Contacts of the helix formed by residues 69 - 105 (chain B) in PDB entry 3C98
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 GLU 69 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PRO 5.3 0.5 - - - +
68B ASP* 1.3 75.2 - - - +
70B LYS* 1.3 62.3 + - - +
71B THR 3.5 0.2 - - - -
72B LYS* 4.0 29.3 + - - +
73B GLU* 3.4 24.8 + - + +
204B LYS* 5.2 5.4 + - - -
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Residues in contact with LYS 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASP* 3.4 14.2 + - + +
69B GLU* 1.3 77.7 - - - +
71B THR* 1.3 61.8 + - + +
72B LYS 3.3 0.4 - - - -
73B GLU* 3.5 18.9 + - + +
74B GLU* 3.1 57.3 + - - +
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LYS* 4.3 13.6 - - - +
60B ALA* 5.5 11.0 - - + +
61B ILE* 4.0 21.7 + - - +
67B PRO* 5.0 1.4 - - - +
68B ASP* 3.0 33.4 + - - +
70B LYS* 1.3 76.9 - - + +
72B LYS* 1.3 65.1 + - - +
73B GLU 3.3 0.4 - - - -
74B GLU* 3.8 17.8 - - - +
75B LEU* 3.2 22.7 + - - +
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Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ILE* 4.1 18.8 - - + -
67B PRO* 3.8 28.4 + - + +
68B ASP 3.6 16.5 + - - +
69B GLU* 4.1 28.8 + - - +
70B LYS 3.3 0.4 - - - -
71B THR* 1.3 76.3 + - - +
73B GLU* 1.3 64.8 + - - +
75B LEU* 3.5 4.0 + - - +
76B GLU* 3.2 30.1 + - - +
197B THR* 3.4 31.5 + - - +
200B SER* 5.9 2.0 + - - -
201B GLU* 3.9 25.2 - - - +
204B LYS* 4.7 11.7 - - - +
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Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLU* 3.4 19.9 + - - +
70B LYS* 3.6 21.2 + - + +
71B THR 3.3 0.2 - - - -
72B LYS* 1.3 78.0 - - - +
74B GLU* 1.3 64.8 + - + +
76B GLU* 3.3 14.0 + - - +
77B GLU* 3.2 20.6 + - - +
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LYS* 3.1 35.3 + - - -
70B LYS* 3.1 45.9 + - - +
71B THR* 4.0 12.6 - - - +
72B LYS 3.3 0.2 - - - -
73B GLU* 1.3 75.0 - - + +
75B LEU* 1.3 65.4 + - - +
77B GLU* 3.1 17.3 + - - +
78B LEU* 3.2 18.1 + - + +
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Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B VAL* 3.7 43.3 - - + +
57B LYS* 4.0 14.3 - - + +
58B HIS* 4.2 18.8 - - + +
61B ILE* 3.8 19.7 - - + -
71B THR 3.2 16.3 + - - +
72B LYS* 3.7 6.3 - - - +
73B GLU 3.3 0.2 - - - -
74B GLU* 1.3 78.3 - - - +
76B GLU* 1.3 63.2 + - + +
78B LEU* 3.4 3.8 + - - +
79B MET* 3.1 44.0 + - + +
141B TYR* 5.1 0.2 - - + -
201B GLU* 3.7 25.1 - - - +
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LYS* 3.2 17.3 - - - +
73B GLU* 3.3 13.8 + - - +
74B GLU 3.2 0.6 - - - -
75B LEU* 1.3 77.5 - - + +
77B GLU* 1.3 63.1 + - - +
79B MET* 3.6 25.7 + - + +
80B SER* 3.3 21.1 + - - -
201B GLU* 5.3 0.8 - - - +
204B LYS* 2.9 43.6 + - + +
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B GLU 3.2 11.6 + - - +
74B GLU* 3.1 13.1 + - - +
76B GLU* 1.3 77.7 - - - +
78B LEU* 1.3 65.3 + - + +
80B SER* 3.4 9.0 + - - -
81B ASP* 3.2 39.2 + - - +
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ASN* 3.8 28.2 + - + +
53B GLU* 3.7 29.6 - - + -
54B VAL* 3.8 22.2 - - + +
57B LYS* 3.9 25.1 - - + -
74B GLU 3.2 14.9 + - - +
75B LEU* 3.7 7.6 - - - +
76B GLU 3.3 0.4 - - - -
77B GLU* 1.3 77.6 - - + +
79B MET* 1.3 59.7 + - - +
81B ASP* 3.2 9.8 + - - +
82B ILE* 2.9 35.6 + - - +
