Contacts of the helix formed by residues 71 - 96 (chain B) in PDB entry 2OB1
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 PHE 71 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B SER 3.7 11.2 - - - -
70B SER* 1.3 81.2 - - - +
72B PRO* 1.3 79.8 - - + +
73B VAL* 3.8 20.0 - - + -
74B MET* 3.1 44.0 + - + +
75B ASN* 2.9 26.6 + - - +
306B GLN* 4.8 1.3 - - - +
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Residues in contact with PRO 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 4.3 6.3 - - - +
71B PHE* 1.3 90.2 - - + -
73B VAL* 1.3 57.1 + - + +
75B ASN* 3.8 0.4 - - + +
76B TYR* 2.8 37.1 + - - -
306B GLN* 3.3 34.1 - - + +
307B PHE 3.8 23.8 - - - +
308B LEU* 4.1 16.6 - - + -
309B ASP 5.4 0.7 - - - +
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 3.2 19.1 + - + -
72B PRO* 1.3 76.5 - - + +
74B MET* 1.3 58.5 + - - +
77B GLY* 3.0 23.7 + - - -
308B LEU* 3.6 24.0 - - + -
310B GLU* 3.7 17.9 - - + +
313B GLU* 4.0 18.2 - - + +
314B LEU* 3.4 33.6 - - + +
317B MET* 3.9 22.7 - - + -
318B GLN* 4.9 0.7 + - - -
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Residues in contact with MET 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B SER* 4.6 2.0 - - - +
15B CYS* 3.5 45.5 - - - +
18B ALA* 4.3 5.6 - - + -
66B ALA* 4.4 11.4 - - + +
69B SER 4.7 1.6 - - - +
70B SER* 3.7 35.9 - - - -
71B PHE* 3.1 37.2 + - + +
73B VAL* 1.3 77.3 - - - +
75B ASN* 1.3 66.2 + - - +
77B GLY* 3.1 3.4 + - - -
78B THR* 3.0 25.9 + - - +
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Residues in contact with ASN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B CYS 4.6 1.2 - - - +
18B ALA* 3.5 26.1 + - - +
19B ALA* 3.7 8.9 + - - +
22B VAL* 3.8 17.7 - - + +
24B TYR* 3.5 22.0 - - + -
70B SER* 3.5 21.1 + - - -
71B PHE 2.9 15.0 + - - +
72B PRO 3.8 1.6 - - - +
74B MET* 1.3 77.2 - - - +
76B TYR* 1.3 65.3 + - - +
78B THR* 3.4 6.5 + - - -
79B TYR* 2.9 24.1 + - - +
306B GLN* 3.0 26.0 + - - +
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Residues in contact with TYR 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 2.9 31.4 - + - -
72B PRO 2.8 30.0 + - - +
75B ASN* 1.3 73.3 - - - +
77B GLY* 1.3 59.4 + - - +
79B TYR* 3.2 6.0 + + - +
80B LEU* 2.9 34.7 + - + +
290B PHE* 4.0 26.5 - + - -
299B ARG* 4.6 5.1 + - + -
302B LEU* 3.4 44.3 - - + +
303B ARG* 4.0 7.8 + - - +
306B GLN 4.2 1.5 + - - -
308B LEU* 3.7 34.1 + - + +
314B LEU* 3.6 31.6 - - + -
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Residues in contact with GLY 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B VAL 3.0 13.4 + - - -
74B MET* 3.1 5.0 + - - -
76B TYR* 1.3 77.6 - - - +
78B THR* 1.3 55.5 + - - +
80B LEU* 3.7 2.2 - - - +
81B ARG* 2.9 31.1 + - - +
231B TYR* 4.3 5.0 + - - -
314B LEU* 4.1 0.6 - - - +
318B GLN* 3.3 33.6 - - - +
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Residues in contact with THR 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ALA 5.5 0.2 - - - +
15B CYS* 3.3 52.9 + - + +
16B LYS* 3.8 12.8 - - - +
19B ALA* 3.7 12.6 - - + -
25B LEU* 4.4 0.4 - - + -
74B MET* 3.0 14.0 + - - +
75B ASN* 3.7 8.2 - - - -
76B TYR 3.3 0.2 - - - -
77B GLY* 1.3 71.7 - - - +
79B TYR* 1.3 65.6 + - - +
81B ARG* 3.4 12.7 + - - +
82B THR* 2.8 38.3 + - - +
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Residues in contact with TYR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ALA* 4.6 0.6 - - - +
24B TYR* 3.4 42.0 - - + -
25B LEU* 3.9 17.0 - - + -
