Contacts of the helix formed by residues 59 - 94 (chain B) in PDB entry 5FW2
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 ALA 59 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A G 2.7 26.1 + - - +
14A U 3.8 27.3 + - - +
64A U 3.6 25.0 + - + +
58B THR* 1.3 71.2 - - - +
60B GLU* 1.3 62.7 + - - +
61B ALA 3.6 0.7 - - - -
62B THR* 3.6 6.6 + - - -
63B ARG* 3.0 22.7 + - - +
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Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A G 4.3 4.8 + - - +
58B THR* 3.2 20.8 + - - +
59B ALA* 1.3 74.6 - - - +
61B ALA* 1.3 68.2 + - - +
63B ARG* 2.8 45.8 + - - +
64B LEU* 2.9 29.4 + - + +
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A U 4.5 4.7 - - - +
58B THR* 4.8 2.9 + - - +
60B GLU* 1.3 79.1 - - - +
62B THR* 1.3 63.6 + - - +
64B LEU* 3.2 12.1 + - - +
65B LYS* 2.9 44.8 + - - +
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Residues in contact with THR 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A G 5.9 0.2 - - - +
63A U 2.7 59.3 + - + +
64A U 3.2 33.8 + - + +
58B THR 5.4 0.2 + - - -
59B ALA* 3.6 10.4 + - - -
60B GLU 3.2 0.2 - - - -
61B ALA* 1.3 77.4 - - - +
63B ARG* 1.3 58.1 + - - +
65B LYS* 3.5 3.4 + - - +
66B ARG* 2.9 41.1 + - - +
69B ARG* 4.4 1.3 + - - +
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Residues in contact with ARG 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A G 4.7 13.1 + - - -
14A U 3.2 65.7 + - - +
15A A 3.3 31.0 + - - +
59B ALA 3.0 14.1 + - - +
60B GLU* 2.8 47.9 + - - +
62B THR* 1.3 76.1 - - - +
64B LEU* 1.3 71.7 + - + +
66B ARG* 3.0 15.1 + - - +
67B THR* 2.8 36.4 + - + +
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Residues in contact with LEU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLU* 2.9 41.7 + - + +
61B ALA* 3.2 10.5 + - - +
63B ARG* 1.3 96.8 - - + +
65B LYS* 1.3 64.7 + - + +
67B THR* 3.1 8.1 + - + +
68B ALA* 3.0 25.1 + - - +
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Residues in contact with LYS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A A 4.9 3.5 + - - +
63A U 3.4 52.9 + - + +
61B ALA* 2.9 34.2 + - - +
62B THR* 3.9 3.8 - - - +
64B LEU* 1.3 79.0 - - + +
66B ARG* 1.3 55.8 + - - +
68B ALA* 3.5 5.8 + - + +
69B ARG* 2.9 45.2 + - - +
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Residues in contact with ARG 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A U 3.3 27.5 + - - -
15A A 2.9 42.3 + - - -
61A C 5.2 1.3 - - - -
62A G 3.3 35.6 + - - +
63A U 4.9 0.6 + - - +
62B THR* 2.9 41.2 + - - +
63B ARG* 3.6 14.1 - - - +
65B LYS* 1.3 77.2 - - - +
67B THR* 1.3 61.4 + - - +
69B ARG* 3.1 33.4 - - - +
70B ARG* 3.1 28.8 + - + +
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Residues in contact with THR 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A A 4.0 26.2 - - - +
16A A 4.0 33.1 + - - +
17A A 6.0 2.9 - - - -
63B ARG* 2.8 25.1 + - + +
64B LEU* 3.1 15.2 + - - +
66B ARG* 1.3 70.4 - - + +
68B ALA* 1.3 67.4 + - - +
70B ARG* 3.1 22.4 + - - +
71B ARG* 3.1 18.5 + - - +
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A A 4.9 5.2 - - - +
64B LEU 3.0 19.7 + - - +
65B LYS* 3.7 6.7 - - + +
67B THR* 1.3 75.7 + - - +
69B ARG* 1.3 65.0 + - - +
71B ARG* 3.0 29.8 + - - +
72B TYR* 3.1 25.9 + - + -
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Residues in contact with ARG 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A A 3.8 34.1 + - - +
