Contacts of the helix formed by residues 59 - 82 (chain E) in PDB entry 2ZJR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 59 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E ALA* 1.3 81.9 - - + +
60E LYS* 1.3 81.9 + - + +
61E HIS 2.6 4.4 + - - +
62E ARG 2.8 0.7 + - - -
63E ALA* 2.7 27.3 + - + +
1045X G 5.1 1.1 + - - -
1046X U 2.5 52.1 + - - +
2728X A 6.5 0.2 - - + -
2729X A 3.3 33.2 + - + +
2730X A 5.9 0.6 + - - -
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Residues in contact with LYS 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59E GLN* 1.3 92.9 - - + +
61E HIS* 1.3 70.1 + - + +
63E ALA* 3.9 4.2 - - - +
64E LEU* 3.6 23.9 + - - +
2737X A 5.0 9.5 + - - +
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Residues in contact with HIS 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40E GLU* 2.9 34.1 + - + +
41E LEU* 4.4 6.2 - - - +
54E ARG* 4.3 5.1 - - + +
55E PRO* 3.8 32.8 - - + +
56E SER* 3.3 49.6 + - - +
57E ASP* 4.4 2.2 - - - +
58E ALA 5.1 0.7 - - - +
59E GLN 2.6 4.4 + - - +
60E LYS* 1.3 83.3 - - + +
62E ARG* 1.3 65.0 + - - +
63E ALA 3.1 2.0 + - - -
64E LEU* 3.2 9.8 + - - +
65E HIS* 3.0 19.9 + - - +
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Residues in contact with ARG 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E ARG* 2.4 44.7 - - - +
57E ASP* 2.9 21.1 + - - +
58E ALA* 2.8 46.9 - - - +
59E GLN 2.8 6.5 + - - -
61E HIS* 1.3 73.5 - - - +
63E ALA* 1.3 54.8 + - - +
65E HIS* 3.0 11.2 + - + +
66E GLY 2.8 25.5 + - - -
2728X A 3.1 5.2 + - - -
2729X A 4.0 16.7 - - - +
2730X A 4.5 11.7 + - - -
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Residues in contact with ALA 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E GLN* 2.7 22.8 + - + +
60E LYS* 3.9 5.8 - - - +
62E ARG* 1.3 68.9 - - - +
64E LEU* 1.3 64.7 + - - +
65E HIS 2.9 5.0 + - - -
66E GLY 3.0 11.3 + - - -
67E LEU* 3.0 14.1 + - - +
2728X A 3.1 40.1 + - + +
2729X A 3.4 10.2 + - - +
2737X A 4.2 12.3 - - + +
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Residues in contact with LEU 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38E ASN* 2.9 51.1 - - + +
40E GLU* 4.4 13.0 - - - +
41E LEU* 3.4 30.2 - - + +
60E LYS 3.6 14.5 + - - +
61E HIS* 3.2 8.6 + - - +
63E ALA* 1.3 78.9 - - + +
65E HIS* 1.3 56.4 + - - +
67E LEU* 2.8 39.4 - - + +
68E THR* 2.9 10.6 + - - -
2737X A 5.5 2.7 - - + -
2738X A 4.4 13.2 - - - +
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Residues in contact with HIS 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E GLY* 4.2 6.0 - - - -
6E LYS* 2.6 45.0 + - + +
7E GLN* 4.6 6.8 - - + +
41E LEU* 3.8 6.9 - - - +
52E VAL* 3.2 35.3 + - + +
53E GLU* 6.0 0.2 - - - -
54E ARG* 2.8 42.4 + - + +
61E HIS 3.0 12.4 + - - +
62E ARG* 3.0 15.4 + - - +
63E ALA 2.9 1.0 - - - -
64E LEU* 1.3 74.8 - - - +
66E GLY* 1.3 54.9 + - - +
67E LEU 2.4 15.8 + - - -
68E THR* 3.3 8.4 + - - -
69E ARG* 3.8 11.6 + - + +
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Residues in contact with GLY 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E GLY* 6.1 1.1 - - - -
6E LYS* 4.5 18.4 - - - -
62E ARG 2.8 14.8 + - - -
63E ALA 3.0 1.5 + - - -
65E HIS* 1.3 71.3 - - - +
67E LEU* 1.3 56.4 + - - +
70E THR* 4.2 6.3 + - - -
2727X G 4.0 1.2 + - - +
2728X A 2.6 60.0 - - - +
2729X A 5.2 0.7 - - - -
