Contacts of the helix formed by residues 1 - 30 (chain C) in PDB entry 2ONK
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 MET 1 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ARG* 1.3 71.5 + - + +
3C LEU* 3.2 8.1 - - - +
4C LEU* 3.3 41.8 - - + +
5C PHE* 4.1 1.9 + - - +
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Residues in contact with ARG 2 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B PRO* 4.2 17.8 - - - +
68B GLU* 3.2 31.1 + - - +
69B ARG* 4.1 30.3 - - - +
1C MET* 1.3 79.8 - - + +
3C LEU* 1.3 62.1 + - + +
4C LEU 3.0 2.2 - - - -
5C PHE* 3.1 9.0 + - + +
6C SER* 2.7 30.8 + - - -
163D ARG* 4.7 4.9 - - - +
168D SER* 4.9 7.5 - - - -
169D PRO* 4.3 25.3 - - + +
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Residues in contact with LEU 3 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET 3.2 5.5 - - - +
2C ARG* 1.3 79.4 - - + +
4C LEU* 1.3 58.2 + - + +
6C SER* 3.7 14.6 - - - +
7C ALA* 2.6 39.4 + - + +
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Residues in contact with LEU 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 3.3 39.5 - - + +
2C ARG 3.0 0.4 - - - -
3C LEU* 1.3 82.5 - - + +
5C PHE* 1.3 57.3 + - - +
7C ALA* 4.2 3.0 - - + +
8C LEU* 2.8 29.9 + - - +
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Residues in contact with PHE 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET 4.1 0.8 + - - +
2C ARG* 3.1 11.6 + - + +
4C LEU* 1.3 75.0 - - - +
6C SER* 1.3 68.2 + - - +
7C ALA 3.1 1.3 - - - -
8C LEU* 3.6 19.0 - - + +
9C LEU* 3.1 64.6 + - + +
74D TYR* 5.5 3.1 - + - -
169D PRO* 4.3 12.8 - - + -
170D LEU* 3.1 63.0 - - + -
173D PHE* 3.9 23.6 - + + -
174D PHE* 3.9 9.6 - + - -
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Residues in contact with SER 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C ARG* 2.7 18.2 + - - -
3C LEU* 3.9 16.9 - - - +
5C PHE* 1.3 83.0 - - - +
7C ALA* 1.3 57.4 + - - +
9C LEU* 4.3 4.6 - - - +
10C ALA* 3.3 22.1 + - - +
75D ILE* 5.6 0.9 - - - +
79D LYS* 4.0 21.2 + - - +
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Residues in contact with ALA 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LEU* 2.6 24.6 + - + +
4C LEU* 4.2 3.8 - - + +
6C SER* 1.3 73.6 - - - +
8C LEU* 1.3 55.7 + - - +
9C LEU 3.1 1.8 - - - -
10C ALA* 3.5 6.2 - - - +
11C LEU* 2.5 40.6 + - + +
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Residues in contact with LEU 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU 2.8 21.0 + - - +
5C PHE* 3.6 26.2 - - + +
7C ALA* 1.3 76.4 - - - +
9C LEU* 1.3 61.0 + - + +
11C LEU* 3.6 10.5 - - + +
12C LEU* 3.0 54.1 + - + +
174D PHE* 6.3 1.8 - - + -
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Residues in contact with LEU 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C PHE* 3.1 58.9 + - + +
6C SER* 4.3 5.4 - - - +
8C LEU* 1.3 84.0 - - + +
10C ALA* 1.3 56.7 + - - +
12C LEU* 5.6 2.5 - - + -
13C SER* 2.6 35.9 + - - -
71D PRO* 3.7 30.3 - - + +
74D TYR* 4.2 23.1 - - + -
75D ILE* 4.3 17.4 - - + +
79D LYS* 5.9 4.3 - - - +
173D PHE* 4.9 10.3 - - + -
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Residues in contact with ALA 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C SER 3.3 19.3 + - - +
7C ALA* 3.0 8.4 + - - +
9C LEU* 1.3 78.9 - - - +
11C LEU* 1.3 57.5 + - - +
13C SER* 3.0 7.2 + - - -
14C SER* 2.9 31.2 + - - -
75D ILE* 4.3 8.5 - - + +
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Residues in contact with LEU 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C ALA* 2.5 22.3 + - + +
8C LEU* 3.6 11.0 - - + +
10C ALA* 1.3 69.6 - - - +
12C LEU* 1.3 74.3 + - + +
14C SER* 2.6 25.9 + - - +
15C ILE* 3.1 26.9 - - + +
