Contacts of the helix formed by residues 86 - 109 (chain B) in PDB entry 2OX4
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 GLY 86 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLY 5.6 0.2 - - - -
85A GLY 3.9 1.3 - - - -
86A GLY* 3.3 19.7 - - - -
85B GLY* 1.3 74.6 - - - -
87B THR* 1.3 66.5 + - - +
88B VAL 3.3 2.7 - - - -
89B ILE 3.9 0.4 - - - -
90B PHE* 2.9 34.3 + - - +
268B TYR* 4.0 10.7 - - - -
501B CL 3.5 2.9 - - - -
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Residues in contact with THR 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A TRP* 3.6 37.1 + - + -
85A GLY 2.9 24.3 + - - -
89A ILE* 3.9 10.1 - - - -
40B ILE* 3.9 18.6 - - + -
86B GLY* 1.3 70.8 - - - +
88B VAL* 1.3 60.9 + - + +
90B PHE* 4.1 1.0 - - - +
91B SER* 3.0 29.1 + - - -
268B TYR* 2.8 40.8 + - + +
291B THR* 4.7 5.4 - - + -
501B CL 3.4 0.8 - - - +
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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
----------------------------------------------------------
48A ALA* 4.0 8.5 - - + -
52A ILE* 4.8 0.4 - - + -
88A VAL* 3.9 9.0 - - + -
89A ILE* 3.9 25.4 - - + -
40B ILE* 4.0 13.5 - - + -
45B GLY* 4.9 0.9 - - - +
48B ALA* 3.4 48.9 - - + +
49B ALA* 4.0 2.2 - - - +
52B ILE* 3.6 19.1 - - + +
87B THR* 1.3 73.5 - - - +
89B ILE* 1.3 68.4 + - - +
91B SER* 2.9 21.3 + - - -
92B GLY 3.1 6.9 + - - -
501B CL 3.1 10.7 - - + +
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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
----------------------------------------------------------
44A VAL 5.1 1.3 - - - +
45A GLY* 5.6 0.9 - - - -
87A THR* 3.9 12.8 - - - +
88A VAL* 4.0 13.0 - - + -
52B ILE* 3.9 18.4 - - + -
56B TYR* 3.1 31.8 + - - +
81B TRP* 3.8 26.0 - - + +
82B GLY* 3.8 27.6 - - - +
85B GLY* 3.5 29.2 - - - +
86B GLY 3.4 3.3 + - - +
88B VAL* 1.3 78.8 - - - +
90B PHE* 1.3 67.5 + - + +
92B GLY 3.4 6.2 + - - -
93B ILE* 3.5 11.9 + - + +
501B CL 3.7 3.8 - - + +
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Residues in contact with PHE 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A LEU* 3.8 20.9 - - + -
72B TRP* 3.7 32.1 - + - -
76B PHE* 4.3 9.0 - + - -
82B GLY 4.3 5.6 - - - -
85B GLY* 3.7 22.4 - - - -
86B GLY 2.9 28.5 + - - +
87B THR 4.4 0.4 - - - +
89B ILE* 1.3 74.1 - - + +
91B SER* 1.3 55.9 + - - +
92B GLY 3.2 1.8 - - - -
93B ILE* 3.3 22.9 + - + +
94B SER* 2.6 37.7 + - - -
268B TYR* 3.7 19.1 - - + -
269B SER* 3.8 25.4 - - - -
271B TRP* 5.0 0.2 - + - -
291B THR 3.1 18.8 - - - +
292B CYS 4.7 3.4 - - - -
293B GLY* 4.2 1.7 + - - -
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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
----------------------------------------------------------
38B ALA* 3.9 6.8 - - - +
40B ILE* 3.6 28.6 - - - +
49B ALA* 4.0 12.1 - - - +
52B ILE* 4.2 1.2 - - - +
87B THR 3.0 18.7 + - - -
88B VAL* 2.9 13.6 + - - -
90B PHE* 1.3 76.4 - - - +
92B GLY* 1.3 58.1 + - - +
94B SER* 3.4 1.7 + - - -
95B ALA* 3.0 30.1 + - - +
290B GLY 3.4 21.6 - - - +
291B THR* 4.0 4.4 + - - +
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Residues in contact with GLY 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ILE* 3.7 22.9 - - - -
53B LEU* 3.7 11.3 - - - +
56B TYR* 3.7 15.0 - - - -
88B VAL 3.1 5.9 + - - -
89B ILE 3.4 0.2 + - - -
90B PHE 3.2 0.2 - - - -
91B SER* 1.3 80.6 + - - +
93B ILE* 1.3 63.9 + - - +
96B PHE* 3.3 28.4 + - - -
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B TYR* 3.8 6.3 - - + +
72B TRP* 3.3 48.2 - - + +
75B LEU* 3.8 44.4 - - + +
76B PHE* 4.0 16.4 - - + +
89B ILE* 3.5 16.1 + - + +
90B PHE* 3.3 32.4 + - + +
92B GLY* 1.3 76.1 - - - +
94B SER* 1.3 63.0 + - - +
96B PHE* 3.5 2.4 + - - +
