Contacts of the helix formed by residues 75 - 105 (chain B) in PDB entry 2Q7N
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 75 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B GLY* 1.3 76.5 - - - +
76B GLU* 1.3 67.7 + - - +
77B LYS* 3.0 15.4 - - - +
78B ALA* 2.8 20.2 + - - +
79B LYS* 3.3 5.2 + - - +
137B TYR* 4.9 4.5 - - - +
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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
----------------------------------------------------------
23B MET* 3.7 33.1 - - + +
75B THR* 1.3 72.3 - - - +
77B LYS* 1.3 53.1 + - - +
79B LYS* 3.3 22.7 + - - +
80B LEU* 2.7 51.4 + - + +
132B ARG* 3.1 40.4 + - - +
137B TYR* 3.2 21.6 - - + +
180B PHE* 5.8 0.2 - - + -
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Residues in contact with LYS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B THR* 2.9 10.9 + - - +
76B GLU* 1.3 77.8 - - - +
78B ALA* 1.3 55.6 + - - +
80B LEU* 3.4 5.4 - - - +
81B VAL* 2.7 44.9 + - + +
133B LEU* 4.1 11.3 - - + +
137B TYR* 3.4 46.0 + - + +
139B VAL* 4.8 19.0 - - + +
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B HIS* 6.3 0.4 - - + -
73B ASN 4.9 1.6 - - - +
74B GLY* 4.3 7.9 - - - -
75B THR* 2.8 26.2 + - - +
77B LYS* 1.3 73.7 - - - +
79B LYS* 1.3 67.2 + - - +
81B VAL* 3.0 10.7 - - - +
82B GLU* 2.8 41.1 + - - +
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Residues in contact with LYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B MET* 5.9 1.6 - - - +
70B PHE* 3.7 19.9 - - + -
71B HIS 5.1 0.4 - - - +
72B ALA 4.7 7.4 - - - +
73B ASN* 3.5 21.1 + - - +
74B GLY 3.4 18.2 - - - +
75B THR* 3.3 0.4 + - - +
76B GLU* 3.6 29.4 - - - +
78B ALA* 1.3 76.8 - - - +
80B LEU* 1.3 56.9 + - - +
82B GLU* 3.7 3.4 + - - +
83B LEU* 2.8 33.2 + - - +
179B ALA* 4.4 9.5 + - + +
180B PHE* 3.7 47.6 - - + +
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B MET* 4.3 10.3 - - - -
26B ILE* 4.4 7.2 - - + -
76B GLU* 2.7 42.1 + - + +
77B LYS 3.5 2.9 - - - +
79B LYS* 1.3 68.9 - - + +
81B VAL* 1.3 70.7 + - - +
83B LEU* 3.5 6.6 + - - +
84B TYR* 3.0 20.4 + - - +
129B VAL* 3.9 17.1 - - + +
132B ARG* 3.7 35.9 - - + -
133B LEU* 3.5 21.4 - - + +
137B TYR* 5.5 1.8 - - + -
180B PHE* 3.4 33.7 - - + -
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LYS* 2.7 28.9 + - + +
78B ALA* 3.0 21.5 - - - +
80B LEU* 1.3 70.2 - - - +
82B GLU* 1.3 79.4 + - + +
84B TYR* 2.8 21.9 + - - +
85B ARG* 3.2 26.7 + - - +
133B LEU* 3.3 16.9 - - + +
139B VAL* 6.0 5.8 - - + -
142B VAL* 3.7 25.8 - - + -
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Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B PRO* 3.8 21.4 - - + +
70B PHE* 3.9 13.4 - - + -
71B HIS* 3.6 46.8 + - - +
73B ASN 5.6 0.5 - - - +
78B ALA* 2.8 40.8 + - - +
79B LYS* 3.7 4.6 + - - +
81B VAL* 1.3 73.3 - - + +
83B LEU* 1.3 65.2 + - - +
85B ARG* 2.9 40.7 + - - +
86B ILE* 3.3 10.3 + - - +
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ILE* 5.2 0.2 - - + -
30B LEU* 3.8 18.4 - - + -
70B PHE* 4.2 5.4 - - + -
79B LYS 2.8 20.8 + - - +
80B LEU* 3.6 2.9 - - - +
82B GLU* 1.3 71.0 - - - +
84B TYR* 1.3 56.0 + - - +
86B ILE* 2.7 32.1 + - - +
87B VAL* 2.9 30.6 + - + +
125B LEU* 3.9 8.7 - - + -
129B VAL* 3.2 37.5 - - + -
176B LEU* 3.8 28.9 - - + -
180B PHE* 3.6 25.1 - - + -
