Contacts of the helix formed by residues 71 - 96 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ARG* 4.4 0.9 - - - +
69C SER 4.1 8.3 - - - +
70C SER* 1.3 74.8 - - - +
72C PRO* 1.3 77.6 - - + +
73C VAL* 3.6 32.5 - - + -
74C MET* 3.0 56.2 + - + +
75C ASN* 3.0 16.3 + - - -
317C MET* 6.3 1.1 - - + -
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Residues in contact with PRO 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ARG* 4.3 8.5 - - - +
24C TYR* 4.0 4.9 - - - +
71C PHE* 1.3 86.5 - - + +
73C VAL* 1.3 64.4 + - + +
75C ASN* 3.1 2.9 + - - +
76C TYR* 2.9 30.4 + - + -
306C GLN* 3.3 38.8 - - + +
307C PHE 3.5 28.5 - - - +
308C LEU* 4.5 9.4 - - + -
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Residues in contact with VAL 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C PHE* 3.2 21.5 + - + -
72C PRO* 1.3 76.6 - - + +
74C MET* 1.3 57.2 + - - +
76C TYR* 3.5 3.6 + - - +
77C GLY* 3.0 23.4 + - - -
308C LEU* 3.5 26.2 - - + -
310C GLU* 4.5 6.3 - - + +
313C GLU* 4.3 11.2 - - + +
314C LEU* 3.8 37.4 - - + +
317C MET* 4.2 23.1 - - + -
318C GLN* 4.7 1.6 + - - -
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Residues in contact with MET 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C CYS* 5.0 19.0 - - - -
66C ALA* 5.0 6.7 - - + +
69C SER* 4.3 4.5 - - - +
70C SER* 3.9 17.5 - - - -
71C PHE* 3.0 64.5 + - + +
73C VAL* 1.3 77.5 - - - +
75C ASN* 1.3 60.7 + - - +
77C GLY* 3.0 4.0 + - - -
78C THR* 2.8 33.3 + - - +
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Residues in contact with ASN 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C CYS* 4.6 2.4 - - - +
18C ALA* 3.7 14.3 - - - +
19C ALA* 4.0 10.2 + - - +
22C VAL* 4.1 5.7 - - - +
24C TYR* 3.3 31.2 - - + -
70C SER* 3.7 25.8 + - - -
71C PHE 3.0 16.8 + - - -
72C PRO 3.5 6.1 - - - +
74C MET* 1.3 74.5 - - - +
76C TYR* 1.3 60.5 + - - +
78C THR* 3.3 6.5 + - - +
79C TYR* 2.9 30.1 + - - +
306C GLN* 3.0 30.3 + - - +
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Residues in contact with TYR 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C TYR* 3.6 24.0 - + - -
72C PRO* 2.9 26.6 + - + -
73C VAL 3.5 9.0 - - - +
75C ASN* 1.3 74.1 - - - +
77C GLY* 1.3 66.3 + - - +
79C TYR* 3.3 3.5 + - - +
80C LEU* 3.0 33.3 + - + +
290C PHE* 3.6 35.8 - + - -
299C ARG 4.7 1.1 + - - -
302C LEU* 3.6 42.2 + - + +
303C ARG* 3.8 13.0 + - - +
306C GLN 5.4 3.2 + - - -
308C LEU* 4.0 32.5 - - + +
314C LEU* 3.5 27.8 - - + -
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Residues in contact with GLY 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C VAL 3.0 12.4 + - - -
74C MET* 3.0 6.1 + - - -
76C TYR* 1.3 74.9 - - - +
78C THR* 1.3 56.8 - - - +
80C LEU* 3.8 1.6 - - - +
81C ARG* 3.0 32.8 + - - +
231C TYR* 4.3 5.8 + - - -
318C GLN* 3.3 32.1 - - - +
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Residues in contact with THR 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C CYS* 3.2 48.8 + - + +
16C LYS* 3.9 15.0 - - + +
19C ALA* 3.9 13.0 - - + -
25C LEU* 4.5 0.4 - - + -
74C MET 2.8 15.6 + - - -
75C ASN* 3.7 6.5 + - - -
76C TYR 3.2 0.2 - - - -
77C GLY* 1.3 75.8 - - - +
79C TYR* 1.3 62.8 + - - +
81C ARG* 3.5 11.4 - - - +
82C THR* 2.8 39.1 + - - +
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Residues in contact with TYR 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ALA* 4.9 0.4 - - - +
24C TYR* 3.4 39.3 - - + -
25C LEU* 3.9 17.2 - - + +
27C SER* 3.9 1.3 - - - -
30C LEU* 3.3 15.8 - - - +
75C ASN 2.9 18.3 + - - +
76C TYR* 3.7 4.3 - + - +
78C THR* 1.3 77.2 - - - +
80C LEU* 1.3 70.1 + - + +
82C THR* 3.3 0.9 + - - -
83C VAL* 2.8 61.3 + - + +
290C PHE* 5.6 0.7 - + - -