97B ASP* 3.0 22.1 + - + +
293B GLY* 4.6 1.1 - - - +
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Residues in contact with SER 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PHE 2.6 23.7 + - - -
91B SER 3.4 1.1 - - - -
92B GLY 3.3 0.2 - - - -
93B ILE* 1.3 76.0 - - - +
95B ALA* 1.3 64.1 + - - +
97B ASP* 3.2 4.0 + - - +
98B ILE* 3.0 28.3 + - - +
289B LEU 3.2 17.9 - - - -
290B GLY 3.4 16.8 - - - -
291B THR 3.3 7.6 - - - -
293B GLY 2.8 22.8 + - - -
294B GLY* 3.5 11.6 - - - +
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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
----------------------------------------------------------
22B ILE 5.6 0.2 - - - +
24B VAL* 3.6 16.3 - - + +
36B GLY* 3.4 11.3 - - - -
37B GLU 3.6 33.0 - - - +
38B ALA* 3.7 5.2 - - + +
53B LEU* 3.8 20.6 - - + -
91B SER 3.0 13.1 + - - +
93B ILE 3.4 0.2 - - - -
94B SER* 1.3 79.8 - - - +
96B PHE* 1.3 63.0 + - - +
98B ILE* 3.4 1.2 + - - -
99B ALA 3.2 16.1 + - - -
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Residues in contact with PHE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ILE* 3.6 31.0 - - + -
24B VAL* 3.6 24.7 - - + -
26B VAL* 3.8 16.8 - - + -
53B LEU* 3.5 41.5 - - + -
56B TYR* 3.7 18.8 - + + -
57B ALA* 4.1 3.8 - - - -
60B LEU* 3.5 22.7 - - + -
75B LEU* 4.8 4.9 - - + -
92B GLY 3.3 21.8 + - - +
93B ILE 3.5 3.7 + - - +
94B SER 3.3 0.2 - - - -
95B ALA* 1.3 75.1 - - - +
97B ASP* 1.3 65.9 + - - +
99B ALA* 3.1 5.4 + - - +
100B PHE* 2.9 44.8 + + + -
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Residues in contact with ASP 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B THR* 4.1 11.4 - - - +
72B TRP* 4.0 9.0 - - + -
93B ILE 3.0 18.9 + - - +
94B SER 3.5 4.5 - - - +
96B PHE* 1.3 75.5 - - - +
98B ILE* 1.3 62.7 + - - +
100B PHE* 3.2 13.4 + - + +
101B TRP* 3.0 37.9 + - - -
293B GLY 4.0 10.3 - - - +
294B GLY* 4.1 0.2 - - - -
295B PHE 2.8 28.5 + - - -
296B THR* 2.6 35.9 + - - -
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU 3.5 14.8 - - - +
36B GLY* 3.8 6.1 - - - -
37B GLU* 3.8 25.1 - - + +
94B SER 3.0 16.5 + - - +
95B ALA 3.7 5.8 - - - +
96B PHE 3.2 0.2 - - - -
97B ASP* 1.3 74.5 - - - +
99B ALA* 1.3 62.4 + - - +
101B TRP* 3.3 4.7 + - - +
102B ASP* 3.0 20.6 + - - +
289B LEU* 3.8 32.8 - - + +
290B GLY 4.2 0.4 - - - +
294B GLY* 4.2 10.8 - - - -
295B PHE* 3.9 27.7 - - + +
321B VAL* 4.9 2.0 - - + -
322B ALA* 6.1 2.5 - - - -
325B ALA* 4.0 16.6 - - + -
373B ILE* 4.5 6.9 - - + +
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B VAL* 4.4 2.5 - - + -
26B VAL* 3.7 27.4 - - + -
34B GLY* 3.5 8.3 - - - +
35B LEU 3.4 27.3 + - - +
36B GLY 3.8 3.4 - - - +
95B ALA 3.2 7.0 + - - +
96B PHE 3.1 8.2 + - - +
98B ILE* 1.3 80.2 - - - +
100B PHE* 1.3 58.1 + - - +
102B ASP* 3.3 3.6 - - - +
103B ILE* 3.0 31.9 + - - +
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Residues in contact with PHE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ILE* 3.6 26.9 - - + -
26B VAL* 4.1 20.2 - - + -
60B LEU* 4.1 15.7 - - + -
65B PRO* 3.6 30.0 - - + +
68B THR* 3.6 17.5 - - + -
71B ILE* 3.6 35.4 - - + -
75B LEU* 5.8 0.2 - - + -
96B PHE* 2.9 43.4 + + + -
97B ASP* 3.2 12.5 + - + +
99B ALA* 1.3 75.5 - - - +
101B TRP* 1.3 60.1 + - - +
103B ILE* 3.2 8.6 + - + +
104B LYS* 2.9 32.1 + - - +
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Residues in contact with TRP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B THR* 3.9 9.9 - - + +
97B ASP* 3.0 40.0 + - - -
98B ILE 3.7 0.4 - - - +
100B PHE* 1.3 72.5 - - - +
102B ASP* 1.3 65.9 + - - +
104B LYS* 3.2 33.7 + - + +
105B GLY 2.9 20.1 + - - -
112B VAL* 3.4 17.0 - - + +
115B LEU* 3.6 39.6 - - + +
116B LEU* 3.9 19.7 - - + -
