Contacts of the helix formed by residues 76 - 110 (chain B) in PDB entry 6XWQ
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 SER 76 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B SER 4.2 1.2 + - - -
75B ILE* 1.3 72.0 - - - +
77B PRO* 1.3 69.8 - - - +
78B ALA* 3.0 17.9 + - - +
79B ARG* 2.8 13.8 + - - +
80B LEU 2.8 24.5 + - - -
168B THR* 4.5 2.7 - - - -
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Residues in contact with PRO 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ILE 3.4 4.5 - - - +
76B SER* 1.3 87.8 - - - +
78B ALA* 1.3 60.4 + - - +
80B LEU* 3.7 13.0 - - + -
81B GLY* 3.0 19.4 + - - -
165B ILE* 4.9 8.3 - - + -
168B THR* 3.7 26.2 - - + +
169B TYR* 3.4 42.6 - - + +
172B ASN* 6.0 0.9 - - - +
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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
----------------------------------------------------------
76B SER* 2.9 13.1 + - - +
77B PRO* 1.3 80.9 - - - +
79B ARG* 1.3 60.4 + - - +
81B GLY* 3.8 0.7 + - - -
82B ARG* 3.7 22.1 + - - +
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Residues in contact with ARG 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B SER 5.1 6.7 + - - -
75B ILE* 3.7 21.7 - - + +
76B SER* 2.8 15.1 + - - +
78B ALA* 1.3 73.9 - - - +
80B LEU* 1.3 65.6 + - - +
82B ARG* 3.3 29.2 + - - +
83B VAL* 3.0 31.1 + - + +
300B GLY* 3.7 29.4 - - - +
301B ILE* 5.3 0.2 - - - +
420B GLU* 3.1 29.1 + - - +
422B GLU* 4.0 18.4 + - - +
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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
----------------------------------------------------------
72B ALA* 3.6 34.3 - - + +
75B ILE* 3.5 28.6 - - + +
76B SER 2.8 19.7 + - - +
77B PRO* 3.8 8.7 - - + -
79B ARG* 1.3 73.2 - - - +
81B GLY* 1.3 57.0 + - - +
83B VAL* 4.6 2.5 - - + -
84B GLY* 2.8 26.2 + - - -
161B ILE* 5.3 2.5 - - + -
165B ILE* 3.7 28.3 - - + -
168B THR* 5.5 0.4 - - + -
304B PHE* 3.6 38.1 - - + -
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Residues in contact with GLY 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PRO 3.0 17.7 + - - -
78B ALA 4.3 1.1 - - - -
79B ARG 3.2 0.2 - - - -
80B LEU* 1.3 77.0 - - - +
82B ARG* 1.3 61.7 + - - +
84B GLY* 3.2 1.5 + - - -
85B VAL* 3.0 32.0 + - - +
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Residues in contact with ARG 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ALA 3.7 13.3 + - - +
79B ARG* 3.3 42.1 + - - +
81B GLY* 1.3 73.8 - - - +
83B VAL* 1.3 59.7 + - + +
85B VAL* 3.4 4.7 + - - +
86B LYS* 2.9 58.4 + - + +
419B THR 5.6 0.4 - - - -
420B GLU* 4.1 19.7 + - - +
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ILE* 5.4 2.0 - - + -
79B ARG* 3.0 25.7 + - + +
80B LEU* 4.0 4.3 - - + +
82B ARG* 1.3 80.7 - - + +
84B GLY* 1.3 59.6 + - - +
86B LYS* 3.4 6.1 + - - +
87B ILE* 2.9 31.5 + - - +
300B GLY 4.9 12.3 - - - +
301B ILE* 4.9 1.6 - - + -
304B PHE* 3.9 16.8 - - + -
305B THR* 3.7 28.0 - - + -
416B VAL* 4.3 13.5 - - + +
420B GLU* 3.3 29.8 - - + +
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Residues in contact with GLY 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU 2.8 19.5 + - - -
81B GLY* 3.7 1.1 - - - -
83B VAL* 1.3 77.6 - - - +
85B VAL* 1.3 56.9 + - - +
87B ILE* 3.1 8.5 - - - +
88B VAL* 2.9 39.2 + - - +
304B PHE* 4.3 11.9 - - - -
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLY* 3.0 20.0 + - - +
82B ARG* 4.0 3.8 - - - +
