Contacts of the helix formed by residues 78 - 116 (chain B) in PDB entry 4CKG
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 78 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B PRO* 3.1 14.2 + - + +
77B ALA* 1.4 76.5 - - + +
79B CYS* 1.4 73.2 + - - +
80B LEU 3.5 0.2 - - - -
81B GLU* 3.2 5.5 + - - +
82B LYS* 2.9 45.4 + - + +
216B TYR* 4.1 11.9 + - - +
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Residues in contact with CYS 79 (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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189A MET* 4.1 0.2 - - + -
74B PRO 4.6 1.8 - - - -
75B MET* 3.0 28.2 + - - +
78B GLU* 1.4 83.8 - - - +
80B LEU* 1.3 61.5 + - - +
82B LYS* 3.0 3.6 + - - +
83B PHE* 2.9 31.1 + - + -
216B TYR* 3.5 35.2 - - + +
220B LEU* 3.9 35.9 - - + -
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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
----------------------------------------------------------
188A ILE* 3.7 22.2 - - + -
189A MET* 3.9 38.3 - - + +
192A VAL* 3.8 31.9 - - + -
63B ILE* 5.1 4.7 - - + +
67B ALA* 3.7 30.3 - - + +
75B MET 3.1 5.7 + - - -
76B MET* 3.3 32.2 + - + +
78B GLU 3.5 0.2 - - - -
79B CYS* 1.3 75.6 - - - +
81B GLU* 1.3 59.9 + - - +
83B PHE* 3.6 4.0 + - - +
84B THR* 3.2 33.0 + - + +
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Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B MET 3.7 4.6 + - - +
77B ALA 3.5 22.8 - - - +
78B GLU* 3.2 4.3 + - - +
79B CYS 3.2 0.2 - - - -
80B LEU* 1.3 77.4 - - - +
82B LYS* 1.3 61.9 + - + +
84B THR* 3.3 6.0 + - - +
85B VAL* 3.0 50.8 + - + +
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Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLU* 2.9 41.1 + - + +
79B CYS 3.0 4.2 + - - +
81B GLU* 1.3 73.7 - - + +
83B PHE* 1.3 63.9 + - - +
85B VAL* 4.2 6.7 - - + +
86B SER* 3.2 24.3 + - - -
213B LEU* 4.9 5.0 - - + +
216B TYR* 4.3 19.3 - - + +
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Residues in contact with PHE 83 (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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189A MET* 4.0 12.8 - - - -
192A VAL* 3.5 28.9 - - + -
193A LEU* 3.7 29.2 - - + -
196A VAL* 3.7 34.5 - - + +
79B CYS* 2.9 28.8 + - + +
80B LEU* 4.0 4.9 - - - +
81B GLU 3.2 0.2 - - - -
82B LYS* 1.3 78.0 - - - +
84B THR* 1.3 60.4 + - - +
86B SER* 3.6 6.1 - - - -
87B LEU* 3.2 26.9 + - - +
213B LEU* 4.0 23.1 - - + -
216B TYR* 3.6 33.2 - + - -
217B ARG* 4.2 7.0 - - - -
220B LEU* 4.3 9.6 - - + -
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Residues in contact with THR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A VAL* 4.8 8.1 - - + -
60B VAL* 3.7 6.1 - - + +
63B ILE* 3.8 30.3 - - + -
64B CYS* 3.7 29.2 - - - +
80B LEU* 3.2 21.6 + - + +
81B GLU* 3.3 9.2 + - - +
82B LYS 3.4 0.2 - - - -
83B PHE* 1.3 76.1 - - - +
85B VAL* 1.3 64.8 + - - +
87B LEU* 3.1 17.3 + - + +
88B ASN* 3.1 30.1 + - - -
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLU* 3.0 38.3 + - + +
82B LYS* 4.2 8.7 - - + +
84B THR* 1.3 74.6 + - - +
86B SER* 1.3 66.3 + - - +
88B ASN* 3.2 9.5 + - - +
89B HIS* 3.0 54.2 + - + +
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Residues in contact with SER 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LYS 3.2 17.4 + - - -
83B PHE 3.6 5.8 - - - -
85B VAL* 1.3 78.0 - - - +
87B LEU* 1.3 56.4 + - - +
89B HIS* 3.4 8.8 - - - +
90B LYS* 3.1 47.4 + - - +
209B GLU* 6.1 0.5 - - - +
210B LEU* 4.5 4.3 - - - +
213B LEU* 3.7 30.4 - - - +
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Residues in contact with LEU 87 (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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192A VAL* 5.4 2.7 - - + -
195A LEU* 5.2 12.1 - - + -
196A VAL* 4.1 24.7 - - + +
199A GLN* 3.4 31.8 + - + +
60B VAL* 3.9 23.3 - - + -
63B ILE* 5.0 10.3 - - + -
83B PHE* 3.2 17.7 + - + +
84B THR* 3.1 22.2 + - + +
86B SER* 1.3 76.3 - - - +
88B ASN* 1.3 60.3 + - - +
