Contacts of the helix formed by residues 41 - 66 (chain B) in PDB entry 2ONF
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 TYR 41 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 4.6 7.9 - + - -
27B VAL* 3.8 5.2 - - - -
28B ASP* 3.3 15.9 - - + +
29B SER 3.5 13.7 - - - -
30B PRO* 3.6 13.0 - - + -
31B PRO* 3.4 15.6 - - + +
36B PRO 2.6 29.1 + - - -
37B GLU* 3.4 4.0 + - - -
38B GLY 3.2 20.4 + - - -
39B GLN* 3.2 29.7 + - + -
40B LEU* 1.3 79.9 - - - +
42B PRO* 1.4 71.8 - - - +
43B GLU* 3.5 19.1 - - + +
44B THR* 3.2 23.8 + - + +
45B LEU* 2.9 23.2 + - - +
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Residues in contact with PRO 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A VAL* 3.7 23.1 - - + -
52A SER* 4.2 2.2 - - - +
53A CYS* 4.1 36.8 - - + +
56A THR* 4.5 7.9 - - + +
121A PHE* 4.1 11.0 - - + -
122A ILE* 4.1 2.0 - - + -
27B VAL* 3.6 15.7 - - + -
28B ASP 3.0 24.5 - - - +
29B SER* 5.0 1.6 - - - -
41B TYR* 1.4 75.4 - - - +
43B GLU* 1.3 66.9 + - - +
46B PHE* 2.9 34.8 + - - +
90B PHE* 4.5 0.3 - - - -
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Residues in contact with GLU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 3.5 51.1 - - + +
121A PHE* 3.1 33.5 - - + -
30B PRO* 3.4 31.9 - - - +
33B PHE* 3.7 11.6 - - - -
41B TYR* 3.1 4.6 - - + +
42B PRO* 1.3 90.9 - - - +
44B THR* 1.3 56.3 + - - +
47B PRO* 3.3 20.4 - - - +
80B LEU* 4.1 7.6 - - + -
90B PHE* 4.0 14.0 - - + -
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Residues in contact with THR 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 3.8 33.2 - - + -
5A GLU 4.3 10.8 - - - +
6A SER* 4.0 3.5 + - - -
20A VAL* 3.8 32.4 - - + +
40B LEU* 4.3 3.1 - - - -
41B TYR* 3.2 30.6 + - + -
43B GLU* 1.3 74.8 - - - +
45B LEU* 1.3 65.7 + - - +
46B PHE 3.5 0.4 - - - -
47B PRO* 3.6 3.8 - - - +
48B SER* 2.6 34.2 + - - -
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Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 4.7 13.7 - - + -
20A VAL* 4.8 1.1 - - + -
25A ILE* 3.7 26.0 - - + -
45A LEU* 5.1 13.9 - - + -
49A VAL* 4.1 22.9 - - + -
25B ILE* 4.5 4.5 - - + -
27B VAL* 3.5 33.9 - - + -
40B LEU* 3.7 31.9 - - + -
41B TYR 2.9 15.6 + - - +
44B THR* 1.3 78.3 + - - +
46B PHE* 1.3 59.6 + - - +
48B SER* 3.4 2.1 + - - -
49B VAL* 2.9 37.3 + - + +
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Residues in contact with PHE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A PHE* 3.2 44.4 - + + +
49A VAL* 4.1 6.7 - - + +
122A ILE* 3.8 31.2 - - + -
125A ALA* 4.8 7.2 - - + -
42B PRO 2.9 16.0 + - - +
45B LEU* 1.3 76.1 - - - +
47B PRO* 1.4 72.7 - - + +
49B VAL* 3.2 5.6 + - + -
50B LEU* 3.0 21.5 + - + +
90B PHE* 4.1 17.9 - + + -
93B ILE* 4.3 16.2 - - + -
122B ILE* 3.8 17.5 - - + -
126B ILE* 3.5 35.2 - - + -
130B VAL* 5.8 0.4 - - + -
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Residues in contact with PRO 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A SER* 5.3 0.4 - - - +
43B GLU 3.3 30.1 - - - +
44B THR* 3.6 7.0 - - - +
46B PHE* 1.4 98.4 - - + +
48B SER* 1.3 59.1 + - - +
50B LEU* 3.4 10.9 - - + +
51B ALA* 3.1 21.8 + - - +
76B VAL* 3.6 25.4 - - + +
78B ALA* 3.4 23.3 - - + -
90B PHE* 4.2 9.2 - - + -
93B ILE* 3.9 14.6 - - + -
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Residues in contact with SER 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A SER* 2.7 28.4 + - - -
8A VAL* 3.6 11.7 - - - +
18A VAL* 3.7 28.1 - - - +
20A VAL* 4.1 1.0 - - - +
44B THR 2.6 24.6 + - - -
45B LEU* 3.5 8.1 - - - -
46B PHE 3.2 0.2 - - - -
47B PRO* 1.3 76.5 - - - +
49B VAL* 1.3 58.8 + - - +
51B ALA* 3.2 1.7 + - - -
52B SER* 2.8 30.9 + - - -
76B VAL* 4.7 0.2 - - - -