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Residues in contact with LEU 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LEU* 3.0 37.0 + - + +
9C LEU* 3.9 3.1 - - + +
11C LEU* 1.3 85.2 - - + +
13C SER* 1.3 58.7 + - - +
15C ILE* 3.2 17.0 + - + +
16C ILE* 2.9 19.2 - - - +
67D ILE* 3.6 22.0 - - + +
68D PHE* 3.3 34.2 - - + -
71D PRO* 3.9 21.1 - - + -
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Residues in contact with SER 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU 2.6 24.6 + - - -
10C ALA* 3.0 15.6 + - - -
12C LEU* 1.3 72.5 - - - +
14C SER* 1.3 59.6 + - - +
15C ILE 3.0 5.6 - - - -
16C ILE* 3.1 20.0 - - - +
17C LEU* 3.3 21.1 - - - +
68D PHE 4.1 2.0 + - - -
71D PRO* 4.4 0.4 - - - +
72D LEU* 3.5 41.9 - - - +
75D ILE* 3.8 7.7 - - - +
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Residues in contact with SER 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ALA 2.9 16.5 + - - -
11C LEU* 2.6 31.0 + - - +
13C SER* 1.3 74.7 + - - +
15C ILE* 1.3 65.1 + - - +
17C LEU* 3.8 13.9 - - - +
18C LEU* 3.1 29.6 + - - +
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Residues in contact with ILE 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU* 3.1 35.0 - - + +
12C LEU* 3.2 11.4 - - + +
13C SER 3.0 0.4 - - - -
14C SER* 1.3 77.3 - - - +
16C ILE* 1.3 58.1 + - - +
17C LEU 2.9 3.1 - - - -
18C LEU* 2.6 35.8 + - + +
19C PHE* 2.8 13.1 + - + -
68D PHE* 3.6 28.5 - - + -
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Residues in contact with ILE 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU 2.9 27.1 - - - +
13C SER* 3.1 18.6 - - - +
15C ILE* 1.3 72.9 - - - +
17C LEU* 1.3 60.7 + - - +
19C PHE* 3.6 17.7 - - + -
20C VAL* 3.0 28.4 + - - +
64D ILE* 5.9 2.0 - - + +
65D ALA* 5.9 2.2 - - - -
68D PHE* 3.1 46.0 - - + +
69D GLY* 4.2 5.6 - - - +
72D LEU* 4.7 10.3 - - + -
136D LEU* 5.0 7.0 - - + -
140D VAL* 3.9 37.7 - - + -
144D ILE* 5.5 0.7 - - + -
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Residues in contact with LEU 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C SER* 3.3 24.3 + - - +
14C SER* 3.8 11.2 - - - +
15C ILE 2.8 1.0 + - - -
16C ILE* 1.3 80.2 - - - +
18C LEU* 1.3 59.7 + - + +
20C VAL* 3.6 0.4 + - - -
21C LEU* 2.9 28.8 + - - +
72D LEU* 4.1 12.6 - - + -
87D VAL* 3.8 39.9 - - + +
90D ILE* 3.6 42.5 - - + +
91D VAL* 4.1 11.7 - - + -
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Residues in contact with LEU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C SER* 3.1 17.0 - - - +
15C ILE* 2.6 20.1 + - + +
17C LEU* 1.3 73.2 - - + +
19C PHE* 1.3 60.7 + - - +
21C LEU* 4.0 14.1 - - + -
22C LEU* 2.5 46.5 + - + +
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Residues in contact with PHE 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ILE* 2.8 10.4 + - + +
16C ILE* 3.5 20.9 - - + +
18C LEU* 1.3 76.4 - - - +
20C VAL* 1.3 69.3 + - + +
22C LEU* 5.0 1.8 - - - -
23C PRO* 2.9 29.1 - - - +
106D LEU* 4.4 4.5 - - + -
110D PHE* 4.3 13.7 - + - -
133D VAL* 3.4 52.5 - - + -
136D LEU* 3.4 30.5 - - + -
137D PHE* 3.4 33.8 - + + -
140D VAL* 4.7 0.4 - - + -
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Residues in contact with VAL 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ILE 3.0 17.6 + - - +
17C LEU 3.8 3.1 - - - +
19C PHE* 1.3 89.9 - - + +
21C LEU* 1.3 60.3 + - - +
23C PRO* 4.3 0.2 - - - -
24C VAL* 3.4 21.0 - - - +
90D ILE* 3.3 28.3 - - + +
91D VAL* 5.1 2.7 - - - +
93D LEU* 3.4 5.9 - - + +
94D PRO* 3.4 26.5 - - + -
137D PHE* 3.6 17.3 - - + +
140D VAL* 4.3 23.8 - - + -
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Residues in contact with LEU 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU 2.9 18.7 + - - +
18C LEU* 2.8 18.2 + - + +