294C ILE* 3.7 15.5 - - + +
298C GLU* 2.6 38.6 + - - +
301C ARG* 3.7 3.8 - - - -
302C LEU* 3.7 28.3 - - + -
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Residues in contact with LEU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C TYR* 3.0 25.4 + - + +
77C GLY 3.8 2.9 - - - +
79C TYR* 1.3 82.9 - - + +
81C ARG* 1.3 59.5 + - - +
83C VAL* 3.9 2.7 - - - +
84C GLY* 2.8 28.9 + - - -
286C MET* 3.2 40.0 - - + +
287C TRP* 6.3 0.2 - - + -
289C ILE* 4.3 4.3 - - + +
290C PHE* 3.8 45.8 - - + +
294C ILE* 3.8 19.3 - - + -
314C LEU* 5.0 2.2 - - + -
318C GLN* 3.7 27.6 - - + +
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Residues in contact with ARG 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASP* 5.6 3.2 + - - -
12C ALA* 3.7 30.7 - - - +
15C CYS* 5.9 7.0 - - - +
77C GLY 3.0 18.3 + - - +
78C THR* 3.5 13.0 - - - +
80C LEU* 1.3 75.9 - - - +
82C THR* 1.3 59.0 + - - +
84C GLY* 4.0 0.2 - - - -
85C ILE* 3.1 35.2 + - - +
201C GLU* 2.5 43.6 + - - +
202C CYS* 3.7 30.3 - - - +
231C TYR* 3.4 44.8 + - + -
286C MET* 3.8 3.1 - - - +
321C TYR* 5.9 1.6 - - - -
323C LEU* 5.1 0.2 - - - +
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Residues in contact with THR 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LYS* 3.1 35.6 + - - +
25C LEU* 3.8 11.6 - - + +
31C GLN* 3.4 23.8 - - - +
41C TYR* 3.9 4.5 - - - +
78C THR* 2.8 22.1 + - - +
79C TYR 3.8 2.7 - - - -
81C ARG* 1.3 76.1 - - - +
83C VAL* 1.3 63.0 + - - +
85C ILE 3.5 0.3 + - - -
86C ASP* 2.9 34.1 + - - +
111C ARG* 3.8 11.6 + - - +
201C GLU* 5.1 0.9 + - - -
2004C PO4 3.9 6.3 - - - +
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Residues in contact with VAL 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C LEU* 3.8 14.6 - - + -
27C SER* 3.7 30.5 - - - +
30C LEU* 3.9 15.6 - - + +
31C GLN* 4.4 5.8 - - + -
79C TYR* 2.8 39.3 + - + +
80C LEU* 3.9 4.9 - - - +
82C THR* 1.3 69.9 - - - +
84C GLY* 1.3 60.3 + - - +
86C ASP* 4.1 5.3 - - - +
87C ALA* 2.8 37.6 + - - +
289C ILE* 5.6 0.4 - - + -
294C ILE* 3.6 30.3 - - + -
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Residues in contact with GLY 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LEU 2.8 19.2 + - - -
81C ARG 4.0 0.7 - - - -
83C VAL* 1.3 79.0 - - - +
85C ILE* 1.3 60.2 + - - +
87C ALA* 3.9 3.4 - - - +
88C ALA* 3.2 19.2 + - - +
286C MET* 4.9 2.9 - - - -
289C ILE* 5.0 8.5 - - - -
293C GLN* 6.2 0.4 - - - -
323C LEU* 3.4 28.7 - - - +
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Residues in contact with ILE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ARG* 3.1 21.4 + - + +
84C GLY* 1.3 73.8 - - - +
86C ASP* 1.3 64.1 + - - +
88C ALA* 3.3 4.5 + - - +
89C ILE* 3.1 32.0 + - + +
111C ARG* 3.6 28.7 - - - +
199C ILE* 4.5 11.0 - - + -
201C GLU* 3.5 45.1 - - + +
229C ILE* 3.9 19.2 - - + +
231C TYR* 4.1 10.5 - - + -
323C LEU* 3.7 18.8 - - + +
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Residues in contact with ASP 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C GLN* 2.7 47.7 - - + +
41C TYR* 5.2 0.2 - - - -
82C THR* 2.9 24.9 + - - +
83C VAL 4.1 1.3 - - - +
85C ILE* 1.3 76.0 - - - +
87C ALA* 1.3 58.8 + - - +
89C ILE* 3.2 9.9 + - - +
90C LEU* 2.9 37.7 + - + +
111C ARG* 2.7 37.0 + - - +
115C LEU* 6.0 1.1 - - - +
2004C PO4 4.8 4.2 + - - -
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Residues in contact with ALA 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 4.2 21.9 + - + +
83C VAL 2.8 24.1 + - - +
84C GLY* 3.9 4.3 - - - +
86C ASP* 1.3 72.0 - - - +
88C ALA* 1.3 57.8 + - - +
90C LEU* 3.3 4.7 + - - +
91C GLU* 3.1 30.5 + - - +
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Residues in contact with ALA 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C GLY 3.2 13.5 + - - +