84B GLY* 1.3 76.0 - - - +
86B LYS* 1.3 59.0 + - + +
88B VAL* 4.9 2.5 - - - -
89B VAL* 3.0 51.5 + - + +
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Residues in contact with LYS 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ARG* 2.9 44.8 + - + +
83B VAL* 4.0 4.0 - - - +
85B VAL* 1.3 78.3 - - + +
87B ILE* 1.3 57.8 + - - +
89B VAL* 4.5 3.9 - - - +
90B TYR* 3.6 16.3 + - - +
416B VAL* 3.6 33.9 + - + +
419B THR* 3.0 56.1 + - + +
420B GLU* 3.9 7.9 - - - +
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Residues in contact with ILE 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B VAL 2.9 23.8 + - - +
84B GLY* 3.1 13.7 - - - +
86B LYS* 1.3 78.8 - - - +
88B VAL* 1.3 71.8 + - + +
89B VAL 3.4 0.4 - - - -
90B TYR* 3.4 3.5 + - + +
91B TYR* 2.9 75.4 + - + +
304B PHE* 4.6 3.1 - - + -
305B THR* 3.8 26.2 - - + -
308B LEU* 4.6 12.6 - - + -
412B GLY* 3.9 17.0 - - - +
416B VAL* 3.6 20.4 - - + -
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLY* 2.9 24.4 + - - +
85B VAL* 4.3 2.2 - - - +
87B ILE* 1.3 80.7 - - + +
89B VAL* 1.3 66.9 + - + +
91B TYR* 3.2 6.6 + - + +
92B LEU* 2.9 52.4 + - + +
304B PHE* 6.4 0.2 - - + -
308B LEU* 4.7 13.2 - - + -
312B ILE* 5.2 9.4 - - + -
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Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B VAL* 3.0 38.1 + - + +
86B LYS* 4.9 3.8 - - - +
88B VAL* 1.3 77.6 - - + +
90B TYR* 1.3 56.6 + - - +
92B LEU* 3.5 5.3 + - - +
93B ALA* 2.9 32.6 + - + +
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Residues in contact with TYR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B LYS 3.6 19.1 + - - +
87B ILE* 3.4 6.7 + - + +
88B VAL 3.2 0.4 - - - -
89B VAL* 1.3 80.0 - - - +
91B TYR* 1.3 86.6 + + - +
93B ALA* 3.3 4.6 + - + +
94B THR* 2.9 56.4 + - + +
249B TYR* 3.7 20.3 - - - -
252B LEU* 3.6 21.3 - - + -
253B LEU* 6.2 0.4 - - + -
313B ASN* 4.5 2.2 - - - -
408B GLY 3.3 20.6 + - - -
411B ALA* 3.7 6.8 - - - +
412B GLY* 3.4 31.9 + - - -
415B ILE* 5.2 15.5 - - + -
416B VAL* 5.5 1.6 - - + -
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Residues in contact with TYR 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ILE* 2.9 53.6 + - + +
88B VAL* 3.2 8.3 + - - +
90B TYR* 1.3 93.3 - + - +
92B LEU* 1.3 59.4 + - + +
94B THR* 3.3 4.1 + - - -
95B SER* 2.4 39.8 + - - +
305B THR* 2.9 24.3 + - - -
306B LEU* 5.0 0.3 - - - +
308B LEU* 4.3 7.4 - - + -
309B GLY* 3.1 26.4 - - - -
312B ILE* 3.7 26.5 - - + -
313B ASN* 3.4 36.1 - - + -
353B ILE* 6.3 0.7 - - + -
409B ASP* 4.8 6.6 + - - -
412B GLY* 4.9 2.7 - - - -
413B THR* 5.3 0.3 + - - -
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B VAL* 2.9 39.4 + - + +
89B VAL* 4.0 4.5 - - - +
91B TYR* 1.3 79.7 - - + +
93B ALA* 1.3 63.7 + - - +
95B SER* 3.3 4.0 + - - -
96B ALA* 3.0 25.8 + - - +
312B ILE* 6.1 1.8 - - + -
349B VAL* 4.6 11.1 - - + +
350B LEU* 6.3 0.4 - - + -
353B ILE* 3.7 29.6 - - + -
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Residues in contact with ALA 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B VAL* 2.9 24.3 + - + +
90B TYR* 3.8 5.6 - - - +
92B LEU* 1.3 76.6 - - - +
94B THR* 1.3 61.2 + - + +
96B ALA* 3.4 4.5 + - - +
97B MET* 2.9 38.1 + - + +
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Residues in contact with THR 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TYR* 2.9 54.8 + - + +
91B TYR* 3.3 4.7 + - - -
93B ALA* 1.3 75.5 - - + +