295B PHE* 3.4 36.1 - + + +
296B THR* 3.0 30.6 + - - -
299B LYS* 6.4 0.2 - - + -
115C LEU 5.2 0.4 - - - -
117C GLY* 5.7 0.2 - - - -
3403C GOL 3.2 35.2 - - - -
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Residues in contact with ASP 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLY* 3.3 7.8 - - - -
35B LEU* 2.8 32.7 + - - +
98B ILE 3.0 13.2 + - - +
99B ALA 3.3 10.3 - - - +
100B PHE 3.3 0.2 - - - -
101B TRP* 1.3 76.2 - - - +
103B ILE* 1.3 61.8 + - - +
105B GLY 3.3 0.2 + - - -
106B LYS* 3.0 42.8 + - - +
112B VAL* 4.1 4.6 - - - +
372B GLY* 3.3 11.8 - - - -
373B ILE* 2.8 37.5 + - + +
374B GLY 4.4 1.0 + - - -
375B GLN 4.5 3.8 - - - +
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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
----------------------------------------------------------
1B LEU* 3.9 17.0 - - + -
26B VAL* 3.5 39.3 - - + +
28B THR* 3.9 16.6 - - + -
32B ILE* 4.0 14.5 - - + +
33B TYR* 3.6 6.5 - - - -
34B GLY 3.4 18.4 - - - +
65B PRO* 3.8 31.4 - - + -
66B PHE* 5.2 0.4 - - + -
99B ALA 3.0 18.2 + - - +
100B PHE* 3.2 8.0 + - - +
102B ASP* 1.3 75.9 - - - +
104B LYS* 1.3 57.9 + - - +
106B LYS* 3.3 2.5 + - - +
107B ALA* 2.8 28.4 + - - +
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Residues in contact with LYS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B PRO 3.8 8.1 - - - +
66B PHE* 3.9 52.8 + - + -
68B THR* 2.8 44.0 + - - -
100B PHE 2.9 15.3 + - - +
101B TRP* 3.2 45.3 + - + +
103B ILE* 1.3 75.4 - - - +
105B GLY* 1.3 62.9 + - - +
107B ALA* 3.4 2.1 + - - +
108B LEU* 3.0 29.1 + - - +
115B LEU* 3.8 14.4 - - + -
114C LYS 5.0 4.6 + - - +
115C LEU 6.1 0.4 - - - -
117C GLY* 4.4 3.8 - - - +
3403C GOL 4.4 4.6 + - - -
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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 TRP 2.9 13.6 + - - -
102B ASP 3.7 1.1 - - - -
104B LYS* 1.3 76.9 - - - +
106B LYS* 1.3 57.0 + - - +
108B LEU 3.2 1.0 + - - -
109B ASN* 2.9 25.3 + - - -
110B LEU* 2.9 30.8 + - - -
112B VAL* 4.9 1.8 - - - -
115B LEU* 3.6 12.5 - - - +
371B PRO* 4.0 0.2 - - - +
372B GLY* 3.5 9.4 - - - -
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Residues in contact with LYS 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ILE* 3.6 21.9 - - + +
33B TYR* 2.9 59.0 + - - +
35B LEU* 5.4 0.2 - - - +
102B ASP* 3.0 36.9 + - - +
105B GLY* 1.3 73.1 - - - +
107B ALA* 1.3 63.6 + - - +
108B LEU 3.3 0.7 + - - -
109B ASN* 3.3 11.3 + - - +
371B PRO* 4.0 26.9 - - + +
372B GLY 3.6 0.8 - - - +
375B GLN 5.1 7.4 + - - -
376B ASP* 4.9 2.8 + - - -
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B LEU* 4.3 6.1 - - + -
32B ILE* 3.9 24.1 - - + +
66B PHE* 4.0 23.1 - - + -
103B ILE 2.8 20.6 + - - +
104B LYS 3.6 4.7 - - - +
105B GLY 3.3 0.2 - - - -
106B LYS* 1.3 71.8 - - - +
108B LEU* 1.3 65.0 + - + +
109B ASN* 3.8 0.3 + - - +
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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
----------------------------------------------------------
66B PHE* 3.9 28.3 - - + -
104B LYS 3.0 18.3 + - - +
105B GLY 4.1 1.6 - - - +
107B ALA* 1.3 83.9 - - + +
109B ASN* 1.3 69.9 + - - +
110B LEU* 3.4 19.7 + - + +
115B LEU* 3.9 24.9 - - + -
108C LEU* 4.4 28.9 - - + +
110C LEU* 3.8 29.6 - - + -
115C LEU* 4.4 2.5 - - + -
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Residues in contact with ASN 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B GLY 2.9 5.5 + - - -
106B LYS 3.3 10.4 + - - +
107B ALA 3.4 0.6 - - - -
108B LEU* 1.3 80.9 - - - +
110B LEU* 1.3 65.1 + - - +
111B PRO* 4.6 1.7 - - - +
371B PRO* 3.4 27.2 - - - +
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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