62A G 3.1 77.5 + - - +
63A U 3.0 52.1 + - - -
62B THR* 4.4 1.6 + - - +
65B LYS* 2.9 18.4 + - - +
66B ARG* 3.1 38.9 - - - +
68B ALA* 1.3 77.2 - - - +
70B ARG* 1.3 64.9 + - + +
72B TYR* 3.2 8.9 + - - +
73B THR* 3.0 22.7 + - + +
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Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A A 2.4 47.7 + - - -
16A A 2.9 21.6 + - - +
60A C 5.1 4.5 - - - +
61A C 2.7 48.0 + - + +
66B ARG* 3.5 33.1 + - + +
67B THR* 3.1 12.0 + - - +
69B ARG* 1.3 77.1 - - + +
71B ARG* 1.3 62.8 + - + +
73B THR* 3.5 9.4 + - - -
74B ARG* 3.2 62.2 + - - +
454B PRO* 3.5 12.4 - - - +
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Residues in contact with ARG 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A A 3.6 43.4 + - + +
18A A 2.5 82.5 + - - +
19A A 4.5 12.5 + - - +
67B THR* 3.1 13.6 + - - +
68B ALA* 3.0 18.7 + - - +
70B ARG* 1.3 75.4 - - + +
72B TYR* 1.3 68.3 + - + +
74B ARG* 3.2 6.9 + - - +
75B ARG* 2.8 33.2 + - - +
78B ARG* 4.8 2.1 + - - +
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Residues in contact with TYR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A A 4.2 15.8 + - - -
21A G 4.4 0.2 + - - -
50A U 3.3 79.4 + + + +
51A A 3.4 32.3 - - - +
68B ALA* 3.1 24.5 + - + -
69B ARG 3.2 6.0 + - - +
71B ARG* 1.3 85.4 - - + +
73B THR* 1.3 62.1 + - + +
75B ARG* 3.5 25.1 + - - +
76B LYS* 3.1 22.3 + - - +
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Residues in contact with THR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A U 3.9 16.5 + - - -
60A C 4.1 14.0 + - + +
61A C 5.1 14.1 - - + +
62A G 5.5 4.7 - - - +
69B ARG* 3.0 23.8 - - + +
70B ARG* 3.7 7.9 + - - +
71B ARG 3.2 0.4 - - - -
72B TYR* 1.3 76.1 - - + +
74B ARG* 1.3 59.7 + - - +
76B LYS* 3.4 8.1 + - - +
77B ASN* 3.0 31.3 + - - +
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Residues in contact with ARG 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A A 2.6 36.1 + - - -
17A A 2.8 32.7 + - - +
59A U 3.4 31.1 + - + +
60A C 2.8 32.1 + - - -
70B ARG* 3.2 38.5 + - - +
71B ARG* 3.9 4.0 - - - +
73B THR* 1.3 83.5 + - - +
75B ARG* 1.3 60.0 + - - +
77B ASN* 3.7 1.7 - - - +
78B ARG* 3.0 37.0 + - - +
448B ILE* 3.5 25.3 - - - +
454B PRO* 4.0 4.2 - - - +
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Residues in contact with ARG 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A A 4.9 7.1 + - - -
50A U 3.1 37.8 + - - -
71B ARG 2.8 17.7 + - - +
72B TYR* 3.9 23.0 + - - +
74B ARG* 1.3 76.0 - - - +
76B LYS* 1.3 63.5 + - - +
78B ARG* 3.4 38.8 + - - +
79B ILE* 3.3 21.9 + - - +
163B LYS* 3.7 56.1 + - + +
164B PHE* 4.2 17.8 - - - -
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Residues in contact with LYS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A A 4.1 11.1 + - - -
49A A 3.2 36.2 + - - +
50A U 6.0 1.8 - - - +
72B TYR 3.1 14.5 + - - +
73B THR* 3.5 12.1 - - - +
75B ARG* 1.3 76.0 - - - +
77B ASN* 1.3 63.5 + - - +
79B ILE* 3.2 17.1 + - + +
80B CYS* 2.9 48.1 + - - +
83B GLN* 5.6 0.8 + - - +
102B GLU* 4.3 25.7 + - - +
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Residues in contact with ASN 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A U 2.5 55.6 + - + +
73B THR* 3.0 21.7 + - - +
74B ARG 3.3 2.4 + - - +
76B LYS* 1.3 77.7 - - - +
78B ARG* 1.3 60.5 + - - +