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Residues in contact with TYR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B PRO 5.0 0.5 + - - -
8B VAL 4.6 2.1 + - - -
10B ALA* 2.5 37.9 - - + +
80B LEU 3.0 9.9 + - - +
81B VAL* 2.8 20.5 + - - +
83B LEU* 1.3 79.0 - - - +
85B ARG* 1.3 60.2 + - - +
87B VAL* 3.4 7.1 + - - +
88B VAL* 3.0 42.0 + - + +
126B LEU* 3.6 28.4 - - + +
129B VAL* 3.8 21.3 - - + -
130B LEU* 3.6 24.7 - - + -
133B LEU* 4.4 1.3 - - + -
142B VAL* 3.3 42.6 - - + -
144B VAL* 3.9 10.3 - - + -
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Residues in contact with ARG 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PRO* 4.2 15.9 - - + -
69B PRO* 4.9 16.2 + - + +
81B VAL* 3.9 27.1 - - - +
82B GLU* 2.9 34.1 + - - +
84B TYR* 1.3 74.7 - - - +
86B ILE* 1.3 54.5 + - - +
88B VAL* 3.1 4.7 + - - +
89B TYR* 2.8 35.5 + - - +
142B VAL* 4.6 3.2 - - + +
143B ASP* 3.2 25.9 + - - +
144B VAL* 4.1 24.0 - - + +
145B THR* 4.8 11.6 - - - +
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE* 4.7 10.1 - - + -
68B PRO* 3.5 41.1 - - + +
69B PRO 3.6 13.9 - - - +
70B PHE* 4.0 22.7 - - + -
82B GLU 3.3 8.9 + - - +
83B LEU* 2.7 14.6 + - - +
85B ARG* 1.3 73.4 - - - +
87B VAL* 1.3 65.9 + - + +
89B TYR* 3.0 3.1 + - - +
90B LEU* 2.9 41.6 + - + +
172B ILE* 4.2 13.2 - - + -
176B LEU* 4.1 25.1 - - + -
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Residues in contact with VAL 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B THR* 4.7 0.4 - - + -
83B LEU* 2.9 27.1 + - + +
84B TYR* 3.4 7.2 - - - +
86B ILE* 1.3 78.7 - - + +
88B VAL* 1.3 69.1 + - - +
89B TYR 2.9 1.0 + - - -
90B LEU* 3.0 11.0 + - + -
91B GLY* 3.2 9.9 + - - -
122B LEU* 3.5 46.7 - - + +
125B LEU* 3.5 26.0 - - + -
126B LEU* 3.4 27.1 - - + +
129B VAL* 6.0 0.7 - - + -
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B THR* 4.1 11.8 - - + +
7B PRO 4.7 12.8 - - - +
8B VAL* 5.1 10.1 - - + +
84B TYR* 3.0 32.2 + - + +
85B ARG 3.3 7.2 - - - +
87B VAL* 1.3 81.1 - - - +
89B TYR* 1.3 56.4 + - - +
91B GLY* 4.0 0.7 - - - -
92B THR* 2.7 43.8 + - + +
126B LEU* 3.8 9.0 - - + -
144B VAL* 3.6 29.4 - - + -
145B THR 3.5 20.6 - - - +
146B TYR* 5.2 0.2 - - - -
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Residues in contact with TYR 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B VAL* 5.5 3.9 - - + +
65B THR 4.7 1.7 + - - -
66B ASP* 3.2 29.4 + - - -
67B PHE* 3.7 30.7 - + + -
68B PRO* 3.6 28.5 - - + -
85B ARG 2.8 12.9 + - - +
86B ILE 3.1 11.0 - - - +
87B VAL 2.9 0.8 + - - -
88B VAL* 1.3 79.2 - - - +
90B LEU* 1.3 64.2 + - + +
92B THR* 2.4 24.3 + - - -
93B SER* 3.2 3.6 + - - -
145B THR* 4.3 17.7 - - + +
146B TYR 3.7 18.5 + - - -
147B GLY* 4.0 7.2 - - - +
148B PRO* 3.5 35.0 - - + +
165B LEU* 4.5 7.6 - - + -
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE* 4.0 28.7 - - + -
86B ILE* 2.9 34.2 + - + +
87B VAL* 3.0 5.6 + - - +
89B TYR* 1.3 71.1 - - - +
91B GLY* 1.3 53.3 + - - +
93B SER* 2.5 13.0 + - - -
94B LEU* 2.4 44.0 + - + -
122B LEU* 4.6 12.3 - - + -
165B LEU* 4.3 16.6 - - + +
169B TYR* 3.8 46.0 - - + +
172B ILE* 5.5 2.9 - - + -
173B ILE* 5.8 2.7 - - + -
176B LEU* 6.1 0.7 - - + -
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Residues in contact with GLY 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PRO* 5.9 0.5 - - - +
5B ILE* 5.3 3.1 + - - -
6B THR* 3.2 31.2 + - - -
