Contacts of the helix formed by residues 45 - 69 (chain E) in PDB entry 1JT6
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 THR 45 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E LEU* 5.3 2.2 - - - -
40E TYR* 4.5 4.0 - - - -
43E PHE* 4.0 4.3 - - - +
44E LYS* 1.3 95.2 - - + +
46E LYS* 1.3 65.1 + - - +
47E GLU* 3.1 21.6 + - - +
48E ASN* 3.0 22.4 + - - +
49E LEU* 2.9 23.3 + - - +
249E SO4 3.3 13.7 - - - +
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Residues in contact with LYS 46 (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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15E PHE* 4.1 14.7 - - + -
20E TYR* 3.3 50.2 + - + +
21E ASN* 4.0 8.1 + - - +
23E THR* 2.6 30.6 + - - -
24E THR* 4.6 4.4 - - - +
25E THR* 5.2 11.9 - - - +
28E ILE* 5.6 4.0 - - + -
39E LEU* 5.6 1.6 - - - -
40E TYR* 4.8 0.8 - - - -
45E THR* 1.3 73.3 - - - +
47E GLU* 1.3 57.3 + - - +
49E LEU* 3.1 12.6 + - + +
50E PHE* 2.8 27.2 + - - +
249E SO4 2.7 36.8 + - - +
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Residues in contact with GLU 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20E TYR* 3.4 17.4 + - - +
45E THR* 3.1 19.4 + - - +
46E LYS* 1.3 81.6 - - - +
48E ASN* 1.3 80.9 + - - +
50E PHE* 3.2 3.2 + - - +
51E LEU* 3.0 27.8 + - + +
102E PHE* 3.8 15.6 - - + -
106E TYR* 3.9 19.0 + - + +
112E ILE* 3.2 40.0 - - + +
249E SO4 5.0 0.4 + - - -
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Residues in contact with ASN 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42E HIS 5.1 0.4 + - - -
43E PHE* 3.9 8.1 - - - +
44E LYS* 3.6 39.1 + - + +
45E THR* 3.0 25.7 + - - +
47E GLU* 1.3 84.5 + - - +
49E LEU* 1.3 67.4 + - - +
51E LEU* 3.3 12.2 + - - +
52E GLU* 3.0 41.8 + - - +
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Residues in contact with LEU 49 (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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7E ILE* 4.2 15.3 - - + -
8E LEU* 3.8 15.7 - - + -
11E ALA* 3.9 14.1 - - + -
15E PHE* 4.7 3.8 - - + -
28E ILE* 3.8 28.7 - - + -
39E LEU* 4.4 11.7 - - + -
43E PHE* 3.5 44.8 - - + +
45E THR 2.9 12.6 + - - +
46E LYS* 3.2 13.2 - - - +
48E ASN* 1.3 77.0 - - - +
50E PHE* 1.3 63.9 + - - +
52E GLU* 3.2 2.9 + - - +
53E ILE* 3.1 25.0 + - + +
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Residues in contact with PHE 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E PHE* 3.5 37.9 - + + -
20E TYR* 3.8 17.5 - + + -
46E LYS 2.8 13.3 + - - +
47E GLU 3.6 7.9 - - - +
48E ASN 3.2 0.2 - - - -
49E LEU* 1.3 77.4 - - - +
51E LEU* 1.3 56.1 + - - +
53E ILE* 3.3 7.2 + - + +
54E LEU* 3.0 61.0 + - + +
95E LEU* 4.6 5.6 - - + -
98E ALA* 3.7 38.4 - - + -
99E ILE* 4.0 6.7 - - + -
102E PHE* 3.4 44.4 - + + -
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Residues in contact with LEU 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E GLU* 3.0 29.5 + - - +
48E ASN* 3.5 12.8 - - - +
50E PHE* 1.3 75.5 - - - +
52E GLU* 1.3 59.8 + - - +
54E LEU* 3.3 11.0 + - + +
55E ASN* 2.9 39.0 + - - +
102E PHE* 3.7 27.6 - - + -
112E ILE* 4.3 19.3 - - + +
115E LYS* 4.7 22.4 - - + -
116E MET* 4.2 13.9 - - + +
119E LEU* 5.1 6.5 - - + -
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Residues in contact with GLU 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E LYS* 4.3 11.8 - - - +
8E LEU* 4.5 10.3 - - + -
42E HIS 4.3 3.4 - - - +
43E PHE* 2.8 39.5 - - + -
48E ASN* 3.0 29.0 + - - +
49E LEU 3.7 7.4 - - - +
51E LEU* 1.3 72.3 - - - +
53E ILE* 1.3 66.7 + - - +
55E ASN* 3.2 7.8 + - + +
56E ILE* 3.0 34.5 + - + +
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Residues in contact with ILE 53 (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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8E LEU* 3.5 24.9 - - + +