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Residues in contact with VAL 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 5.6 1.1 - - + -
27A VAL* 4.9 5.4 - - + -
42A PRO* 3.7 25.1 - - + -
45A LEU* 3.5 34.5 - - + -
46A PHE* 4.0 15.7 - - + +
49A VAL* 5.4 1.3 - - + -
45B LEU* 2.9 22.3 + - + +
46B PHE* 3.8 6.1 - - - +
48B SER* 1.3 74.6 - - - +
50B LEU* 1.3 65.5 + - - +
52B SER* 3.4 6.3 + - - +
53B CYS* 2.9 23.2 + - - +
122B ILE* 3.5 20.2 - - + -
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PHE* 3.0 15.1 + - + +
47B PRO* 3.4 8.1 - - + +
49B VAL* 1.3 77.8 - - - +
51B ALA* 1.3 55.8 + - - +
53B CYS* 3.2 3.1 + - - +
54B LEU* 2.9 27.0 + - + +
93B ILE* 4.0 32.5 - - + -
95B ILE* 4.1 10.1 - - + -
120B CYS* 4.2 0.9 - - - -
122B ILE* 3.7 23.6 - - + +
123B SER* 3.4 44.4 - - - +
126B ILE* 3.8 22.2 - - + -
132B GLU* 3.7 14.6 - - - +
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Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 3.9 13.3 - - + +
47B PRO 3.1 8.7 + - - +
48B SER 3.7 6.7 - - - +
50B LEU* 1.3 71.6 - - - +
52B SER* 1.3 64.9 + - - +
54B LEU* 3.5 5.1 + - - +
55B LEU* 3.1 23.7 + - - +
72B TRP* 5.3 1.6 + - - -
74B SER* 4.3 2.7 - - - +
76B VAL* 3.5 31.9 - - + -
95B ILE* 3.9 24.9 - - + +
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Residues in contact with SER 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 3.4 9.6 - - - +
16A THR* 2.9 26.2 + - - +
18A VAL* 3.3 25.6 - - - +
27A VAL* 3.8 20.7 - - - +
42A PRO* 4.7 2.2 - - - -
48B SER 2.8 12.5 + - - -
49B VAL* 3.8 5.6 - - - -
50B LEU 3.3 0.2 - - - -
51B ALA* 1.3 76.4 - - - +
53B CYS* 1.3 56.7 + - - +
55B LEU* 3.3 3.2 + - - +
56B THR* 2.9 34.5 + - - +
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Residues in contact with CYS 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A PRO* 4.0 14.9 - - + +
49B VAL 2.9 19.5 + - - +
50B LEU 3.6 3.8 - - - +
52B SER* 1.3 68.5 - - - +
54B LEU* 1.3 57.6 + - - +
56B THR* 3.2 8.4 + - - -
57B THR* 2.8 41.7 + - - -
120B CYS* 3.5 19.5 - - - -
121B PHE* 3.6 28.3 - - - -
122B ILE* 3.9 21.5 - - + -
140B COA 4.7 6.7 - - - -
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Residues in contact with LEU 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 2.9 16.9 + - + +
51B ALA* 3.6 6.7 - - - +
53B CYS* 1.3 74.6 - - - +
55B LEU* 1.3 58.1 + - - +
57B THR* 3.4 2.3 + - - -
58B PHE* 2.9 27.0 + - - +
72B TRP* 4.5 17.0 - - + -
95B ILE* 4.1 24.2 - - + -
97B VAL* 4.8 0.4 - - + -
113B MSE 4.9 4.0 - - + +
116B ALA* 3.9 6.9 - - + +
117B GLU* 3.6 43.1 - - + +
120B CYS* 3.7 12.9 - - + -
123B SER* 4.8 3.1 - - - +
132B GLU* 5.0 1.1 - - - +
134B VAL* 3.8 35.4 - - + -
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 4.4 5.2 - - + -
9A SER 3.8 2.7 - - - +
10A TRP* 3.7 28.7 - - + +
16A THR* 3.4 33.2 - - + -
51B ALA 3.1 14.1 + - - +
52B SER 3.6 2.5 - - - +
54B LEU* 1.3 79.2 - - - +
56B THR* 1.3 58.8 + - - +
58B PHE* 3.0 4.1 + - + +
59B LEU* 2.9 50.4 + - + +
72B TRP* 3.6 52.5 - - + +
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Residues in contact with THR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 4.1 12.2 + - - +
16A THR* 3.6 21.8 - - + -
28A ASP* 4.3 1.8 - - - -
29A SER* 3.2 38.4 + - - +
42A PRO* 4.8 2.5 - - + +
52B SER* 2.9 20.7 + - - +
53B CYS* 3.2 13.5 + - - -
55B LEU* 1.3 75.0 - - - +
57B THR* 1.3 58.7 + - - +
59B LEU* 3.4 12.0 + - + +
60B GLU 3.4 15.1 + - - -
140B COA 3.3 30.8 - - - +
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Residues in contact with THR 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B CYS* 2.8 26.7 + - - -
54B LEU 3.7 1.8 - - - -
56B THR* 1.3 69.0 + - - +
58B PHE* 1.3 67.0 + - - +
60B GLU* 3.2 12.5 + - - +
61B PHE* 3.3 31.0 + - + -