87B VAL 3.2 7.7 + - - -
88B VAL 4.1 0.2 - - - -
90B LEU* 1.3 78.2 - - - +
92B THR* 1.3 59.4 + - - +
94B LEU* 3.8 13.4 - - - +
95B GLY* 3.3 16.3 + - - -
119B ALA* 5.9 2.7 - - - +
122B LEU* 3.6 14.9 - - - +
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Residues in contact with THR 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B THR* 5.0 12.1 - - - +
8B VAL* 5.1 9.4 - - + -
88B VAL* 2.7 38.5 + - + +
89B TYR 2.4 24.9 + - - -
90B LEU 2.7 4.9 + - - -
91B GLY* 1.3 77.7 - - - +
93B SER* 1.3 64.2 + - - -
95B GLY* 3.7 0.9 + - - -
96B ASN* 3.4 22.2 + - - +
146B TYR* 4.7 7.4 - - + -
147B GLY* 2.8 26.1 + - - +
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Residues in contact with SER 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TYR 3.8 5.4 - - - -
90B LEU 2.5 11.4 + - - -
92B THR* 1.3 77.8 + - - +
94B LEU* 1.3 58.0 + - - -
96B ASN* 3.0 13.0 + - - +
97B ILE* 2.8 38.6 + - - +
148B PRO* 2.7 52.6 + - - +
165B LEU* 3.8 17.7 - - - +
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LEU* 5.5 3.6 - - + -
90B LEU* 2.4 38.2 + - + +
91B GLY* 3.8 12.6 - - - +
93B SER* 1.3 66.5 - - - +
95B GLY* 1.3 66.8 + - - +
97B ILE* 3.4 9.6 + - + +
98B THR* 2.9 24.5 + - - +
115B LEU* 4.2 31.2 - - + +
118B THR* 3.6 35.4 - - + +
119B ALA* 4.2 12.6 - - + -
122B LEU* 4.8 4.7 - - + -
165B LEU* 4.4 4.0 - - + +
166B LEU* 4.5 19.7 - - + -
169B TYR* 6.4 1.3 - - + -
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Residues in contact with GLY 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PRO* 4.6 20.3 - - - +
5B ILE 5.9 0.4 - - - -
91B GLY 3.3 15.1 + - - -
92B THR 4.1 1.8 - - - -
93B SER 3.4 0.2 - - - -
94B LEU* 1.3 77.4 - - - +
96B ASN* 1.3 64.5 + - - +
98B THR* 2.9 23.3 + - - -
99B ARG* 3.1 7.9 + - - +
119B ALA* 5.9 0.2 - - - +
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Residues in contact with ASN 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B THR 3.4 17.1 + - - +
93B SER* 3.0 8.3 + - - +
95B GLY* 1.3 72.0 - - - +
97B ILE* 1.3 56.4 + - + +
98B THR 2.6 13.5 + - - -
99B ARG* 2.8 18.9 + - - +
100B ASP* 3.0 11.3 + - - -
148B PRO 3.5 21.8 + - - -
149B ASP* 4.0 19.8 + - + +
8D VAL* 4.6 12.7 - - - +
9D ASN* 3.1 33.7 + - - +
146D TYR* 5.1 3.2 + - - -
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TYR* 3.6 31.2 - - + +
93B SER* 2.8 31.5 + - - +
94B LEU* 3.8 10.1 - - + +
95B GLY 3.4 0.2 - - - -
96B ASN* 1.3 71.2 - - - +
98B THR* 1.3 54.7 + - - +
100B ASP* 3.2 19.0 - - - +
101B GLN* 3.2 21.0 + - - +
115B LEU* 5.5 5.8 - - + -
148B PRO* 5.9 1.1 - - + -
149B ASP* 3.9 18.8 - - - +
158B LYS 4.9 1.8 - - - +
161B LEU* 4.5 4.9 - - + +
162B GLY* 3.7 29.8 - - - +
165B LEU* 3.5 26.9 - - + -
166B LEU* 5.2 4.7 - - + -
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Residues in contact with THR 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B PRO 5.9 0.2 - - - +
4B PRO* 4.9 10.4 - - + +
94B LEU* 2.9 15.6 + - - +
95B GLY* 2.9 12.0 + - - -
96B ASN 2.6 4.0 + - - -
97B ILE* 1.3 70.5 - - - +
99B ARG* 1.3 52.5 + - - +
100B ASP 2.7 4.4 + - - -
101B GLN* 2.6 10.7 + - - +
102B LYS* 2.4 58.6 + - + +
112B HIS* 4.5 9.6 - - + -
115B LEU* 3.9 29.7 + - + +
116B ASN* 4.3 14.8 - - - +
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Residues in contact with ARG 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B SER* 4.9 9.1 + - - -