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Residues in contact with MET 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B VAL* 5.0 5.8 - - + -
58B HIS* 6.2 0.7 - - - -
75B LEU* 3.1 31.1 + - + +
76B GLU* 3.6 34.8 - - + +
77B GLU 3.3 0.2 - - - -
78B LEU* 1.3 76.7 - - - +
80B SER* 1.3 59.6 + - - +
82B ILE* 3.7 7.0 + - - +
83B LYS* 3.3 22.5 + - - +
134B TYR* 3.9 19.0 + - + +
138B GLN* 3.9 21.1 - - - +
204B LYS* 4.8 20.2 - - + +
205B LEU* 5.5 2.7 - - - -
208B SER* 4.4 19.4 + - - +
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Residues in contact with SER 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLU 3.3 15.8 + - - -
77B GLU* 3.8 14.4 - - - -
78B LEU 3.2 0.6 - - - -
79B MET* 1.3 80.0 - - - +
81B ASP* 1.3 60.5 + - - +
83B LYS* 3.9 6.4 - - - +
84B LYS* 3.0 48.7 + - - +
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Residues in contact with ASP 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LYS* 6.3 0.2 - - + -
50B ASN* 3.7 18.2 + - - +
77B GLU* 3.2 30.7 + - - +
78B LEU* 3.2 14.3 + - - +
80B SER* 1.3 77.4 - - - +
82B ILE* 1.3 60.4 + - - +
83B LYS 3.2 0.2 - - - -
84B LYS* 4.5 8.6 - - - +
85B THR* 2.9 39.4 + - - +
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Residues in contact with ILE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 4.2 24.2 - - + +
50B ASN* 3.7 23.3 - - + +
51B VAL* 4.2 8.3 - - + -
54B VAL* 4.0 18.8 - - + -
78B LEU 2.9 22.3 + - - +
79B MET* 3.9 6.1 - - - +
81B ASP* 1.3 76.6 - - - +
83B LYS* 1.3 56.4 + - - +
85B THR* 4.2 2.7 - - - -
86B ALA* 3.1 28.1 + - - +
131B MET* 4.3 15.9 - - + -
134B TYR* 3.5 44.6 - - + -
212B LEU* 5.4 1.6 - - + -
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Residues in contact with LYS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B MET 3.3 15.4 + - - +
80B SER* 3.9 6.3 - - - +
81B ASP 3.2 0.4 - - - -
82B ILE* 1.3 78.2 - - - +
84B LYS* 1.3 72.9 + - + +
86B ALA* 3.2 6.8 + - - +
87B ASN* 3.1 42.2 + - - +
208B SER* 5.9 2.2 - - - +
211B GLU* 3.3 51.7 + - + +
212B LEU* 4.4 24.0 - - + -
215B MET* 5.1 0.2 - - - +
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Residues in contact with LYS 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B SER* 3.0 35.7 + - - +
81B ASP* 4.3 9.0 - - - +
83B LYS* 1.3 86.8 - - - +
85B THR* 1.3 61.4 + - - +
87B ASN* 3.5 13.3 + - - +
88B LYS* 3.5 29.1 + - - +
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Residues in contact with THR 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 3.6 35.5 - - + +
46B LYS* 4.8 12.7 - - + +
47B ILE* 3.6 27.1 - - + -
50B ASN* 5.5 0.6 + - - -
81B ASP* 2.9 24.8 + - - +
84B LYS* 1.3 76.4 - - - +
86B ALA* 1.3 65.5 + - - +
88B LYS* 3.3 15.7 + - - +
89B VAL* 3.2 20.6 + - - +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 4.0 7.8 - - + +
82B ILE 3.1 20.3 + - - +
83B LYS* 3.2 7.4 + - - +
85B THR* 1.3 77.4 - - - +
87B ASN* 1.3 56.3 + - - +
89B VAL* 3.2 3.5 + - - +
90B ARG* 2.9 29.1 + - - +
127B PHE* 3.7 13.4 - - + -
131B MET* 4.0 22.4 - - + -
212B LEU* 5.1 1.1 - - + -
215B MET* 3.9 17.9 - - + -
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Residues in contact with ASN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LYS* 3.1 39.6 + - - +
84B LYS* 3.6 14.2 - - - +