27B SER* 4.0 1.1 - - - -
30B LEU* 3.4 9.4 - - - +
75B ASN 2.9 17.7 + - - +
76B TYR* 3.4 8.5 - + - +
78B THR* 1.3 76.7 - - - +
80B LEU* 1.3 66.1 + - + +
82B THR* 3.7 0.5 - - - -
83B VAL* 2.9 51.7 + - + +
290B PHE* 5.9 0.7 - + - -
294B ILE* 3.6 26.8 - - + +
298B GLU* 2.6 45.2 + - - +
301B ARG* 3.8 3.4 - - - -
302B LEU* 3.7 25.4 - - + -
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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
----------------------------------------------------------
76B TYR* 2.9 24.0 + - + +
77B GLY 3.7 3.8 - - - +
79B TYR* 1.3 83.7 - - + +
81B ARG* 1.3 55.9 + - - +
83B VAL* 3.8 2.7 - - - +
84B GLY* 2.8 29.1 + - - -
286B MET* 3.2 36.3 - - + +
289B ILE* 4.7 3.7 - - + +
290B PHE* 3.8 31.9 - - + +
294B ILE* 3.6 33.0 - - + -
314B LEU* 4.7 7.6 - - + -
318B GLN* 3.9 26.9 - - + +
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Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ALA* 3.8 29.5 - - - +
15B CYS* 5.8 6.5 - - - +
77B GLY 2.9 18.7 + - - +
78B THR* 3.4 12.6 - - - +
80B LEU* 1.3 74.3 - - - +
82B THR* 1.3 64.7 + - - +
85B ILE* 3.1 32.3 + - + +
201B GLU* 2.7 38.7 + - - +
202B CYS* 3.7 34.2 - - - +
231B TYR* 3.4 44.3 + - + -
286B MET* 3.7 3.1 - - - +
321B TYR* 5.7 2.4 - - - -
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Residues in contact with THR 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LYS* 3.3 23.9 + - - +
25B LEU* 3.6 13.6 - - + +
31B GLN* 3.3 28.9 - - - +
41B TYR* 3.8 12.6 - - - +
78B THR* 2.8 18.9 + - - +
79B TYR 3.7 2.7 - - - -
81B ARG* 1.3 81.0 - - - +
83B VAL* 1.3 58.3 + - - +
86B ASP* 2.9 37.7 + - - +
111B ARG* 3.5 11.5 + - - +
201B GLU* 5.3 1.4 + - - -
2003B PO4 3.9 7.0 - - - +
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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
----------------------------------------------------------
25B LEU* 3.9 15.5 - - + -
27B SER* 3.9 13.2 - - - -
30B LEU* 3.9 18.9 - - + +
31B GLN* 4.2 6.5 - - + -
79B TYR* 2.9 46.3 + - + +
80B LEU* 3.8 4.7 - - - +
82B THR* 1.3 74.6 - - - +
84B GLY* 1.3 63.5 + - - +
86B ASP* 4.3 5.8 - - - -
87B ALA* 2.9 31.7 + - - +
289B ILE* 5.7 0.4 - - + -
293B GLN* 5.0 0.4 - - - +
294B ILE* 3.6 31.2 - - + -
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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 19.9 + - - -
81B ARG 4.1 0.2 - - - -
83B VAL* 1.3 78.9 - - - +
85B ILE* 1.3 62.2 + - - +
87B ALA* 4.0 1.6 - - - +
88B ALA* 3.2 18.7 + - - +
286B MET* 4.8 0.4 - - - -
289B ILE* 4.5 5.8 - - - -
293B GLN* 4.3 14.6 - - - +
323B LEU* 3.4 28.0 - - - +
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG* 3.1 22.1 + - + +
84B GLY* 1.3 75.0 - - - +
86B ASP* 1.3 57.6 + - - +
88B ALA* 3.1 5.2 + - - +
89B ILE* 2.9 41.5 + - + +
111B ARG* 3.5 27.8 - - - +
199B ILE* 4.7 8.7 - - + -
201B GLU* 3.3 43.3 - - + +
229B ILE* 4.0 13.4 - - + +
231B TYR* 3.9 13.7 - - + -
323B LEU* 3.8 23.5 - - + +
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Residues in contact with ASP 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU 4.8 0.4 - - - +
31B GLN* 2.7 44.7 + - + +
82B THR* 2.9 22.0 + - - +
83B VAL 4.0 2.7 - - - +
85B ILE* 1.3 77.7 - - - +
87B ALA* 1.3 52.1 + - - +
89B ILE* 3.3 7.8 + - - +
90B LEU* 2.8 50.3 + - + +
111B ARG* 2.6 38.1 + - - +
115B LEU* 5.6 3.1 - - - +
2003B PO4 4.9 3.6 + - - -
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 4.4 19.4 + - + +
32B ARG* 4.7 3.5 + - - +
83B VAL 2.9 19.8 + - - +
84B GLY 4.0 2.7 - - - +