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Residues in contact with LEU 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E ALA 3.3 6.3 - - - +
64E LEU* 2.8 35.9 - - + +
65E HIS 2.4 17.8 + - - -
66E GLY* 1.3 70.2 - - - +
68E THR* 1.3 64.0 + - - +
69E ARG 3.4 1.0 + - - -
70E THR* 3.5 6.4 + - - -
71E LEU* 3.1 46.3 + - + +
2727X G 4.2 17.7 - - - +
2728X A 5.0 0.2 - - - +
2737X A 3.3 33.0 - - + +
2738X A 3.7 38.1 - - + +
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Residues in contact with THR 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E TYR* 3.2 42.1 - - + -
41E LEU* 2.7 32.8 - - + +
43E VAL* 4.6 5.8 - - + -
52E VAL* 3.9 27.6 - - + -
64E LEU 2.9 6.3 + - - -
65E HIS 3.3 0.9 + - - -
67E LEU* 1.3 73.1 - - - +
69E ARG* 1.3 73.6 + - - +
71E LEU* 2.9 4.2 + - - +
72E VAL* 2.7 31.7 + - + +
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Residues in contact with ARG 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E LYS* 3.5 52.9 - - + +
7E GLN* 3.8 9.8 - - - +
8E PRO* 3.2 42.4 + - - +
9E ILE* 4.4 19.3 - - + +
51E LEU* 6.1 0.2 - - + -
52E VAL* 4.0 14.9 - - + +
65E HIS* 3.8 10.9 + - + +
66E GLY 5.8 0.2 - - - -
67E LEU 3.5 0.6 - - - -
68E THR* 1.3 75.5 - - - +
70E THR* 1.3 63.0 + - - +
72E VAL* 2.6 12.4 + - - +
73E ALA* 2.5 45.1 + - + +
2731X G 5.5 1.6 + - - -
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Residues in contact with THR 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E LYS* 4.0 17.0 + - - +
66E GLY 4.2 1.9 + - - -
67E LEU 3.5 7.3 + - - -
68E THR 3.4 0.4 - - - -
69E ARG* 1.3 82.3 + - - +
71E LEU* 1.3 59.5 + - - +
73E ALA* 3.3 10.4 + - + +
74E ASN* 2.5 45.7 + - - +
138E LYS* 5.4 0.7 - - - +
2727X G 3.2 28.5 - - - +
2728X A 3.0 33.2 + - - +
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Residues in contact with LEU 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E VAL* 4.9 14.1 - - + +
36E PRO 4.8 3.1 - - - +
37E TYR* 3.3 30.2 + - + +
67E LEU* 3.1 36.6 + - + +
68E THR 2.9 9.9 + - - +
69E ARG 2.8 0.6 + - - -
70E THR* 1.3 76.9 - - - +
72E VAL* 1.3 63.3 + - - +
74E ASN* 3.0 26.6 + - + +
75E ALA* 3.3 4.9 + - - +
139E GLN* 4.8 8.1 - - - +
2726X U 3.9 21.3 - - - +
2727X G 4.3 12.3 - - - -
2738X A 4.6 16.4 - - + +
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Residues in contact with VAL 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ILE* 5.9 7.2 - - + -
17E VAL* 5.4 13.2 - - + -
24E PHE* 5.6 2.2 - - + +
26E VAL* 5.3 6.5 - - + -
35E VAL* 4.8 6.5 - - + -
37E TYR* 2.7 29.0 + - + +
43E VAL* 5.9 2.7 - - + -
50E LEU* 5.6 9.0 - - + -
52E VAL* 4.8 5.2 - - + -
68E THR* 2.7 29.8 - - + +
69E ARG* 2.6 13.8 + - - +
71E LEU* 1.3 66.3 - - - +
73E ALA* 1.3 52.4 - - - +
74E ASN 2.7 6.8 + - - -
75E ALA* 2.6 34.2 + - + +
76E VAL* 3.0 15.4 + - + +
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Residues in contact with ALA 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ILE* 5.5 7.7 - - + +
69E ARG* 2.5 31.3 + - + +
70E THR* 3.3 17.3 - - - +
72E VAL* 1.3 72.1 - - - +
74E ASN* 1.3 58.4 + - - +
76E VAL* 3.1 27.8 - - - +
77E LYS* 3.3 21.8 + - + +
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Residues in contact with ASN 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E THR* 2.5 37.1 + - - +
71E LEU* 3.0 21.4 + - - +
72E VAL 2.7 4.6 + - - -
73E ALA* 1.3 74.0 - - - +
75E ALA* 1.3 58.0 + - - +
76E VAL 2.9 1.6 - - - -