85B THR 3.2 0.2 - - - -
86B ALA* 1.3 76.1 - - - +
88B LYS* 1.3 61.9 + - + +
90B ARG* 3.5 9.2 + - - +
91B SER* 3.1 24.1 + - - -
215B MET* 3.2 22.4 - - - +
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Residues in contact with LYS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 4.0 41.8 - - + -
84B LYS* 3.5 18.8 + - - +
85B THR* 3.3 17.0 + - - +
86B ALA 3.3 0.6 - - - -
87B ASN* 1.3 77.9 - - + +
89B VAL* 1.3 52.7 + - - +
91B SER* 3.0 6.0 + - - -
92B LYS* 2.7 44.7 + - - +
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Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ILE* 4.2 14.6 - - + +
43B PHE* 3.7 26.9 - - + -
44B ILE* 4.4 11.7 - - + -
47B ILE* 4.7 3.8 - - + -
85B THR 3.4 15.3 - - - +
86B ALA 3.2 6.8 + - - +
88B LYS* 1.3 72.7 - - - +
90B ARG* 1.3 67.6 + - - +
92B LYS* 4.1 4.9 - - - +
93B LEU* 2.9 46.1 + - + +
127B PHE* 3.7 37.5 - - + -
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Residues in contact with ARG 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ALA 2.9 16.4 + - - +
87B ASN* 3.7 10.8 + - - +
89B VAL* 1.3 76.8 - - - +
91B SER* 1.3 58.2 + - - +
93B LEU* 3.9 5.0 - - - +
94B LYS* 3.1 31.3 + - + +
127B PHE* 4.4 9.1 - - + -
214B ASP* 3.5 25.4 + - - +
215B MET* 3.5 56.8 - - - +
218B ASP* 3.2 35.3 + - + +
219B MET* 6.0 3.8 - - + -
222B LEU* 6.4 2.2 - - + -
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Residues in contact with SER 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ASN 3.1 16.4 + - - -
88B LYS* 3.0 6.6 + - - -
90B ARG* 1.3 78.5 - - - +
92B LYS* 1.3 65.2 + - - +
94B LYS* 3.2 8.3 + - - +
95B SER* 3.0 22.3 + - - -
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Residues in contact with LYS 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLN* 4.0 23.5 + - - +
39B GLU* 2.9 32.6 + - + +
40B ILE* 3.8 29.6 - - + -
43B PHE* 3.7 27.6 - - + -
88B LYS* 2.7 27.0 + - - +
89B VAL* 4.1 2.2 - - - +
91B SER* 1.3 73.9 - - - +
93B LEU* 1.3 62.0 + - - +
95B SER* 3.3 9.0 + - - -
96B ILE* 3.2 26.2 + - - +
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ILE* 3.5 23.3 - - + -
89B VAL* 2.9 40.9 + - + +
90B ARG* 3.9 4.3 - - - +
92B LYS* 1.3 75.6 - - - +
94B LYS* 1.3 60.2 + - - +
96B ILE* 3.4 5.7 + - + +
97B GLU 2.9 23.4 + - - -
120B HIS* 3.2 30.7 + - + +
123B LEU* 3.8 24.9 - - + -
124B SER* 3.9 28.5 - - - +
127B PHE* 4.2 12.6 - - + -
222B LEU* 6.3 2.9 - - + -
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Residues in contact with LYS 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ARG* 3.1 22.5 + - + +
91B SER* 3.2 8.9 + - - +
93B LEU* 1.3 76.0 - - - +
95B SER* 1.3 63.9 + - - +
97B GLU* 3.0 38.2 + - - +
98B GLN* 3.0 38.2 + - + +
218B ASP* 5.0 12.2 + - - -
222B LEU* 4.6 12.0 - - - +
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Residues in contact with SER 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLN* 5.9 1.8 - - - -
91B SER 3.0 13.1 + - - -
92B LYS* 3.5 11.7 - - - -
93B LEU 3.2 0.2 - - - -
94B LYS* 1.3 77.3 - - - +
96B ILE* 1.3 62.3 + - - +
98B GLN* 3.2 16.7 + - - +
99B SER* 3.2 20.4 + - - -
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Residues in contact with ILE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PHE* 3.6 40.6 - - + -
36B GLN* 4.5 19.3 - - + +