2B PRO 5.7 2.8 + - - -
3B LEU* 5.3 2.4 - - - +
4B PRO* 6.0 3.2 - - - +
95B GLY 3.1 6.5 + - - +
96B ASN* 2.8 14.2 + - - +
98B THR* 1.3 74.5 - - - +
100B ASP* 1.3 61.1 + - - +
102B LYS* 4.0 30.1 - - - +
103B ILE* 3.6 18.8 - - - +
5D ILE* 3.3 33.6 - - - +
7D PRO* 4.2 20.2 - - - +
9D ASN* 3.5 30.2 - - - +
14D ILE* 4.8 4.9 - - - +
16D HIS* 4.1 17.4 + - - -
123D ARG* 3.4 29.9 - - - +
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Residues in contact with ASP 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ASN 3.0 8.8 + - - +
97B ILE* 3.2 24.9 - - - +
98B THR 2.7 0.2 + - - -
99B ARG* 1.3 76.8 - - - +
101B GLN* 1.3 59.6 + - - +
102B LYS 2.8 2.9 - - - -
103B ILE* 2.6 31.7 + - - +
104B LEU* 3.0 24.4 - - + +
149B ASP* 4.0 9.0 - - - +
158B LYS* 2.7 55.7 + - + +
9D ASN* 4.1 2.8 + - - -
14D ILE* 3.0 14.2 - - - +
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Residues in contact with GLN 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B TYR* 3.3 27.6 + - + -
48B GLN* 3.0 28.5 + - - +
97B ILE 3.2 15.2 + - - +
98B THR* 2.6 12.6 + - - +
100B ASP* 1.3 79.8 - - - +
102B LYS* 1.3 55.5 - - - +
103B ILE 3.0 1.1 - - - -
104B LEU* 3.8 14.6 - - - +
105B ASN* 2.9 72.8 + - + +
111B LEU* 4.6 7.9 - - + +
112B HIS* 4.0 11.2 - - + -
115B LEU* 4.5 9.2 - - + -
158B LYS 5.3 1.0 + - - -
159B LYS* 5.2 1.8 - - - +
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Residues in contact with LYS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ILE* 4.6 5.2 - - - +
1B SER* 3.5 26.0 - - - +
2B PRO* 3.9 38.4 + - - +
98B THR* 2.4 34.8 + - + +
99B ARG* 4.0 28.5 - - - +
100B ASP 2.7 0.8 + - - -
101B GLN* 1.3 72.3 - - - +
103B ILE* 1.3 73.1 + - + +
106B PRO* 3.5 17.9 - - - +
112B HIS* 3.2 40.3 + - - +
116B ASN* 4.8 2.0 + - - +
16D HIS* 5.8 4.5 - - + +
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Residues in contact with ILE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A VAL* 3.9 18.9 - - - +
316A PRO* 3.6 30.1 - - + -
317A ARG* 4.8 3.4 + - - +
337A ILE* 4.4 17.2 - - + +
99B ARG* 3.6 23.3 - - + +
100B ASP 2.6 13.5 + - - +
102B LYS* 1.3 85.9 - - + +
104B LEU* 1.3 62.1 + - - +
105B ASN 3.7 0.2 - - - -
106B PRO* 4.4 5.4 - - - -
14D ILE* 3.7 30.2 - - + +
15D ARG* 4.5 12.3 - - - +
16D HIS* 4.3 25.1 - - + +
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ASN* 3.0 38.1 - - - +
262A SER* 4.3 20.2 - - - +
280A PHE* 5.1 4.9 - - + -
314A VAL* 4.2 0.2 - - - +
100B ASP* 3.0 45.6 + - + +
101B GLN* 3.8 15.9 - - - +
103B ILE* 1.3 82.5 - - - +
105B ASN* 1.3 63.4 + - - +
106B PRO* 3.2 2.6 - - - +
155B VAL* 4.3 27.4 - - + +
158B LYS* 6.0 3.4 - - + -
159B LYS* 4.5 17.7 - - + -
14D ILE* 4.0 19.1 - - + -
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Residues in contact with ASN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A GLU* 5.0 2.4 - - - +
261A ASN* 3.8 6.4 + - - +
262A SER* 3.3 28.9 + - - -
47B ALA* 3.1 34.3 + - + +
48B GLN* 3.4 10.7 - - - +
101B GLN* 2.9 39.0 + - + +
104B LEU* 1.3 81.9 - - - +
106B PRO* 1.3 59.3 - - - +
107B SER* 3.0 10.4 + - - +
108B ALA* 3.9 12.9 + - + +
111B LEU* 5.2 4.1 - - + +
112B HIS* 3.3 13.7 + - - -
----------------------------------------------------------
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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