86B ASP* 1.3 75.8 - - - +
88B ALA* 1.3 62.8 + - - +
90B LEU* 4.0 3.9 - - - +
91B GLU* 3.1 36.1 + - + +
293B GLN* 4.3 15.5 - - - +
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLY 3.2 11.5 + - - +
85B ILE 3.1 10.4 + - - +
87B ALA* 1.3 78.6 - - - +
89B ILE* 1.3 67.2 + - - +
91B GLU* 3.6 6.5 + - - +
92B PHE* 3.5 12.6 + - - +
227B LEU* 3.7 12.6 - - + +
229B ILE* 3.6 21.8 - - + -
323B LEU* 5.1 0.9 - - + -
325B LYS* 3.8 31.4 - - + +
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Residues in contact with ILE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE* 2.9 22.6 + - + +
86B ASP* 3.5 10.8 - - - +
88B ALA* 1.3 75.7 - - - +
90B LEU* 1.3 65.3 + - + +
92B PHE* 3.1 5.4 + - - +
93B LEU* 2.9 47.8 + - + +
101B VAL* 5.2 2.2 - - + -
111B ARG* 3.5 33.4 - - - +
115B LEU* 4.0 18.6 - - + -
197B ILE* 3.9 14.8 - - + +
199B ILE* 3.6 20.2 - - + -
229B ILE* 3.4 21.3 - - + +
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU 3.6 20.0 - - - +
31B GLN* 3.4 24.9 - - - +
32B ARG* 3.8 26.0 - - + +
86B ASP* 2.8 31.5 + - + +
87B ALA* 3.4 3.3 + - - +
89B ILE* 1.3 73.1 - - - +
91B GLU* 1.3 59.1 + - - +
93B LEU* 3.9 2.4 - - - +
94B VAL* 2.9 36.5 + - - +
115B LEU* 3.8 19.5 - - + -
118B MET* 3.8 12.3 - - + -
119B PHE* 3.6 31.4 - - + -
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Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ARG* 3.8 18.6 - - - +
87B ALA* 3.1 25.8 + - - +
88B ALA* 3.9 6.0 - - - +
89B ILE 3.2 0.2 - - - -
90B LEU* 1.3 76.8 - - - +
92B PHE* 1.3 61.7 + - - +
94B VAL* 3.6 4.8 + - - +
95B ALA* 3.2 22.2 + - - +
325B LYS* 5.6 5.0 + - - -
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Residues in contact with PHE 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ALA 3.5 1.4 + - - -
89B ILE 3.1 8.1 + - - +
91B GLU* 1.3 78.4 - - - +
93B LEU* 1.3 59.5 - - - +
95B ALA* 3.2 2.3 + - - -
96B ASN* 2.8 63.5 + - - +
99B VAL* 3.8 23.1 - - + -
195B PRO* 3.9 18.2 - - + -
196B THR 4.4 0.4 - - - -
197B ILE* 3.4 25.6 - - + -
225B HIS* 5.2 0.9 - - + -
226B GLY* 4.1 21.3 - - - -
227B LEU* 3.8 36.6 - - + -
327B GLN* 4.0 22.9 - - - +
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 2.9 38.1 + - + +
90B LEU* 3.9 1.3 - - + +
92B PHE* 1.3 75.1 - - - +
94B VAL* 1.3 61.3 + - - +
96B ASN 3.0 21.7 + - - +
97B GLU* 4.0 3.3 + - - -
99B VAL* 3.1 37.9 - - + +
101B VAL* 4.3 0.4 - - + -
115B LEU* 3.9 8.7 - - + -
119B PHE* 3.5 54.5 - - + -
122B LEU* 3.9 17.3 - - + -
197B ILE* 3.5 19.5 - - + -
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLY* 5.3 5.4 - - - +
32A ARG* 3.7 43.7 - - + +
32B ARG* 3.4 23.1 - - - +
90B LEU* 2.9 21.2 + - + +
91B GLU* 3.9 4.5 - - - +
93B LEU* 1.3 78.6 - - - +
95B ALA* 1.3 60.7 + - - +
96B ASN 3.5 1.0 + - - -
97B GLU* 5.0 1.9 + - - +
119B PHE* 4.1 19.7 - - + -
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLU 3.2 15.4 + - - +
92B PHE* 3.2 3.3 + - - -
94B VAL* 1.3 77.0 - - - +
96B ASN* 1.3 74.9 + - - +
97B GLU 4.0 1.2 + - - -
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Residues in contact with ASN 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PHE* 2.8 65.0 + - + +
93B LEU 3.0 12.2 - - - +
94B VAL 3.3 1.2 - - - -
95B ALA* 1.3 90.7 - - - +
97B GLU* 1.3 66.6 + - - +
98B LYS 3.4 4.8 + - - +
99B VAL* 3.6 13.0 - - + +
195B PRO* 4.0 22.5 - - + +
----------------------------------------------------------
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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