80B CYS* 3.7 10.5 - - - +
81B TYR* 2.8 47.3 + - + -
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Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A A 6.1 0.6 - - - -
18A A 3.1 24.0 + - - -
59A U 6.1 1.6 - - - +
71B ARG* 4.8 2.4 + - - +
74B ARG* 3.0 15.0 + - - +
75B ARG* 3.4 49.6 - - - +
76B LYS 3.2 0.4 - - - -
77B ASN* 1.3 78.2 - - - +
79B ILE* 1.3 64.1 + - - +
81B TYR* 3.2 9.9 + - + +
82B LEU* 3.0 21.7 + - - +
162B ILE* 2.6 49.0 + - + +
163B LYS 3.9 5.3 + - - -
165B ARG* 3.5 32.3 - - - +
443B ILE* 3.6 37.8 - - + +
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Residues in contact with ILE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A A 3.8 14.8 - - - +
75B ARG* 3.3 14.6 + - - +
76B LYS* 3.2 20.3 + - + +
78B ARG* 1.3 74.6 - - - +
80B CYS* 1.3 57.9 + - - +
82B LEU* 3.1 7.7 + - + +
83B GLN* 2.9 40.3 + - - +
155B TYR* 3.4 21.1 - - - +
159B ALA* 4.0 21.5 - - + +
162B ILE* 4.5 7.4 - - + -
163B LYS* 3.8 44.0 - - + +
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Residues in contact with CYS 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B LYS* 2.9 39.8 + - - +
77B ASN* 3.7 14.4 - - - +
79B ILE* 1.3 75.3 - - - +
81B TYR* 1.3 65.9 + - + +
83B GLN* 3.2 14.3 + - - +
84B GLU* 2.9 25.1 + - - +
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Residues in contact with TYR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A U 3.6 51.2 + + - -
77B ASN* 2.8 37.1 + - + +
78B ARG* 3.4 13.2 - - + +
80B CYS* 1.3 73.8 - - + +
82B LEU* 1.3 62.1 + - - +
84B GLU* 3.3 16.9 + - - +
85B ILE* 3.3 25.5 + - + +
443B ILE* 3.6 24.2 - - + -
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ARG 3.0 12.6 + - - +
79B ILE* 3.1 11.0 + - - +
81B TYR* 1.3 75.0 - - - +
83B GLN* 1.3 64.8 + - - +
85B ILE* 3.1 13.4 + - + +
86B PHE* 3.1 35.4 + - + -
155B TYR* 3.6 28.7 - - + -
158B LEU* 4.1 8.7 - - + -
159B ALA* 3.9 28.7 - - + +
162B ILE* 3.9 18.4 - - + -
440B ILE* 4.0 24.0 - - + -
443B ILE* 3.9 6.7 - - + +
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Residues in contact with GLN 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A A 4.3 1.6 + - - -
76B LYS* 5.6 1.2 + - - +
79B ILE* 2.9 27.6 + - - +
80B CYS* 3.2 12.7 + - - +
82B LEU* 1.3 75.9 - - - +
84B GLU* 1.3 56.6 + - - +
86B PHE 3.3 1.0 + - - -
87B SER* 3.0 31.7 + - - -
98B PHE* 3.9 35.8 - - + +
101B LEU* 4.9 2.4 - - - +
102B GLU* 3.3 36.8 + - - +
155B TYR* 2.9 36.0 + - + +
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Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B CYS 2.9 16.9 + - - +
81B TYR* 3.6 19.1 - - - +
82B LEU 3.1 0.4 - - - -
83B GLN* 1.3 77.1 - - - +
85B ILE* 1.3 62.1 + - + +
86B PHE 3.6 0.2 + - - -
87B SER* 3.8 14.3 + - - -
88B ASN 5.2 0.5 + - - -
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B TYR* 3.3 13.4 + - + +
82B LEU* 3.1 9.7 + - + +
84B GLU* 1.3 79.1 - - + +
86B PHE* 1.3 66.4 + - + +
87B SER 3.7 0.3 + - - -
88B ASN* 5.1 1.2 + - - +
89B GLU* 5.6 0.7 + - - +
432B PHE* 3.3 25.9 - - + -
436B ASN* 3.7 33.8 + - + +
439B LYS* 3.7 38.4 - - + -
440B ILE* 4.1 20.0 - - + -
443B ILE* 4.3 11.4 - - + -
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Residues in contact with PHE 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 3.1 43.2 + - + +
83B GLN 3.3 0.4 + - - +
85B ILE* 1.3 83.0 - - + +
87B SER* 1.3 62.5 + - - +
88B ASN 3.4 2.1 + - - -