77E LYS* 3.5 2.4 + - - +
78E GLY* 2.8 27.4 + - - -
83E TYR* 3.4 12.4 + - - -
138E LYS* 2.6 52.3 + - + +
2726X U 4.6 2.2 + - - -
2727X G 3.5 14.5 + - - -
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Residues in contact with ALA 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E VAL* 4.2 27.8 - - + -
33E LEU* 4.3 21.2 - - + +
35E VAL* 4.2 17.3 - - + -
71E LEU 3.3 2.9 + - - +
72E VAL* 2.6 20.4 + - + +
74E ASN* 1.3 74.6 - - - +
76E VAL* 1.3 65.1 + - + +
78E GLY* 4.8 0.2 - - - -
79E VAL* 3.0 28.6 + - - +
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Residues in contact with VAL 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ILE* 5.3 3.4 - - + -
10E ALA 3.4 26.0 - - - +
11E VAL* 4.7 17.9 - - + -
12E PRO* 3.9 17.5 - - + -
15E VAL* 4.6 11.0 - - + -
17E VAL* 6.5 0.9 - - + -
72E VAL* 3.0 17.0 + - + +
73E ALA* 3.1 17.0 - - - +
74E ASN 2.9 0.4 - - - -
75E ALA* 1.3 75.0 - - + +
77E LYS* 1.3 68.8 + - + +
78E GLY 2.5 15.2 + - - -
79E VAL* 3.4 5.7 - - - +
80E SER* 2.9 24.9 + - - -
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Residues in contact with LYS 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E ALA* 4.3 22.9 + - - +
12E PRO* 5.8 2.6 - - + +
73E ALA* 3.3 20.5 + - + +
74E ASN* 3.8 0.9 - - - +
76E VAL* 1.3 88.5 - - + +
78E GLY* 1.3 62.9 + - - +
80E SER* 3.9 7.6 - - - +
81E ASP* 3.0 25.9 + - + +
82E GLY* 3.1 9.4 + - - +
83E TYR* 4.0 22.9 - - + +
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Residues in contact with GLY 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E LYS* 3.2 4.1 - - - +
33E LEU* 6.1 2.0 - - - -
74E ASN 2.8 15.1 + - - -
75E ALA* 3.6 2.2 - - - -
76E VAL 2.5 8.1 + - - -
77E LYS* 1.3 70.4 - - - +
79E VAL* 1.3 55.4 + - - -
80E SER 2.6 14.2 + - - -
81E ASP 2.9 0.2 + - - -
82E GLY* 2.5 34.2 + - - -
83E TYR* 4.3 10.3 - - - -
136E ILE* 4.6 10.8 - - - -
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Residues in contact with VAL 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E VAL* 4.1 18.6 - - + -
26E VAL* 4.2 17.0 - - + -
27E LYS 4.2 2.7 - - - -
28E GLY* 3.4 28.5 - - - +
29E PRO* 2.7 26.2 - - + +
30E LYS* 2.6 29.2 + - + +
31E GLY 2.8 30.1 - - - +
33E LEU* 4.4 10.0 - - + +
75E ALA 3.0 20.9 + - - +
76E VAL 3.4 3.6 - - - +
78E GLY* 1.3 69.0 - - - -
80E SER* 1.3 53.5 + - - +
136E ILE* 5.0 4.8 - - + +
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Residues in contact with SER 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12E PRO* 4.6 11.8 - - - +
15E VAL* 5.0 7.6 - - - -
29E PRO* 4.0 10.9 - - - +
30E LYS* 3.4 9.0 - - - -
76E VAL* 2.9 29.4 + - - -
77E LYS* 3.9 5.9 - - - +
78E GLY 2.6 4.6 + - - -
79E VAL* 1.3 81.6 - - - +
81E ASP* 1.3 75.8 + - - +
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Residues in contact with ASP 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E LYS* 3.5 18.2 + - - +
77E LYS* 3.0 15.9 + - + +
78E GLY 2.9 2.2 + - - -
80E SER* 1.3 95.9 + - - +
82E GLY* 1.3 68.7 + - - +
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Residues in contact with GLY 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E LYS* 3.9 8.7 - - - +
77E LYS 3.1 5.7 + - - +
78E GLY* 2.5 26.3 + - - -
81E ASP* 1.3 82.9 - - - +
83E TYR* 1.3 68.3 + - - -
84E THR* 4.5 5.4 - - - +
135E GLY 3.7 7.9 - - - -
136E ILE* 5.0 3.4 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il