116B ALA* 3.4 31.9 - - - +
119B TYR* 3.9 9.8 + - + +
120B CYS* 3.5 23.9 - - - +
121B PHE* 4.7 0.7 + - - -
140B COA 3.8 26.4 + - + +
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Residues in contact with PHE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU 2.9 15.1 + - - +
55B LEU 3.3 8.7 - - - +
57B THR* 1.3 76.8 - - - +
59B LEU* 1.3 59.2 + - + +
61B PHE* 3.0 6.0 + - - +
62B LYS* 2.7 58.0 + - + -
67B ILE* 4.7 1.8 - - + -
69B LEU* 4.1 13.2 - - + -
72B TRP* 3.3 34.3 - + + -
99B ILE* 5.1 2.0 - - + -
109B ILE* 4.0 22.4 - - + -
112B ALA* 3.6 35.7 - - + -
113B MSE 3.6 30.3 - - + -
116B ALA* 3.6 12.2 - - + +
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TRP* 3.7 24.7 - - + +
13A ASP 3.5 19.7 - - - +
14A ARG* 3.7 27.4 - - - +
15A ARG 4.7 0.4 - - - +
55B LEU* 2.9 32.6 + - + +
56B THR* 3.7 16.6 - - + +
57B THR 3.2 0.8 - - - -
58B PHE* 1.3 78.6 - - + +
60B GLU* 1.3 61.9 + - - +
62B LYS* 3.3 15.6 + - - +
63B ASP* 3.0 27.5 + - - -
69B LEU* 3.4 33.2 - - + -
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Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 3.0 35.3 + - - +
56B THR 3.4 3.8 + - - -
57B THR 3.2 11.9 + - - +
59B LEU* 1.3 79.4 - - - +
61B PHE* 1.3 58.8 + - + +
63B ASP* 3.4 2.9 + - - +
64B ARG* 2.8 69.6 + - - +
140B COA 3.9 43.1 - - + +
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Residues in contact with PHE 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B THR* 3.3 34.0 + - + -
58B PHE* 3.0 6.5 + - - +
60B GLU* 1.3 75.1 - - + +
62B LYS* 1.3 56.3 + - - +
64B ARG* 3.6 10.9 - - - -
65B MSE 2.8 45.5 + - - +
67B ILE* 5.0 0.7 - - - -
112B ALA* 4.5 17.5 - - + +
115B LEU* 3.8 41.3 - - + -
116B ALA* 4.0 13.0 - - - -
119B TYR* 4.1 7.2 - + + -
140B COA 3.5 71.1 - + + -
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Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A TRP* 4.4 14.5 - - - -
13A ASP* 5.5 2.2 + - - +
14A ARG* 5.7 0.8 - - - +
58B PHE* 2.7 35.2 + - + +
59B LEU* 3.4 29.5 - - - +
61B PHE* 1.3 72.3 - - - +
63B ASP* 1.3 85.2 + - - +
65B MSE 3.4 0.3 + - - -
66B GLY 3.1 3.8 + - - -
67B ILE* 3.0 69.4 + - + +
69B LEU* 3.9 26.9 - - + +
112B ALA* 5.4 0.2 - - - +
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Residues in contact with ASP 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 2.8 31.8 + - - +
59B LEU 3.0 9.3 + - - +
60B GLU* 3.8 6.7 - - - +
62B LYS* 1.3 106.0 + - - +
64B ARG* 1.3 64.0 + - + +
65B MSE 3.3 0.5 + - - -
66B GLY* 3.3 11.4 + - - -
67B ILE 5.4 0.4 - - - -
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Residues in contact with ARG 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLU* 2.8 49.2 + - - +
61B PHE* 3.2 13.4 + - - +
63B ASP* 1.3 79.3 - - + +
65B MSE 1.3 58.5 + - - +
66B GLY 3.4 0.6 + - - -
140B COA 3.0 96.9 + - + +
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Residues in contact with MSE 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B PHE* 2.8 28.0 + - + +
64B ARG* 1.3 72.6 - - + +
66B GLY* 1.3 63.5 + - - +
67B ILE* 3.3 12.6 - - + -
108B LYS* 3.0 55.3 + - + +
111B ARG* 3.9 22.0 - - + -
112B ALA* 3.8 30.7 - - - -
115B LEU* 4.8 2.5 - - - -
140B COA 3.4 35.7 - - + +
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Residues in contact with GLY 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LYS 3.1 4.5 + - - -
63B ASP* 3.3 10.6 + - - -
64B ARG 3.4 1.4 + - - -
65B MSE 1.3 79.1 - - - +
67B ILE* 1.3 61.7 + - - +
68B ASN* 3.7 9.9 + - - -
105B ASP* 3.5 4.7 - - - +
108B LYS* 3.4 13.7 + - - -
----------------------------------------------------------
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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