89B GLU* 3.6 3.8 + - - +
90B MET* 2.9 35.7 + - + +
98B PHE* 3.8 17.9 - - + -
151B LEU* 3.8 22.7 - - + -
154B ILE* 4.3 2.2 - - + -
155B TYR* 3.7 38.1 - + + -
158B LEU* 3.6 26.0 - - + -
432B PHE* 4.0 13.7 - + - -
433B LEU* 3.8 20.4 - - + -
440B ILE* 4.2 4.0 - - + -
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Residues in contact with SER 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLN 3.0 15.7 + - - -
84B GLU* 3.8 13.4 + - - -
85B ILE 3.4 2.8 - - - -
86B PHE* 1.3 77.1 - - - +
88B ASN* 1.3 69.7 + - - +
90B MET* 3.4 1.4 + - - +
91B ALA* 3.0 25.2 + - - +
98B PHE* 4.2 13.3 - - - -
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Residues in contact with ASN 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU 5.2 0.6 + - - -
85B ILE 5.1 1.6 + - - +
86B PHE 3.5 0.2 - - - -
87B SER* 1.3 84.1 + - - +
89B GLU* 1.3 71.2 + - + +
91B ALA* 3.2 20.9 + - - +
92B LYS* 3.6 16.1 + - - +
----------------------------------------------------------
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Residues in contact with GLU 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE 5.6 0.2 + - - -
86B PHE 3.6 4.2 + - - +
87B SER 3.5 0.2 - - - -
88B ASN* 1.3 80.7 - - + +
90B MET* 1.3 62.2 + - - +
92B LYS* 3.1 48.3 + - - +
93B VAL* 3.5 18.0 + - - +
151B LEU* 3.8 18.9 - - + +
430B TYR* 5.6 5.1 - - + -
431B PRO* 6.5 0.7 - - - -
432B PHE* 3.6 36.3 - - + -
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Residues in contact with MET 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PHE* 2.9 32.1 + - + +
87B SER 3.9 3.1 - - - +
89B GLU* 1.3 72.3 - - - +
91B ALA* 1.3 57.9 + - - +
92B LYS 3.0 5.1 + - - -
93B VAL* 3.1 8.6 + - - +
94B ASP* 2.8 42.9 + - - +
97B PHE* 3.8 33.4 - - + -
98B PHE* 4.0 24.9 - - + -
151B LEU* 3.7 30.2 - - + +
152B ARG* 3.4 30.7 - - - -
155B TYR* 4.2 1.8 - - + -
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Residues in contact with ALA 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B SER 3.0 14.7 + - - +
88B ASN* 3.2 14.8 + - - +
90B MET* 1.3 75.6 - - - +
92B LYS* 1.3 59.3 + - + +
94B ASP 4.0 6.2 - - - -
95B ASP* 4.4 22.4 + - - +
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Residues in contact with LYS 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ASN* 3.6 16.4 - - - +
89B GLU* 3.1 41.8 + - - +
90B MET 3.0 0.8 - - - -
91B ALA* 1.3 80.1 - - + +
93B VAL* 1.3 65.4 + - + +
----------------------------------------------------------
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLU 3.5 13.7 + - - +
90B MET* 3.1 10.6 + - - +
91B ALA 5.0 0.2 - - - -
92B LYS* 1.3 82.4 - - + +
94B ASP* 1.3 59.9 + - + +
150B ASP* 4.6 8.7 - - - +
151B LEU* 4.5 19.7 - - + +
152B ARG* 4.1 35.3 + - + +
430B TYR* 5.7 5.4 - - + +
----------------------------------------------------------
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Residues in contact with ASP 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B MET* 2.8 32.4 + - - +
91B ALA* 4.0 2.1 - - - -
93B VAL* 1.3 76.9 - - - +
95B ASP* 1.3 69.6 + - - +
96B SER* 3.2 11.6 + - - -
97B PHE* 3.8 14.3 + - + -
100B ARG* 2.7 38.7 + - - -
119B PHE 4.4 3.5 - - - +
152B ARG* 3.0 38.8 + - + +
----------------------------------------------------------
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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