Contacts of the helix formed by residues 1 - 31 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 6.2 2.0 - - - +
2D ARG* 1.3 71.6 + - + +
3D LEU* 3.3 9.3 - - - +
4D LEU* 3.3 40.9 - - + +
5D PHE* 4.1 1.6 + - - +
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Residues in contact with ARG 2 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PRO* 2.8 42.8 - - - +
68A GLU* 2.5 35.0 + - - +
69A ARG* 4.2 19.1 - - - +
163C ARG* 4.2 6.6 - - - +
168C SER* 5.2 3.8 - - - -
169C PRO* 4.2 24.3 - - + +
1D MET* 1.3 79.2 - - + +
3D LEU* 1.3 62.0 + - + +
4D LEU 3.0 2.2 - - - -
5D PHE* 3.1 10.2 + - + +
6D SER* 2.7 30.6 + - - -
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Residues in contact with LEU 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MET 3.3 5.7 - - - +
2D ARG* 1.3 79.2 - - - +
4D LEU* 1.3 58.4 + - + +
6D SER* 3.7 12.8 - - - +
7D ALA* 2.7 40.1 + - + +
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Residues in contact with LEU 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MET* 3.3 39.7 - - + +
2D ARG 3.0 0.2 - - - -
3D LEU* 1.3 82.6 - - + +
5D PHE* 1.3 56.5 + - - +
7D ALA* 4.2 3.4 - - + +
8D LEU* 2.8 30.0 + - - +
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Residues in contact with PHE 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C TYR* 5.5 3.6 - + - -
169C PRO* 4.0 16.6 - - + -
170C LEU* 3.3 60.8 - - + +
173C PHE* 3.8 26.7 - + + -
174C PHE* 4.2 8.7 - + - -
1D MET 4.1 1.3 + - - +
2D ARG* 3.1 11.8 + - + +
4D LEU* 1.3 75.2 - - - +
6D SER* 1.3 67.7 + - - +
7D ALA 3.1 1.6 - - - -
8D LEU* 3.6 18.1 - - + +
9D LEU* 3.1 63.9 + - + +
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Residues in contact with SER 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ILE* 5.6 1.0 - - - +
79C LYS* 4.0 21.3 + - - +
2D ARG* 2.7 18.9 + - - -
3D LEU* 3.9 16.7 - - - +
5D PHE* 1.3 82.2 - - - +
7D ALA* 1.3 56.7 + - - +
9D LEU* 4.3 5.4 - - - +
10D ALA* 3.3 21.9 + - - +
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Residues in contact with ALA 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LEU* 2.7 24.1 + - + +
4D LEU* 4.2 4.3 - - + +
6D SER* 1.3 73.2 - - - +
8D LEU* 1.3 56.3 + - - +
9D LEU 3.1 1.6 - - - -
10D ALA* 3.5 6.0 - - - +
11D LEU* 2.5 40.1 + - + +
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Residues in contact with LEU 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170C LEU* 5.9 0.9 - - + -
174C PHE* 6.2 2.9 - - + -
4D LEU 2.8 21.6 + - - +
5D PHE* 3.6 25.4 - - + +
7D ALA* 1.3 77.6 - - - +
9D LEU* 1.3 61.1 - - + +
11D LEU* 3.7 9.9 - - + +
12D LEU* 3.0 54.2 + - + +
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Residues in contact with LEU 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C PRO* 3.8 28.8 - - + +
74C TYR* 4.2 24.7 - - + -
75C ILE* 4.3 15.5 - - + -
79C LYS* 6.0 4.3 - - - +
173C PHE* 4.9 12.1 - - + -
5D PHE* 3.1 56.9 + - + +
6D SER* 4.3 5.6 - - - +
8D LEU* 1.3 87.0 - - + +
10D ALA* 1.3 54.3 + - - +
12D LEU* 5.6 2.2 - - + -
13D SER* 2.7 36.2 + - - -
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Residues in contact with ALA 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ILE* 4.3 9.6 - - + +
6D SER 3.3 18.8 + - - +
7D ALA* 3.0 8.2 + - - +
9D LEU* 1.3 80.0 - - - +
11D LEU* 1.3 56.5 + - - +
13D SER* 3.1 7.9 + - - -
14D SER* 2.9 30.5 + - - -
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Residues in contact with LEU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ALA* 2.5 23.0 + - + +
8D LEU* 3.7 11.9 - - + +
10D ALA* 1.3 69.7 - - - +
12D LEU* 1.3 75.3 + - + +
14D SER* 2.6 26.0 + - - +
15D ILE* 3.1 26.7 - - + +
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Residues in contact with LEU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ILE* 3.6 22.2 - - + +
68C PHE* 3.3 33.7 - - + -
71C PRO* 3.8 20.4 - - + -
8D LEU* 3.0 36.8 + - + +
9D LEU* 3.9 3.8 - - + +