95B SER* 1.3 61.3 + - - +
97B MET* 3.7 8.1 - - - +
98B ALA* 2.8 26.3 + - - +
244B GLN* 4.5 2.0 + - - -
248B THR* 4.6 11.2 - - + -
249B TYR* 4.8 1.6 - - - -
252B LEU* 4.3 11.9 - - + -
313B ASN* 3.8 5.0 + - - -
315B ASP* 3.0 30.1 + - - +
----------------------------------------------------------
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Residues in contact with SER 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B TYR* 2.4 29.6 + - - +
92B LEU* 3.7 7.2 - - - +
93B ALA 3.3 0.2 - - - -
94B THR* 1.3 77.0 + - - +
96B ALA* 1.3 57.7 + - - +
98B ALA* 3.3 4.3 + - - +
99B VAL* 3.0 32.7 + - - +
313B ASN* 4.5 4.7 + - - -
314B MET 4.7 8.1 + - - -
315B ASP* 3.3 13.6 + - - -
318B ALA* 4.3 8.6 - - - +
349B VAL* 3.8 23.1 - - - -
352B SER* 5.2 2.2 - - - -
353B ILE* 5.2 6.4 - - - +
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Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU 3.0 16.5 + - - +
93B ALA* 3.8 4.9 - - - +
95B SER* 1.3 76.9 - - - +
97B MET* 1.3 59.9 + - + +
99B VAL* 3.3 2.6 + - - +
100B PHE* 2.9 28.1 + - - +
345B VAL* 3.9 19.8 - - + +
349B VAL* 3.9 12.2 - - + +
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Residues in contact with MET 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ALA* 2.9 25.3 + - + +
94B THR* 3.8 8.1 - - - +
95B SER 3.3 0.2 - - - -
96B ALA* 1.3 75.9 - - + +
98B ALA* 1.3 57.8 + - - +
100B PHE* 3.3 12.4 + - - +
101B PHE* 2.9 46.9 + - + -
244B GLN* 4.2 0.9 - - - +
248B THR* 4.6 19.1 - - + +
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B THR 2.8 18.1 + - - +
95B SER 3.3 4.7 + - - +
97B MET* 1.3 74.8 - - - +
99B VAL* 1.3 61.8 + - - +
101B PHE* 3.3 1.2 + - - -
102B GLY 2.9 23.9 + - - -
244B GLN* 3.2 27.7 + - + +
315B ASP* 3.6 31.0 - - + +
318B ALA* 4.8 0.2 - - + -
319B LEU* 3.4 17.1 - - + +
----------------------------------------------------------
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B SER 3.0 21.8 + - - +
96B ALA 3.3 4.7 + - - +
98B ALA* 1.3 75.2 - - - +
100B PHE* 1.3 58.4 + - - +
102B GLY* 3.2 2.0 + - - +
103B LEU* 2.9 33.9 + - + +
318B ALA* 3.6 34.3 - - + +
319B LEU* 4.7 1.1 - - - +
322B GLY* 4.6 12.2 - - - -
344B VAL* 4.3 2.2 - - + +
345B VAL* 3.6 33.2 - - + +
348B ALA* 3.9 20.0 - - + -
349B VAL* 4.7 7.6 - - + -
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Residues in contact with PHE 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ALA 2.9 17.4 + - - +
97B MET* 3.7 13.7 - - - +
99B VAL* 1.3 78.5 - - - +
101B PHE* 1.3 72.7 + + - +
103B LEU* 3.2 9.5 + - + +
104B ILE* 2.9 61.0 + - + +
341B GLN* 3.7 28.0 - - + -
345B VAL* 4.8 6.0 - - + +
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Residues in contact with PHE 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B MET* 2.9 37.8 + - + +
98B ALA* 3.7 6.1 - - - +
100B PHE* 1.3 87.2 - + - +
102B GLY* 1.3 57.8 + - - +
104B ILE* 3.3 9.8 + - + +
105B VAL* 2.9 35.3 + - + +
240B GLY 5.1 1.8 - - - +
243B LEU* 3.8 42.8 - - + -
244B GLN* 4.5 6.3 - - - +
247B ILE* 3.6 33.9 - - + -
248B THR* 4.1 17.3 - - - -
319B LEU* 4.3 10.8 - - + -
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Residues in contact with GLY 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ALA 2.9 11.5 + - - -
99B VAL 3.2 4.0 + - - -
100B PHE 3.2 0.2 - - - -
101B PHE* 1.3 76.3 - - - +
103B LEU* 1.3 57.4 + - - +
105B VAL* 3.1 5.9 - - - +
106B GLY* 2.9 24.6 + - - -
319B LEU* 3.6 18.0 - - - +
322B GLY 5.1 0.2 - - - -