20C VAL* 1.3 79.2 - - - +
22C LEU* 1.3 68.1 + - - +
23C PRO 3.3 0.5 - - - -
24C VAL* 3.3 3.6 + - + +
25C ALA* 2.7 42.4 + - + +
90D ILE* 3.9 26.0 - - + -
93D LEU* 3.9 19.1 - - + -
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Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C LEU* 2.5 27.3 + - + +
19C PHE* 4.4 2.2 - - - +
21C LEU* 1.3 71.9 - - - +
23C PRO* 1.3 63.9 - - + +
25C ALA* 4.2 4.5 - - + -
26C ALA* 2.6 49.0 + - + +
109D VAL* 4.1 21.5 - - + -
115D LEU* 5.1 15.0 - - + -
116D ILE* 4.2 16.6 - - + -
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Residues in contact with PRO 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PHE 2.9 28.9 - - - +
20C VAL 4.0 7.4 - - - +
21C LEU 3.6 0.2 - - - -
22C LEU* 1.3 89.7 - - + +
24C VAL* 1.3 71.6 + - - +
26C ALA* 3.0 4.7 + - - +
27C THR* 2.9 21.9 + - - +
105D ALA* 3.5 28.0 - - + +
106D LEU* 4.0 14.8 - - + +
109D VAL* 3.5 21.7 - - + -
110D PHE* 5.7 2.7 - - + -
137D PHE* 4.2 13.7 - - + -
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Residues in contact with VAL 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C VAL 3.4 20.9 - - - +
21C LEU* 3.8 3.8 - - + +
23C PRO* 1.3 75.5 - - + +
25C ALA* 1.3 66.6 + - - +
27C THR* 3.5 4.0 + - - -
28C VAL* 3.3 23.4 + - + +
237C ILE* 3.5 40.6 - - + -
241C LEU* 5.6 1.6 - - + -
93D LEU* 3.9 21.1 - - + -
97D ILE* 3.4 29.6 - - + -
105D ALA* 4.1 4.9 - - + +
137D PHE* 3.9 12.3 - - + -
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Residues in contact with ALA 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C LEU* 2.7 45.4 + - + +
22C LEU* 3.3 6.1 - - + +
23C PRO 2.9 0.4 + - - -
24C VAL* 1.3 72.6 - - - +
26C ALA* 1.3 65.4 + - - +
28C VAL* 2.9 17.6 + - - +
29C THR* 2.9 17.3 + - - +
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Residues in contact with ALA 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LEU* 2.6 33.0 + - + +
23C PRO* 3.0 4.9 + - + +
25C ALA* 1.3 72.1 - - - +
27C THR* 1.3 56.0 + - + +
29C THR* 2.7 31.2 + - - -
30C LEU* 2.9 23.0 + - + +
108D VAL* 4.8 7.0 - - + +
109D VAL* 4.6 9.4 - - + -
115D LEU* 5.9 6.5 - - + -
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Residues in contact with THR 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C PRO 2.9 18.8 + - - +
24C VAL 4.0 0.4 - - - +
26C ALA* 1.3 74.5 - - - +
28C VAL* 1.3 64.0 + - - +
30C LEU* 3.7 2.1 + - - +
31C GLN* 3.3 28.0 + - - +
230C MET* 4.3 21.3 - - - +
233C ALA* 4.9 6.1 - - - +
234C ALA* 4.3 8.2 + - - -
237C ILE* 3.3 22.0 - - - +
104D ILE* 5.8 0.9 - - - -
105D ALA* 3.5 33.9 - - + -
108D VAL* 4.1 15.0 - - + +
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Residues in contact with VAL 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C VAL* 3.3 16.4 + - + +
25C ALA* 2.9 7.4 + - - +
27C THR* 1.3 74.6 + - - +
29C THR* 1.3 69.4 + - - +
31C GLN* 3.2 14.7 + - + +
32C LEU* 4.6 3.5 - - - +
38C PHE* 5.9 0.2 - - + -
234C ALA* 4.0 13.5 - - + -
237C ILE* 3.8 32.3 - - + -
238C LEU* 3.3 38.1 - - + -
241C LEU* 6.3 0.2 - - + -
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Residues in contact with THR 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ALA* 2.9 18.3 + - - +
26C ALA* 2.7 19.0 + - - -
28C VAL* 1.3 72.8 - - - +
30C LEU* 1.3 65.6 + - + +
31C GLN 2.6 13.3 + - - -
32C LEU* 2.9 35.3 + - + +
33C PHE* 4.9 9.4 - - + -
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ALA* 2.9 17.2 + - + +
27C THR 4.1 4.9 - - - +
29C THR* 1.3 86.8 - - + +
31C GLN* 1.3 59.4 + - - +
32C LEU 2.9 8.1 + - - -
33C PHE* 3.2 44.1 + - + +
34C ASN* 3.7 8.8 + - - +
230C MET* 4.0 25.4 - - + -
108D VAL* 4.0 16.6 - - + -
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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