11D LEU* 1.3 87.6 - - + +
13D SER* 1.3 59.6 + - - +
15D ILE* 3.2 15.2 + - + +
16D ILE* 2.9 18.6 - - - +
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Residues in contact with SER 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C PHE 4.0 1.5 + - - -
71C PRO 4.2 0.4 - - - -
72C LEU* 3.5 42.3 - - - +
75C ILE* 3.7 8.9 - - - +
9D LEU 2.7 23.6 + - - -
10D ALA* 3.1 15.6 + - - -
12D LEU* 1.3 72.9 - - - +
14D SER* 1.3 59.3 + - - +
15D ILE 3.0 5.6 - - - -
16D ILE* 3.1 20.5 - - - +
17D LEU* 3.3 21.0 + - - +
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Residues in contact with SER 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ALA 2.9 16.3 + - - -
11D LEU* 2.6 31.4 + - - +
13D SER* 1.3 76.2 + - - +
15D ILE* 1.3 63.9 + - - +
17D LEU* 3.8 13.7 - - - +
18D LEU* 3.2 29.9 + - - +
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Residues in contact with ILE 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C PHE* 3.5 28.7 - - + -
11D LEU* 3.1 34.5 - - + +
12D LEU* 3.2 11.4 - - + +
13D SER 3.0 0.4 - - - -
14D SER* 1.3 77.6 - - - +
16D ILE* 1.3 58.2 + - - +
17D LEU 2.9 2.9 - - - -
18D LEU* 2.6 35.5 + - + +
19D PHE* 2.8 12.7 + - + +
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Residues in contact with ILE 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C ILE* 5.8 3.1 - - + +
65C ALA* 5.8 2.0 - - - -
68C PHE* 3.0 45.8 - - + +
69C GLY* 4.0 5.2 - - - +
72C LEU* 4.7 7.2 - - + -
136C LEU* 5.3 4.7 - - + -
140C VAL* 3.8 38.1 - - + -
144C ILE* 5.2 4.0 - - + -
12D LEU 2.9 26.9 - - - +
13D SER* 3.1 18.4 - - - +
15D ILE* 1.3 73.2 - - - +
17D LEU* 1.3 60.3 + - - +
19D PHE* 3.7 17.3 - - + -
20D VAL* 3.0 28.4 + - - +
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Residues in contact with LEU 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LEU* 4.0 14.6 - - + -
87C VAL* 3.8 44.6 - - + +
90C ILE* 3.6 36.5 - - + +
91C VAL* 4.1 12.8 - - + -
13D SER* 3.3 23.7 + - - +
14D SER* 3.8 11.0 - - - +
15D ILE 2.9 1.0 - - - -
16D ILE* 1.3 81.2 - - - +
18D LEU* 1.3 59.3 + - + +
20D VAL 3.6 0.2 + - - -
21D LEU* 3.0 29.2 + - - +
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Residues in contact with LEU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D SER* 3.2 17.5 - - - +
15D ILE* 2.6 20.1 + - + +
17D LEU* 1.3 73.2 - - + +
19D PHE* 1.3 60.8 + - - +
21D LEU* 2.8 14.8 + - + -
22D LEU* 2.5 46.0 + - + +
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Residues in contact with PHE 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU* 4.5 3.1 - - + -
110C PHE* 4.0 32.8 - + - -
116C ILE* 6.3 0.9 - - + -
133C VAL* 3.6 31.4 - - + -
136C LEU* 3.4 33.7 - - + -
137C PHE* 3.4 33.8 - + + -
140C VAL* 4.5 0.4 - - + -
15D ILE* 2.8 10.1 + - + +
16D ILE* 3.5 24.0 - - + +
18D LEU* 1.3 76.4 - - - +
20D VAL* 1.3 69.3 + - + +
22D LEU* 5.0 2.0 - - - -
23D PRO* 2.9 29.1 - - - +
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Residues in contact with VAL 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C ILE* 3.2 29.6 - - + +
91C VAL* 5.6 3.1 - - - +
93C LEU* 3.4 13.9 - - + +
94C PRO* 3.4 27.6 - - + -
137C PHE* 3.7 14.4 - - + +
140C VAL* 4.2 24.0 - - + -
16D ILE 3.0 16.9 + - - +
17D LEU* 4.1 3.1 - - - +
19D PHE* 1.3 90.8 - - + +
21D LEU* 1.3 60.1 + - - +
23D PRO* 4.3 0.7 - - - -
24D VAL* 3.4 12.5 - - - +
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Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C ILE* 3.8 27.1 - - + -
93C LEU* 3.9 18.8 - - + -
17D LEU 3.0 17.8 + - - +
18D LEU* 2.8 18.2 + - + +
20D VAL* 1.3 79.0 - - - +
22D LEU* 1.3 66.9 + - - +
23D PRO 3.3 0.3 - - - -
24D VAL* 3.3 3.8 + - + +
25D ALA* 2.7 43.4 + - + +
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Residues in contact with LEU 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C VAL* 4.1 7.4 - - + -
115C LEU* 3.9 27.4 - - + -
116C ILE* 3.4 37.5 - - + -
18D LEU* 2.5 29.0 + - + +
19D PHE* 4.4 2.0 - - - +