85C ILE 3.5 9.0 - - - +
86C ASP 3.2 0.2 - - - -
87C ALA* 1.3 73.1 - - - +
89C ILE* 1.3 63.5 + - - +
91C GLU* 3.7 9.3 + - - +
92C PHE 3.3 15.8 + - - -
227C LEU* 3.5 12.6 - - + +
229C ILE* 3.6 20.9 - - + -
323C LEU* 4.9 0.7 - - + -
325C LYS* 3.6 34.0 - - + +
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Residues in contact with ILE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ILE* 3.1 20.2 + - + +
86C ASP* 3.2 11.2 + - - +
88C ALA* 1.3 73.6 - - - +
90C LEU* 1.3 64.5 + - + +
92C PHE* 3.3 4.3 + - - +
93C LEU* 3.1 41.1 + - + +
101C VAL* 5.4 1.6 - - + -
111C ARG* 3.6 31.9 - - - +
115C LEU* 4.0 26.5 - - + -
197C ILE* 3.8 21.3 - - + +
199C ILE* 3.7 17.3 - - + -
229C ILE* 3.5 16.6 - - + -
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Residues in contact with LEU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C GLY 5.4 0.2 - - - +
30C LEU 3.3 26.2 - - - +
31C GLN* 3.5 22.9 - - - +
32C ARG* 3.9 19.4 + - + +
86C ASP* 2.9 25.5 + - + +
87C ALA* 3.3 4.5 + - - +
89C ILE* 1.3 73.5 - - + +
91C GLU* 1.3 61.8 + - - +
93C LEU* 3.3 6.0 + - - +
94C VAL* 3.2 25.9 + - - +
115C LEU* 4.5 7.9 - - + -
118C MET* 4.2 13.9 - - + -
119C PHE* 3.8 33.1 - - + -
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Residues in contact with GLU 91 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ALA 3.1 17.0 + - - +
88C ALA* 3.7 9.4 - - - +
90C LEU* 1.3 74.8 - - - +
92C PHE* 1.3 64.4 + - - +
94C VAL* 3.2 24.3 + - + +
95C ALA* 3.6 6.2 + - - +
325C LYS* 4.2 19.1 + - - +
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Residues in contact with PHE 92 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ALA 3.3 1.6 + - - -
89C ILE 3.3 8.4 + - - +
91C GLU* 1.3 80.1 - - - +
93C LEU* 1.3 56.0 - - - +
95C ALA* 3.4 2.7 + - - -
96C ASN* 2.8 69.3 + - + +
99C VAL* 3.8 21.3 - - + -
195C PRO* 3.9 15.5 - - + -
196C THR 4.5 0.4 - - - -
197C ILE* 3.5 21.3 - - + -
225C HIS* 5.2 1.3 - - + -
226C GLY* 3.9 24.7 - - - -
227C LEU* 3.6 43.3 - - + -
327C GLN* 4.1 21.5 - - + +
328C TRP 5.7 0.7 - - - -
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Residues in contact with LEU 93 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ILE* 3.1 37.8 + - + +
90C LEU* 3.6 9.2 - - - +
91C GLU 3.1 0.4 - - - -
92C PHE* 1.3 75.6 - - - +
94C VAL* 1.3 67.7 + - - +
96C ASN 3.3 30.3 + - - +
97C GLU* 3.8 9.0 + - - +
99C VAL* 3.5 20.9 - - + -
115C LEU* 4.2 1.3 - - + -
119C PHE* 3.5 55.9 - - + -
122C LEU* 3.7 22.7 - - + -
197C ILE* 4.4 4.3 - - + -
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Residues in contact with VAL 94 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ARG* 4.5 16.8 - - - +
90C LEU 3.2 15.8 + - - +
91C GLU* 3.5 11.7 - - + +
93C LEU* 1.3 79.0 - - - +
95C ALA* 1.3 62.4 + - + +
97C GLU* 5.0 5.9 + - - +
119C PHE* 5.3 0.4 - - - -
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Residues in contact with ALA 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C GLU 3.6 5.1 + - - +
92C PHE* 3.4 4.7 + - - +
93C LEU 3.3 0.2 - - - -
94C VAL* 1.3 79.9 - - + +
96C ASN* 1.3 75.0 + - - +
97C GLU 4.1 1.2 + - - -
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Residues in contact with ASN 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C PHE* 2.8 54.3 + - + +
93C LEU* 3.3 16.3 + - - +
95C ALA* 1.3 92.4 - - - +
97C GLU* 1.3 59.2 + - - +
98C LYS 3.5 2.2 - - - +
99C VAL* 2.8 34.5 - - + +
195C PRO* 3.6 23.9 - - + +
327C GLN* 5.6 0.4 + - - -
----------------------------------------------------------
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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