323B VAL* 3.3 30.8 - - - +
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 2.9 24.0 + - + +
100B PHE* 3.6 11.7 - - + +
102B GLY* 1.3 75.7 - - - +
104B ILE* 1.3 60.5 + - + +
106B GLY* 3.4 0.7 + - - -
107B ARG* 2.9 36.0 + - + +
322B GLY* 3.2 26.2 - - - +
325B VAL* 6.3 0.2 - - + -
326B LEU* 3.7 27.1 - - + +
336B LEU* 5.4 3.6 - - + -
341B GLN* 3.5 41.3 - - + +
344B VAL* 3.8 26.2 - - + -
345B VAL* 5.4 1.6 - - + -
----------------------------------------------------------
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Residues in contact with ILE 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PHE* 2.9 56.7 + - + +
101B PHE* 3.6 11.7 - - + +
102B GLY 3.2 0.2 - - - -
103B LEU* 1.3 78.6 - - + +
105B VAL* 1.3 61.0 + - + +
107B ARG* 3.2 29.6 + - - +
108B LEU* 2.9 40.7 + - + +
243B LEU* 5.7 4.9 - - + -
341B GLN* 6.2 0.4 - - - +
----------------------------------------------------------
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PHE* 2.9 19.1 + - + +
102B GLY* 3.1 22.4 - - - +
104B ILE* 1.3 76.0 - - + +
106B GLY* 1.3 58.4 + - - +
108B LEU* 3.4 16.4 - - + +
109B PHE* 2.9 37.1 + - + +
236B ALA* 4.2 11.8 - - + +
239B THR* 4.7 8.3 - - + -
240B GLY* 4.0 27.8 - - - +
243B LEU* 3.8 28.9 - - + -
323B VAL* 4.1 9.4 - - + -
----------------------------------------------------------
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Residues in contact with GLY 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLY 2.9 17.3 + - - -
103B LEU 3.7 1.6 - - - -
105B VAL* 1.3 77.5 - - - +
107B ARG* 1.3 52.9 + - - +
110B ASN* 2.7 36.0 + - - -
111B VAL* 3.9 8.8 + - - -
323B VAL* 4.6 14.8 - - - -
326B LEU* 4.4 18.8 - - - +
----------------------------------------------------------
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Residues in contact with ARG 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 2.9 24.0 + - + +
104B ILE* 3.2 27.3 + - - +
106B GLY* 1.3 74.9 - - - +
108B LEU* 1.3 59.9 + - - +
110B ASN* 4.2 7.6 + - - +
326B LEU* 4.2 17.5 - - + +
336B LEU 6.0 1.6 - - - -
341B GLN* 4.8 12.9 + - - -
----------------------------------------------------------
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ILE* 2.9 30.6 + - + +
105B VAL* 3.4 26.2 - - + +
106B GLY 3.1 0.2 - - - -
107B ARG* 1.3 79.9 - - - +
109B PHE* 1.3 92.8 + - + +
110B ASN* 3.5 1.0 - - - +
239B THR* 5.9 1.8 - - + -
243B LEU* 5.5 4.7 - - + -
----------------------------------------------------------
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Residues in contact with PHE 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B VAL* 2.9 17.9 + - + +
108B LEU* 1.3 100.5 - - + +
110B ASN* 1.3 72.4 + - - +
111B VAL* 4.2 13.2 - - + -
232B LYS* 3.6 35.3 + - - -
235B GLY 3.5 22.2 - - - -
236B ALA* 3.4 24.9 - - + -
239B THR* 4.0 22.2 - - + -
----------------------------------------------------------
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Residues in contact with ASN 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B GLY 2.7 19.2 + - - -
107B ARG* 4.2 6.7 - - - +
108B LEU 3.5 1.9 - - - +
109B PHE* 1.3 76.7 - - - +
111B VAL* 1.3 60.7 + - - +
112B GLY 3.7 1.2 + - - -
113B ALA* 3.4 31.9 + - - +
232B LYS* 4.8 5.4 + - - +
330B ASN* 3.5 24.2 - - - +
----------------------------------------------------------
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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