21D LEU* 1.3 72.9 - - - +
23D PRO* 1.3 63.7 - - + +
25D ALA* 4.2 4.5 - - + -
26D ALA* 2.6 40.6 + - + +
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Residues in contact with PRO 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ALA* 3.6 26.9 - - + +
106C LEU* 4.1 16.2 - - + +
109C VAL* 3.6 21.0 - - + -
110C PHE* 5.7 3.6 - - + -
137C PHE* 4.0 19.5 - - + -
19D PHE 2.9 29.2 - - - +
20D VAL 4.1 2.0 - - - +
21D LEU 3.6 0.2 - - - -
22D LEU* 1.3 89.3 - - + +
24D VAL* 1.3 71.4 + - - +
26D ALA* 3.0 5.0 + - - +
27D THR* 2.9 22.1 + - - +
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Residues in contact with VAL 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C LEU* 3.8 20.6 - - + -
97C ILE* 3.4 29.2 - - + -
105C ALA* 4.2 4.0 - - + +
137C PHE* 3.9 12.6 - - + -
20D VAL 3.4 21.3 - - - +
21D LEU* 3.3 3.8 + - + +
23D PRO* 1.3 74.7 - - - +
25D ALA* 1.3 66.6 + - - +
27D THR* 3.5 3.7 + - - -
28D VAL* 3.3 23.4 + - - +
237D ILE* 3.4 43.7 - - + -
241D LEU* 5.5 1.6 - - + -
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Residues in contact with ALA 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU* 2.7 44.8 + - + +
22D LEU* 3.3 6.1 - - + +
23D PRO 2.9 0.2 + - - -
24D VAL* 1.3 74.6 - - - +
26D ALA* 1.3 63.6 - - - +
28D VAL* 2.9 18.0 + - - +
29D THR* 2.9 17.7 + - - +
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Residues in contact with ALA 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C VAL* 4.9 5.4 - - + -
109C VAL* 4.3 11.4 - - + -
115C LEU* 4.2 24.7 - - + -
22D LEU* 2.6 25.1 + - + +
23D PRO 3.0 2.7 + - - +
25D ALA* 1.3 72.5 - - - +
27D THR* 1.3 66.6 + - - +
29D THR* 2.7 22.6 + - - -
30D LEU* 2.9 22.7 + - + +
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Residues in contact with THR 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ILE* 5.8 0.7 - - - -
105C ALA* 3.5 37.9 - - + +
108C VAL* 4.1 10.7 - - + +
23D PRO 2.9 18.1 + - - +
24D VAL 3.5 0.8 + - - +
26D ALA* 1.3 74.3 - - - +
28D VAL* 1.3 64.3 + - - +
30D LEU* 3.7 2.1 + - - +
31D GLN* 3.3 28.2 + - - +
230D MET* 4.4 21.1 - - - -
233D ALA* 4.9 5.2 - - - +
234D ALA* 4.1 10.2 + - - +
237D ILE* 3.3 21.5 - - - +
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Residues in contact with VAL 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D VAL 3.3 16.2 - - - +
25D ALA* 2.9 6.9 + - - +
27D THR* 1.3 73.9 + - - +
29D THR* 1.3 69.6 + - - +
31D GLN* 3.2 14.2 + - + +
32D LEU* 4.6 3.6 - - - +
234D ALA* 4.0 13.0 - - + -
237D ILE* 3.7 32.5 - - + -
238D LEU* 3.2 39.7 - - + -
241D LEU* 6.2 0.4 - - + -
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Residues in contact with THR 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ALA* 2.9 18.0 + - - +
26D ALA* 2.7 19.2 + - - -
28D VAL* 1.3 73.7 - - - +
30D LEU* 1.3 64.3 + - + +
31D GLN 2.6 13.2 + - - -
32D LEU* 2.9 35.2 + - + +
33D PHE* 4.6 8.7 - - + -
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Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C VAL* 4.0 27.8 - - + -
115C LEU* 5.8 12.3 - - + -
26D ALA* 2.9 19.8 + - + +
27D THR 4.1 4.5 - - - +
29D THR* 1.3 82.9 - - + +
31D GLN* 1.3 60.8 + - - +
32D LEU 2.8 7.8 + - - -
33D PHE* 3.1 44.2 + - + +
34D ASN* 3.7 8.3 + - - +
230D MET* 4.1 13.7 - - + -
----------------------------------------------------------
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Residues in contact with GLN 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D THR 3.3 10.5 + - - +
28D VAL* 3.2 12.8 + - + +
29D THR 2.6 6.4 + - - -
30D LEU* 1.3 77.4 + - - +
32D LEU* 1.3 59.5 + - - -
34D ASN* 4.1 10.1 + - - +
35D PHE* 3.5 25.7 - - - -
38D PHE* 3.5 35.8 + - + +
230D MET* 3.7 31.1 - - - +
231D PRO* 3.5 29.6 - - - +
234D ALA* 3.3 28.9 - - + -
----------------------------------------------------------
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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