90B LYS* 3.7 4.4 + - - +
91B LEU* 3.3 27.6 + - - +
213B LEU* 5.7 0.2 - - + -
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Residues in contact with ASN 88 (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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57B ARG* 3.4 32.9 + - - +
60B VAL* 3.4 30.8 - - - +
61B VAL* 6.1 0.4 - - - +
64B CYS* 5.0 5.5 - - - -
84B THR 3.1 21.7 + - - -
85B VAL* 3.2 9.7 + - - +
87B LEU* 1.3 75.1 - - - +
89B HIS* 1.4 57.2 + - - +
91B LEU* 3.3 5.0 + - - +
92B ASP* 2.8 38.2 + - - +
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Residues in contact with HIS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B VAL* 3.0 43.8 + - + +
86B SER* 3.4 9.9 - - - +
88B ASN* 1.4 74.6 - - - +
90B LYS* 1.4 68.6 + - + +
92B ASP* 3.4 11.4 + - - +
93B SER* 3.0 29.4 + - - -
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Residues in contact with LYS 90 (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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199A GLN* 4.5 24.7 - - - +
203A PHE* 5.1 8.1 - - + -
86B SER* 3.1 25.6 + - - +
87B LEU 4.0 4.9 - - - +
88B ASN 3.4 0.2 - - - -
89B HIS* 1.4 87.7 - - - +
91B LEU* 1.4 62.1 + - + +
93B SER* 3.3 10.7 + - - -
94B HIS* 3.0 25.0 + - - +
202B HIS* 4.7 5.3 - - + -
206B GLY* 4.3 17.7 - - - -
209B GLU* 2.8 32.0 + - - +
210B LEU* 4.0 30.5 - - + -
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Residues in contact with LEU 91 (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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53B LEU* 3.7 32.0 - - + +
56B SER* 3.5 24.5 - - - +
57B ARG* 3.6 57.7 + - + +
60B VAL* 4.8 4.0 - - + -
87B LEU 3.3 17.6 + - - +
88B ASN* 3.3 13.8 + - - +
90B LYS* 1.4 74.9 - - - +
92B ASP* 1.3 58.0 + - - +
94B HIS* 3.5 1.3 + - + -
95B ALA* 2.9 27.5 + - - +
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Residues in contact with ASP 92 (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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57B ARG* 2.7 33.5 + - - -
88B ASN* 2.8 19.7 + - - +
89B HIS* 3.5 11.5 + - - +
91B LEU* 1.3 75.3 - - - +
93B SER* 1.4 58.7 + - - +
95B ALA* 3.4 9.8 - - - +
96B GLU* 3.2 27.8 + - - +
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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 HIS 3.0 17.7 + - - -
90B LYS* 3.7 14.0 - - - +
92B ASP* 1.4 74.5 - - - +
94B HIS* 1.3 58.3 + - - +
96B GLU* 3.0 29.6 + - - +
97B LEU* 3.1 9.9 + - - +
202B HIS* 3.4 23.7 + - - -
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Residues in contact with HIS 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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52A TYR* 3.0 37.0 + + - -
52B TYR* 5.6 2.8 - + - -
53B LEU* 3.8 26.9 - - + -
90B LYS 3.0 17.5 + - - +
91B LEU 3.9 3.4 - - - +
93B SER* 1.3 73.4 - - - +
95B ALA* 1.4 62.0 + - - +
97B LEU* 3.1 27.2 + - + +
98B LEU* 3.0 24.4 + - + +
202B HIS* 3.0 29.2 + + + +
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Residues in contact with ALA 95 (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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50B ARG* 3.7 20.1 + - - +
53B LEU* 3.6 13.3 - - + +
57B ARG* 5.3 3.4 - - - +
91B LEU 2.9 18.6 + - - +
92B ASP* 3.4 13.9 - - - +
94B HIS* 1.4 73.6 - - - +
96B GLU* 1.4 57.2 + - + +
98B LEU* 3.2 5.0 + - - +
99B ASP* 2.9 34.8 + - - +
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Residues in contact with GLU 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 ASP 3.2 12.9 + - - +
93B SER* 3.0 21.2 + - - +
95B ALA* 1.4 73.9 - - + +
97B LEU* 1.4 55.8 + - - +
99B ASP* 3.3 9.1 + - + +
100B ALA* 2.8 29.7 + - - +
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B SER 3.1 9.6 + - - +
94B HIS* 3.1 38.8 + - + +
96B GLU* 1.4 76.0 - - - +
98B LEU* 1.4 58.6 + - + +
100B ALA* 3.3 6.2 + - + +
101B THR* 2.8 37.0 + - - +
195B LEU 5.7 0.4 - - - +
198B ALA* 3.6 37.2 - - + +
199B GLN* 4.2 14.4 - - + +