37B VAL* 5.4 0.9 - - + -
40B ILE* 3.8 28.7 - - + -
92B LYS 3.2 9.5 + - - +
93B LEU* 3.7 11.2 - - + +
94B LYS 3.3 0.2 - - - -
95B SER* 1.3 76.5 - - - +
97B GLU* 1.3 62.8 + - - +
99B SER* 3.3 9.1 + - - -
100B ILE* 3.2 27.0 + - + +
116B ARG* 4.3 4.0 - - + +
120B HIS* 4.2 21.8 - - + +
123B LEU* 5.1 6.5 - - + -
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU 2.9 13.6 + - - +
94B LYS* 3.0 46.5 + - + +
96B ILE* 1.3 76.9 - - - +
98B GLN* 1.3 63.2 + - + +
100B ILE* 3.2 19.3 + - - +
101B GLU* 3.3 31.1 + - + +
120B HIS* 3.7 21.1 + - + +
222B LEU* 3.9 25.6 - - - +
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Residues in contact with GLN 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LYS* 3.0 32.4 + - + +
95B SER* 3.5 16.3 + - - +
97B GLU* 1.3 76.1 - - - +
99B SER* 1.3 63.7 + - - +
101B GLU* 3.0 24.9 + - - +
102B GLN* 3.1 14.1 + - - +
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Residues in contact with SER 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B SER 3.2 10.5 + - - -
96B ILE* 3.3 13.2 + - - -
98B GLN* 1.3 78.8 - - - +
100B ILE* 1.3 62.7 + - - +
102B GLN* 3.4 11.6 + - - +
103B GLU* 3.1 31.6 + - - +
116B ARG* 4.0 23.2 + - - -
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ILE* 3.2 16.1 + - + +
97B GLU* 3.4 10.3 - - - +
98B GLN 3.1 0.6 - - - -
99B SER* 1.3 75.1 - - - +
101B GLU* 1.3 67.6 + - + +
103B GLU* 3.3 3.6 + - - +
104B GLU* 3.0 43.4 + - - +
113B LEU* 4.1 15.9 - - + +
116B ARG* 3.6 27.8 - - + +
117B LYS* 3.5 42.8 - - + +
120B HIS* 4.3 16.4 - - + -
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Residues in contact with GLU 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLU* 3.3 29.9 + - + +
98B GLN* 3.0 16.4 + - - +
100B ILE* 1.3 78.7 - - + +
102B GLN* 1.3 63.8 + - - +
104B GLU* 3.2 12.8 + - - +
105B GLY* 3.0 21.0 + - - -
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Residues in contact with GLN 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLN 3.1 10.8 + - - +
99B SER* 3.7 12.6 - - - +
101B GLU* 1.3 78.4 - - - +
103B GLU* 1.3 66.3 + - - +
105B GLY* 3.4 2.8 + - - -
106B LEU* 3.2 41.8 + - + +
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Residues in contact with GLU 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B SER* 3.1 27.4 + - - +
100B ILE* 3.6 4.9 - - - +
102B GLN* 1.3 82.9 + - - +
104B GLU* 1.3 61.0 + - - +
106B LEU* 3.1 17.3 + - - +
108B ARG* 2.9 69.0 + - + +
112B ASP* 5.6 3.2 - - - +
113B LEU* 3.9 20.9 - - + +
116B ARG* 5.3 10.1 - - - +
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Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ILE* 3.0 28.1 + - + +
101B GLU* 3.2 11.9 + - - +
103B GLU* 1.3 75.7 - - - +
105B GLY* 1.3 58.5 + - - +
106B LEU 3.1 0.4 - - - -
107B ASN* 3.1 18.5 + - - +
108B ARG 4.8 2.7 - - - +
113B LEU* 4.0 21.7 - - + +
117B LYS* 3.0 37.6 + - - +
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Residues in contact with GLY 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLU 3.0 14.3 + - - -
102B GLN* 3.4 6.3 + - - -
103B GLU 3.2 0.4 - - - -
104B GLU* 1.3 75.6 - - - +
106B LEU* 1.3 62.5 + - - +
107B ASN* 3.2 1.9 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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