Detailed description of each field in our dataset


 

No.

Field name

Description

1

id

The ID of the SAP

2

ss_wt

The secondary structure of the SAP site in the wildtype protein. Values could be {H,C,T,G,B,E}, assigned by STRIDE.

3

ss_equal

Whether the secondary structures of the SAP site are the same between in the wildtype protein and in the variant protein. Values could be {Y,N}.

4

ss3_equal

Whether the secondary structures of the SAP site plus its 2 neighboring residues are the same between in the wildtype protein and in the variant protein. Values could be {Y,N}.

5

absdiff_phi

The absolute value of the difference of the angles of the SAP site between in the variant protein and the corresponding wildtype protein.

6

absdiff_psi

The absolute value of the difference of the angles of the SAP site between in the variant protein and the corresponding wildtype protein.

7

absdiff_chi1

The absolute value of the difference of the 1 angles of the SAP site between in the variant protein and the corresponding wildtype protein.

8

nac5

The total-sidechain absolute solvent accessibility of the SAP site in wildtype protein, calculated by NACCESS.

9

nac7

The total-sidechain relative solvent accessibility of the SAP site in wildtype protein, calculated by NACCESS.

10

diff_hbond

The difference of the putative hydrogen bonds formed by the SAP site residue between in the variant protein and the corresponding wildtype protein, calculated by HBPLUS.

11

diff_ssbond

The difference of the putative disulfide bonds formed by the SAP site residue between in the variant protein and the corresponding wildtype protein, parsed from the accesary log files of HBPLUS.

12

tango_wt

The TANGO score of the SAP site residue in the wildtype protein, calculated by TANGO.

13

diff_tango

The difference of TANGO scores of the SAP site between in the variant protein and in the corresponding wildtype protein.

14

frag_equal

Whether the SAP altered the propensity of beta-aggregation of a small sequence fragment. Values could be {Y,N}.

15

cbeta_wt

The C density of the SAP site in wildtype protein.

16

back5

The backbone RMSD of 5 consecutive residues at the SAP site between the variant protein and the corresponding wildtype protein.

17

diff_energy

The difference of the energy scores between the variant protein and the corresponding wildtype protein after evaluated by MODELLER.

18

blosum

The BLOSUM62 score of the SAP substitution.

19

grantham

The GRANTHAM score of the SAP substitution.

20

wt_freq

The wildtype residue frequency in the multiple sequence alignment.

21

mt_freq

The variant residue frequency in the multiple sequence alignment.

22

diff_freq

The difference between variant residue frequency and wildtype residue frequency.

23

neibor3L

The conservation score of the 3rd left residue from the SAP site.

24

neibor2L

The conservation score of the 2nd left residue from the SAP site.

25

neibor1L

The conservation score of the 1st left residue from the SAP site.

26

conserv

The conservation score of the SAP site.

27

neibor1R

The conservation score of the 1st right residue from the SAP site.

28

neibor2R

The conservation score of the 2nd right residue from the SAP site.

29

neibor3R

The conservation score of the 3rd right residue from the SAP site.

30

rad13A_wt

The ALA component of the 13A structural neighbor profile at the SAP site in the wildtype protein structure.

31

rad13C_wt

The CYS component

32

rad13D_wt

The ASP component

33

rad13E_wt

The GLU component

34

rad13F_wt

The PHE component

35

rad13G_wt

The GLY component

36

rad13H_wt

The HIS component

37

rad13I_wt

The ILE component

38

rad13K_wt

The LYS component

39

rad13L_wt

The LEU component

40

rad13M_wt

The MET component

41

rad13N_wt

The ASN component

42

rad13P_wt

The PRO component

43

rad13Q_wt

The GLN component

44

rad13R_wt

The ARG component

45

rad13S_wt

The SER component

46

rad13T_wt

The THR component

47

rad13V_wt

The VAL component

48

rad13W_wt

The TRP component

49

rad13Y_wt

The TYR component

50

act_struct_neibor

The structural distance between the SAP site and its nearest residue holding the functional site with Feature Key of ACT_SITE. If the value exceeds 14A, it is set to 14A.

51

binding_struct_neibor

The structural distance between the SAP site and its nearest residue holding the functional site with Feature Key of BINDING. If the value exceeds 14A, it is set to 14A.

52

metal_struct_neibor

The structural distance between the SAP site and its nearest residue holding the functional site with Feature Key of METAL. If the value exceeds 14A, it is set to 14A.

53

modres_struct_neibor

The structural distance between the SAP site and its nearest residue holding the functional site with Feature Key of MOD_RES. If the value exceeds 14A, it is set to 14A.

54

disulfid_struct_neibor

The structural distance between the SAP site and its nearest residue holding the functional site with Feature Key of DISULFID. If the value exceeds 14A, it is set to 14A.

55

act_seq_neibor

The sequence distance between the SAP site and its nearest residue holding the functional site with Feature Key of ACT_SITE. If the value exceeds 30, it is set to 30.

56

binding_seq_neibor

The sequence distance between the SAP site and its nearest residue holding the functional site with Feature Key of BINDING. If the value exceeds 30, it is set to 30.

57

metal_seq_neibor

The sequence distance between the SAP site and its nearest residue holding the functional site with Feature Key of METAL. If the value exceeds 30, it is set to 30.

58

modres_seq_neibor

The sequence distance between the SAP site and its nearest residue holding the functional site with Feature Key of MOD_RES. If the value exceeds 30, it is set to 30.

59

transmem

Whether the SAP site is in the transmembrane region. Values could be {0,1}. 1 means Yes while 0 means No.

60

in_disorder

Whether the SAP site is in the disordered region. Values could be {0,1}. 1 means Yes while 0 means No.

61

is_HLA

Whether the protein containing the SAP is HLA. Values could be {0,1}. 1 means Yes while 0 means No.

62

status

The status of the SAP: Disease-associated (deleterious) or Polymorphism (tolerated, neutral). (Only occured in our provided dataset, for the user' prediction, please refer to "prediction result" in the output page.)

 

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