

25.9

0

26.1

0

26

63

8

LEU

CD1

1

23.7

0

25.3

0

25.1

0

25.2

0

25

0

25.6

0

24.9

0

999

0

25.7

0

24.8

64

8

LEU

CD2

1

25.3

0

25.6

0

23.4

0

20.1

0

23.2

0

999

0

27.2

0

23

0

22.9

0

22.8

65

8

LEU

CG

1

27.1

0

25.1

0

999

0

25

0

25.6

0

25.3

0

24.9

0

25.2

0

24.8

0

22.9

66

8

LEU

HA

1

4.26

0

1.72

0

1.71

0

1.75

0

1.86

0

1.85

0

1.84

0

1.83

0

1.82

0

999

67

8

LEU

HB2

1

1.71

0

1.75

0

1.88

0

1.82

0

1.67

0

1.85

0

1.86

0

1.89

0

0.4

0

999

68

8

LEU

HB3

1

1.71

0

1.75

0

1.88

0

1.82

0

1.85

0

1.86

0

0.4

0

0.42

0

0.44

0

999

69

8

LEU

HD1

1

0.93

0

0.96

0

1

0

0.99

0

0.97

0

999

0

0.4

0

0.39

0

0.37

0

0.36

70

8

LEU

HD2

1

0.98

0

0.91

0

0.89

0

0.88

0

0.4

0

0.39

0

0.87

0

0.37

0

999

0

0.36

71

8

LEU

HG

1

1.82

0

1.72

0

1.71

0

0.96

0

0.97

0

999

0

0.4

0

0.42

0

0.44

0

0.15

72

9

THR

CA

1

61.4

0

69

0

68.9

0

999

0

57.7

0

57.6

0

57.4

0

57.3

0

57.1

0

57

73

9

THR

CB

1

69

0

61.3

0

61.1

0

999

0

61

0

60.3

0

60.8

0

60.6

0

60.5

0

60.4

74

9

THR

CG2

1

21.8

0

18.1

0

999

0

19.1

0

17

0

18.2

0

17.1

0

16.9

0

17.2

0

20.1

75

9

THR

HA

1

4.37

0

4.54

0

999

0

999

0

999

0

999

0

999

0

999

0

999

0

999

76

9

THR

HB

1

4.54

0

4.37

0

1.45

0

1.46

0

1.3

0

1.43

0

999

0

1.31

0

1.33

0

1.34

77

9

THR

HG2

1

1.21

0

1.3

0

1.31

0

999

0

1.45

0

1.33

0

1.34

0

1.35

0

1.38

0

1.39

78

10

GLY

CA

0.997

45.3

0.002

45.4

0.001

45.2

0

45.5

0

45.1

0

45.6

0

45

"> 0

45.7

0

44.9

0

999

79

10

GLY

HA2

0.916

4.3

0.084

3.56

0

999

0

3.95

0

3.9

0

3.94

0

3.93

0

3.92

0

3.96

0

3.97

80

10

GLY

HA3

0.918

3.56

0.082

4.3

0

4.08

0

4.07

0

4.06

0

4.1

0

4.11

0

999

0

4.15

0

4.14

81

11

LYS

CA

0.997

56.2

0.002

56.3

0

56.1

0

56

0

57.5

0

57.6

0

57.4

0

57.3

0

57.2

0

999

82

11

LYS

CB

1

33.3

0

29.5

0

999

0

999

0

999

0

999

0

999

0

999

0

0

999

0

999

83

11

LYS

CD

1

25

0

999

0

29.5

0

29.4

0

29.3

0

29.2

0

29.1

0

29

0

28.9

0

28.8

84

11

LYS

CE

0.546

42

0.453

41.9

0

41.8

0

42.1

0

41.7

0

42.2

0

41.6

0

42.3

0

42.4

0

999

85

11

LYS

CG

0.996

25

0.003

25.1

0.001

25.2

0

24.9

0

24.8

0

25.3

0

24.7

0

999

0

24.6

0

24.5

86

11

LYS

HA

1

4.3

0

4.61

0

999

0

3.1

0

5.15

0

999

0

999

0

999

0

999

0

999

87

11

LYS

HB2

1

1.7

0

1.76

0

1.37

0

1.19

0

1.64

0

2.87

0

1.81

0

1.82

0

3.1

0

999

88

11

LYS

HB3

1

1.7

0

1.76

0

1.37

0

1.19

0

1.64

0

999

0

1.83

0

1.84

0

1.87

0

1.88

89

11

LYS

HD2

0.501

1.19

0.499

1.37

0

1.76

0

2.87

0

1.64

0

1.67

0

1.7

0

1.69

0

999

0

3.14

90

11

LYS

HD3

0.667

1.37

0.333

1.19

0

1.76

0

1.64

0

1.68

0

1.7

0

1.69

0

999

0

3.14

0

3.05

91

11

LYS

HE2

1

2.87

0

3.14

0

3.05

0

2.97

0

3.01

0

3.02

0

2.98

0

3

0

2.99

0

999

92

11

LYS

HE3

1

2.87

0

3.14

0

3.05

0

2.97

0

3.01

0

3.02

0

2.98

0

3

0

2.99

0

999

93

11

LYS

HG2

0.54

1.37

0.46

1.19

0

1.76

0

2.87

0

1.41

0

1.64

0

1.42

0

1.43

0

1.45

0

999

94

11

LYS

HG3

0.673

1.37

0.326

1.19

0.001

1.38

0

1.76

0

1.41

0

1.64

0

1.42

0

1.45

0

1.46

0

999

...

...

...