202B HIS* 4.0 21.3 - - + +
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Residues in contact with LEU 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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52A TYR* 3.6 24.5 - - + +
45B LEU* 5.3 2.9 - - + -
46B LEU* 3.3 39.8 - - + +
49B GLY* 3.6 30.7 - - - -
50B ARG* 3.7 23.6 - - + +
53B LEU* 3.8 20.4 - - + -
94B HIS* 3.0 16.7 + - + +
95B ALA 3.2 7.2 + - - +
97B LEU* 1.4 74.2 - - + +
99B ASP* 1.3 64.5 + - - +
101B THR* 4.4 3.8 - - + +
102B GLN* 3.2 21.1 + - - +
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Residues in contact with ASP 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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50B ARG* 2.6 28.6 + - - +
95B ALA* 2.9 19.8 + - - +
96B GLU* 3.6 11.5 - - + +
98B LEU* 1.3 74.2 - - - +
100B ALA* 1.3 61.8 + - - +
102B GLN* 3.3 18.2 + - - +
103B HIS* 3.1 21.0 + - - +
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Residues in contact with ALA 100 (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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96B GLU 2.8 20.4 + - - +
97B LEU* 3.9 11.0 - - + +
98B LEU 3.3 0.2 - - - -
99B ASP* 1.3 73.5 - - - +
101B THR* 1.4 61.3 + - - +
103B HIS* 3.2 8.2 + - - +
104B THR* 3.0 28.0 + - - -
198B ALA* 5.4 9.9 - - + -
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Residues in contact with THR 101 (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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59A PHE* 5.8 5.4 - - + -
42B GLY* 5.3 3.6 - - - +
45B LEU* 5.5 10.8 - - + -
46B LEU* 3.7 22.7 - - + -
97B LEU* 2.8 30.3 + - - +
98B LEU* 4.4 4.7 - - + +
100B ALA* 1.4 70.5 - - - +
102B GLN* 1.3 54.3 + - - +
104B THR* 3.4 2.4 + - - -
105B LEU* 2.9 34.1 + - + +
191B PHE* 5.5 0.8 - - + -
195B LEU* 3.6 30.5 - - + +
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Residues in contact with GLN 102 (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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46B LEU* 3.8 26.4 - - + +
50B ARG* 4.8 5.2 + - - -
98B LEU 3.2 12.5 + - - +
99B ASP* 3.3 25.6 + - - +
101B THR* 1.3 74.7 - - - +
103B HIS* 1.4 53.1 + - - +
105B LEU* 3.3 4.4 + - + +
106B GLN* 2.7 56.4 + - + +
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Residues in contact with HIS 103 (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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99B ASP 3.1 10.0 + - - +
100B ALA* 3.2 13.7 + - - +
102B GLN* 1.4 77.9 - - - +
104B THR* 1.3 56.6 + - - +
106B GLN* 3.6 7.8 - - + +
107B GLN* 2.7 65.0 + - + +
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Residues in contact with THR 104 (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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100B ALA 3.0 16.1 + - - -
101B THR 3.5 6.1 - - - -
103B HIS* 1.3 81.2 + - - +
105B LEU* 1.3 54.2 + - - +
107B GLN* 3.7 9.4 - - - +
108B GLN* 3.2 30.5 + - + +
191B PHE* 3.6 26.8 - - + -
194B ARG* 3.6 33.4 - - + +
195B LEU* 3.9 18.3 - - + +
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Residues in contact with LEU 105 (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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59A PHE* 5.3 4.0 - - + -
38B LEU 4.5 2.9 - - - +
39B LEU* 4.2 19.5 - - + +
42B GLY* 3.5 42.0 - - - +
43B THR* 3.7 11.4 - - - +
46B LEU* 4.0 14.4 - - + -
101B THR* 2.9 22.6 + - + +
102B GLN* 3.6 4.9 - - + +
104B THR* 1.3 71.1 - - - +
106B GLN* 1.4 58.9 + - - +
109B ILE* 3.0 48.7 + - + -
110B GLN* 3.1 12.1 + - - +
191B PHE* 3.9 18.6 - - + -
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Residues in contact with GLN 106 (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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102B GLN* 2.7 40.9 + - + +
103B HIS* 3.7 7.1 - - + +
105B LEU* 1.4 70.9 - - - +
107B GLN* 1.3 61.7 + - - +
110B GLN* 3.7 39.0 + - - +
111B THR* 3.2 20.3 + - - -