11E ALA* 3.7 16.8 - - + -
12E LYS* 3.6 32.3 - - + +
15E PHE* 3.7 20.6 - - + -
49E LEU* 3.1 15.8 + - + +
50E PHE* 3.5 8.5 - - + +
52E GLU* 1.3 75.4 - - - +
54E LEU* 1.3 60.7 + - + +
56E ILE* 3.2 4.1 + - - +
57E GLU* 3.0 28.1 + - + +
95E LEU* 4.1 25.4 - - + -
399E SO4 3.7 16.6 + - - +
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Residues in contact with LEU 54 (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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50E PHE* 3.0 53.1 + - + +
51E LEU* 3.6 12.3 - - + +
52E GLU 3.2 0.4 - - - -
53E ILE* 1.3 77.1 - - + +
55E ASN* 1.3 65.3 + - - +
57E GLU* 3.4 5.4 + - + +
58E GLU* 3.1 24.6 + - - +
92E TYR* 6.1 1.8 - - + -
95E LEU* 4.1 18.2 - - + -
99E ILE* 3.9 25.1 - - + -
116E MET* 3.4 33.0 - - + -
119E LEU* 3.8 17.5 - - + +
123E TYR* 4.3 4.5 + - + +
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Residues in contact with ASN 55 (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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51E LEU* 2.9 27.2 + - - +
52E GLU* 3.2 8.7 + - + +
54E LEU* 1.3 77.3 - - - +
56E ILE* 1.3 64.8 + - + +
58E GLU* 3.6 5.3 + - - +
59E SER* 3.3 21.5 + - - -
115E LYS* 6.1 0.9 - - - +
119E LEU* 4.1 25.7 - - - +
122E LYS* 6.2 0.4 - - - +
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Residues in contact with ILE 56 (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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8E LEU* 4.0 22.2 - - + -
52E GLU* 3.0 20.4 + - + +
53E ILE 3.6 6.3 - - - +
54E LEU 3.1 0.2 - - - -
55E ASN* 1.3 75.9 - - + +
57E GLU* 1.3 66.6 + - - +
59E SER* 3.0 7.4 + - - +
60E LYS* 2.9 39.4 + - + +
399E SO4 3.4 41.1 - - - +
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Residues in contact with GLU 57 (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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12E LYS* 2.8 44.3 + - - +
53E ILE* 3.0 22.3 + - + +
54E LEU* 3.9 6.7 - - + +
56E ILE* 1.3 76.5 - - - +
58E GLU* 1.3 58.0 + - - +
60E LYS* 3.2 5.2 + - - +
61E TRP* 2.8 30.7 + - - +
90E GLU 3.6 1.4 - - - +
91E TYR* 3.2 19.4 - - - +
92E TYR* 3.0 32.6 + - + +
94E PRO* 5.2 0.5 - - - +
95E LEU* 3.8 23.5 - - + +
123E TYR* 3.7 5.8 - - - +
399E SO4 3.5 11.8 + - - -
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Residues in contact with GLU 58 (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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54E LEU 3.1 12.6 + - - +
55E ASN* 4.0 7.6 - - - +
57E GLU* 1.3 75.4 - - - +
59E SER* 1.3 68.1 + - - +
61E TRP* 3.7 2.1 - - - +
62E GLN* 2.6 59.1 + - - +
119E LEU* 3.5 24.9 - - + -
122E LYS* 3.5 34.8 + - + +
123E TYR* 2.8 40.7 + - + +
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Residues in contact with SER 59 (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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55E ASN 3.3 13.0 + - - -
56E ILE* 3.0 10.5 + - - +
58E GLU* 1.3 87.4 - - - +
60E LYS* 1.3 64.7 + - - +
62E GLN* 3.8 4.9 - - - +
63E GLU* 2.9 30.1 + - - +
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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
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699A SO4 3.7 29.8 + - - -
56E ILE* 2.9 36.7 + - + +
57E GLU 3.8 1.1 - - - +
59E SER* 1.3 80.3 + - - +
61E TRP* 1.3 57.6 + - - +
63E GLU* 3.4 5.1 + - + +
64E GLN* 2.9 30.8 + - - +
91E TYR* 3.6 46.1 + - + +
399E SO4 5.3 2.9 - - - +
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Residues in contact with TRP 61 (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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57E GLU 2.8 17.5 + - - +
58E GLU* 3.7 5.4 - - - +
60E LYS* 1.3 75.6 - - - +
62E GLN* 1.3 62.8 + - + +
64E GLN* 2.9 35.7 - - + -
65E TRP* 3.0 32.0 + - + +
82E TYR* 3.2 47.8 + + - -
85E LEU* 4.1 24.7 - - + -
86E SER* 4.0 13.2 - - - -
89E THR* 3.5 24.2 - - + -
91E TYR* 4.1 13.6 - - + -
92E TYR* 4.7 4.0 - - + -
93E TYR* 3.9 15.3 - + - -
123E TYR* 3.4 32.0 - + + +
126E ALA* 5.6 2.0 - - - +
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Residues in contact with GLN 62 (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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58E GLU* 2.6 57.2 + - - +
59E SER* 3.8 5.5 - - - +
61E TRP* 1.3 81.3 - - + +
63E GLU* 1.3 58.6 + - - +
65E TRP* 3.3 6.1 + - - +
66E LYS* 2.9 31.8 + - + +
122E LYS* 4.0 16.0 + - - +
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Residues in contact with GLU 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 SER 2.9 17.9 + - - +
60E LYS* 3.7 7.2 - - + +
62E GLN* 1.3 74.7 - - - +
64E GLN* 1.3 65.7 + - - +
66E LYS* 3.2 33.1 + - - +
67E LYS* 3.2 37.9 + - + +
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Residues in contact with GLN 64 (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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60E LYS 2.9 17.9 + - - +
61E TRP* 2.9 29.9 - - + +
63E GLU* 1.3 77.1 - - - +
65E TRP* 1.3 57.7 + - - +
67E LYS* 3.1 9.3 + - - +
68E GLU* 3.0 34.8 + - - +
85E LEU* 5.3 8.0 - - + +
89E THR* 2.4 37.1 + - - -
90E GLU* 5.2 2.3 + - - +
91E TYR* 3.8 17.1 - - + -
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Residues in contact with TRP 65 (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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61E TRP* 3.0 26.1 + - + +
62E GLN* 3.9 4.9 - - - +
64E GLN* 1.3 75.4 - - - +
66E LYS* 1.3 67.3 + - - +
68E GLU* 4.3 1.1 - - - +
69E GLN* 3.0 72.3 + - + +
78E LYS* 3.1 33.9 - - + -
81E LEU* 4.2 7.4 - - + -
82E TYR* 3.4 54.4 - + + -
85E LEU* 3.6 23.8 - - + -
126E ALA* 4.2 17.7 + - + +
130E ILE* 3.9 17.2 - - + +
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Residues in contact with LYS 66 (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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62E GLN* 2.9 18.8 + - + +
63E GLU* 3.4 24.8 + - - +
65E TRP* 1.3 77.8 - - - +
67E LYS* 1.3 61.5 + - + +
69E GLN* 3.9 12.2 - - - +
70E ILE* 3.9 19.9 - - - +
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Residues in contact with LYS 67 (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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63E GLU* 3.2 35.3 + - + +
64E GLN* 3.1 10.6 + - - +
65E TRP 3.1 0.4 - - - -
66E LYS* 1.3 81.7 - - + +
68E GLU* 1.3 63.6 + - - +
69E GLN 3.5 0.2 - - - -
70E ILE* 3.9 15.3 + - - +
71E LYS* 4.5 8.8 - - - +
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Residues in contact with GLU 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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64E GLN* 3.0 22.4 + - - +
65E TRP* 3.3 2.9 + - + +
67E LYS* 1.3 78.4 - - - +
69E GLN* 1.3 64.7 + - - +
70E ILE 3.1 2.9 - - - -
71E LYS* 2.8 58.2 + - - +
81E LEU* 3.5 14.7 - - + +
85E LEU* 3.3 43.0 - - + +
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Residues in contact with GLN 69 (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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65E TRP* 3.0 69.5 + - + +
66E LYS* 3.9 9.2 - - - +
68E GLU* 1.3 75.4 - - - +
70E ILE* 1.3 81.3 + - + +
71E LYS 3.0 0.2 - - - -
72E ALA* 3.1 22.2 + - - +
78E LYS* 3.4 29.5 - - - +
81E LEU* 4.6 1.8 - - - -
129E VAL* 5.5 9.7 - - - +
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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