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Residues in contact with GLN 107 (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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103B HIS* 2.7 48.3 + - + +
104B THR* 3.7 9.3 - - - +
106B GLN* 1.3 73.2 - - - +
108B GLN* 1.3 88.7 + - - +
111B THR* 2.9 24.5 + - - +
190B GLU* 4.8 5.7 - - - +
194B ARG* 5.1 12.1 + - - +
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Residues in contact with GLN 108 (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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104B THR* 3.2 17.9 + - + +
107B GLN* 1.3 111.3 - - - +
109B ILE* 1.3 67.0 + - + +
110B GLN 3.5 0.4 - - - -
111B THR* 3.9 0.5 - - - -
112B LEU* 2.8 35.1 + - + +
187B ASP* 3.5 48.7 + - + +
190B GLU* 2.7 33.3 + - + +
191B PHE* 4.1 21.3 - - + -
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Residues in contact with ILE 109 (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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35B LEU* 3.6 50.5 - - + +
38B LEU* 4.1 10.3 - - + -
39B LEU* 3.9 16.4 - - + +
105B LEU* 3.0 18.4 + - + +
108B GLN* 1.3 83.0 - - + +
110B GLN* 1.3 58.0 + - - +
112B LEU* 3.9 4.6 - - + +
113B VAL* 3.0 28.1 + - + +
187B ASP 5.6 0.4 - - - +
188B ILE* 4.4 8.1 - - + -
191B PHE* 3.4 52.5 - - + -
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Residues in contact with GLN 110 (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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39B LEU* 3.7 27.7 - - + +
105B LEU* 3.1 11.1 + - - +
106B GLN* 3.7 52.0 + - - +
109B ILE* 1.3 73.2 - - - +
111B THR* 1.3 59.4 - - - +
113B VAL* 3.5 2.1 + - - +
114B LYS* 2.9 38.6 + - + +
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Residues in contact with THR 111 (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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106B GLN 3.2 9.9 + - - -
107B GLN* 2.9 26.4 + - - +
108B GLN 3.9 1.1 - - - -
109B ILE 3.5 0.4 - - - -
110B GLN* 1.3 76.0 - - - +
112B LEU* 1.3 59.5 + - - +
114B LYS* 4.6 1.3 - - - -
115B GLU* 2.9 61.4 + - + +
116B GLY* 3.2 4.8 + - - -
183B LYS* 5.6 7.0 - - - +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 5.7 4.0 - - + -
35B LEU* 4.3 35.0 - - + -
108B GLN* 2.8 21.2 + - + +
109B ILE* 3.9 5.8 - - + +
110B GLN 3.3 0.2 - - - -
111B THR* 1.3 78.6 - - - +
113B VAL* 1.3 63.5 + - - +
116B GLY* 3.0 34.2 + - - +
117B LEU* 3.9 16.2 + - + +
180B ILE* 6.3 1.6 - - + -
183B LYS* 3.8 28.9 - - + +
184B ARG* 5.8 3.1 - - - +
187B ASP* 3.7 37.9 - - + +
188B ILE* 5.1 7.9 - - + -
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Residues in contact with VAL 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLU* 4.7 18.7 - - + +
35B LEU* 3.7 32.5 - - + -
36B GLU* 3.5 46.7 - - + +
39B LEU* 3.9 13.7 - - + -
109B ILE* 3.0 18.8 + - + +
110B GLN 3.9 3.1 - - - +
112B LEU* 1.3 77.5 - - - +
114B LYS* 1.4 60.5 + - - +
116B GLY 5.0 0.2 + - - -
117B LEU* 5.1 8.3 + - - +
121B ARG* 5.8 0.3 + - - -
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Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLN* 2.9 27.5 + - + +
111B THR* 4.2 2.2 - - - +
112B LEU 3.4 0.2 - - - -
113B VAL* 1.4 76.8 - - - +
115B GLU* 1.3 80.2 + - + +
118B ARG* 4.9 15.9 + - - +
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B THR* 2.9 35.9 + - + +
114B LYS* 1.3 96.8 + - + +
116B GLY* 1.4 62.8 + - - +
117B LEU 3.6 2.2 - - - -
118B ARG* 3.7 37.6 + - - +
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Residues in contact with GLY 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B THR* 3.2 7.0 + - - -
112B LEU* 3.0 19.0 + - - +
115B GLU* 1.4 77.3 - - - +
117B LEU* 1.3 65.3 + - - +
118B ARG 3.5 2.9 - - - -
119B GLY 5.4 0.2 + - - -
120B PHE* 5.7 0.3 - - - +
180B ILE* 5.0 5.4 - - - +
183B LYS* 3.7 36.5 - - - +
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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