Contacts of the helix formed by residues 40 - 66 (chain B) in PDB entry 1VGO
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 ASP 40 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASP* 2.6 34.0 + - - +
235A LEU* 3.6 10.7 - - - +
236A GLY* 5.9 0.4 - - - -
38B VAL* 3.7 3.5 - - + +
39B THR* 1.3 82.1 + - - +
41B LYS* 1.3 65.2 + - - +
43B ALA* 2.9 36.5 + - + +
44B ARG* 3.1 21.3 + - - +
235B LEU* 3.7 10.9 - - + +
236B GLY 2.8 36.4 + - - +
237B GLU* 3.7 5.9 - - - +
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Residues in contact with LYS 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLY 2.6 30.3 + - - -
39A THR* 3.6 20.1 - - + +
39B THR 3.1 3.6 + - - -
40B ASP* 1.3 71.4 + - - +
42B GLU* 1.3 70.4 + - + +
44B ARG* 3.1 19.9 + - - +
45B GLU* 3.6 16.4 + - - +
236B GLY 3.5 10.5 - - - +
237B GLU* 3.1 31.4 + - - +
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Residues in contact with GLU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS* 1.3 78.8 - - + +
43B ALA* 1.3 66.9 + - - +
45B GLU* 2.9 34.4 + - - +
46B TYR* 3.2 27.8 + - + -
107B LYS* 3.2 25.7 + - - +
168B ARG* 4.7 6.4 + - - -
234B ILE 3.4 12.1 - - - +
235B LEU 4.9 0.7 - - - +
236B GLY* 3.0 36.9 + - - +
237B GLU* 3.2 2.1 + - - -
238B THR* 3.0 30.6 + - - +
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 3.6 13.2 - - + -
40B ASP* 2.9 34.6 + - + +
42B GLU* 1.3 76.1 - - - +
44B ARG* 1.3 61.7 + - - +
46B TYR* 3.4 3.6 + - - +
47B TYR* 3.2 28.4 + - - -
234B ILE* 3.0 35.8 + - + +
235B LEU* 4.4 4.9 - - + -
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Residues in contact with ARG 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A THR* 5.4 0.7 - - - -
35B GLY 3.9 13.1 + - - -
36B TRP* 4.5 2.8 + - - +
38B VAL* 2.9 35.2 + - + +
39B THR 3.8 10.3 - - - -
40B ASP 3.1 11.9 + - - +
41B LYS* 3.5 10.3 - - - +
42B GLU 3.0 0.6 - - - -
43B ALA* 1.3 75.2 - - - +
45B GLU* 1.3 63.0 + - + +
47B TYR* 3.8 7.3 - - - +
48B ALA* 3.2 23.2 + - - +
402B SO4 3.4 33.6 + - - -
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Residues in contact with GLU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LYS* 3.6 14.7 + - - +
42B GLU* 2.9 33.4 + - - +
44B ARG* 1.3 76.0 - - - +
46B TYR* 1.3 68.4 + - + +
48B ALA* 3.4 4.8 + - - +
49B ILE* 3.1 37.4 + - + +
104B LEU* 4.3 19.2 - - + +
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Residues in contact with TYR 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLU* 3.2 34.9 + - + -
43B ALA 3.4 5.4 + - - +
45B GLU* 1.3 79.5 - - + +
47B TYR* 1.3 55.9 + - - +
49B ILE* 3.7 1.3 - - - +
50B THR* 2.6 37.4 + - - -
101B ASP* 3.4 43.7 - - - +
104B LEU* 3.1 43.9 + - + +
105B LEU* 3.1 21.2 + - + +
107B LYS* 5.7 0.5 - - - -
168B ARG* 4.9 2.4 + - - -
228B LEU* 4.4 3.6 - - + -
229B LEU* 3.9 9.9 - - + -
233B ALA 4.7 1.6 + - - -
234B ILE* 3.2 49.4 - - + -
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Residues in contact with TYR 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE* 3.2 32.5 - + - -
34B ARG* 3.0 42.3 + - + +
35B GLY* 3.4 19.7 - - - +
38B VAL* 3.7 24.6 - - + +
43B ALA 3.2 22.8 + - - -
44B ARG* 3.8 9.6 - - - +
46B TYR* 1.3 78.3 - - - +
48B ALA* 1.3 55.2 + - - +
50B THR* 4.6 0.2 - - - -
51B ILE* 2.7 49.1 + - + +
229B LEU* 3.5 38.5 + - + +
234B ILE* 4.0 14.8 - - + -
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ARG 3.2 14.8 + - - +
45B GLU* 3.7 7.0 - - - +
46B TYR 3.4 0.2 - - - -
47B TYR* 1.3 79.6 - - - +
49B ILE* 1.3 64.3 + - + +
51B ILE* 3.9 8.5 - - - +
52B LEU* 3.2 27.9 + - - +
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Residues in contact with ILE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLU* 3.1 22.7 + - + +
46B TYR 3.7 2.5 - - - +
48B ALA* 1.3 79.7 - - + +
50B THR* 1.3 64.1 + - - +
52B LEU* 3.3 23.8 + - - +
53B VAL* 3.6 8.1 + - - +
97B LEU* 3.4 41.8 - - + +
100B LEU* 4.3 17.3 - - + -
101B ASP* 3.7 14.6 - - - +
104B LEU* 3.5 32.1 - - + -
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Residues in contact with THR 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE* 4.3 6.1 - - + -
46B TYR 2.6 25.8 + - - -
47B TYR 3.9 0.4 - - - -
49B ILE* 1.3 70.2 - - - +
51B ILE* 1.3 61.0 + - - +
53B VAL* 3.0 14.1 + - + +
54B PRO* 2.8 28.2 - - - +
98B LEU* 5.6 0.9 - - + -
101B ASP* 2.9 24.4 + - - +
221B LYS 4.9 2.5 - - - +
224B PHE* 5.2 3.1 - - + -
225B GLY* 3.7 23.1 - - - -
228B LEU* 3.6 8.3 - - + +
229B LEU* 3.6 28.4 - - + +
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Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B THR* 3.9 7.8 - - + +
31B PHE* 3.7 28.2 - - + +
32B ILE* 3.6 48.0 - - + +
35B GLY* 5.6 1.6 - - - -
47B TYR* 2.7 38.9 + - + +
48B ALA* 3.9 8.7 - - - +
50B THR* 1.3 72.9 - - - +
52B LEU* 1.3 68.5 + - + +
53B VAL 3.2 0.2 + - - -
54B PRO* 3.4 8.1 - - - +
55B GLY* 3.1 19.3 + - - -
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Residues in contact with LEU 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ALA 3.2 17.5 - - - +
49B ILE* 3.3 12.3 + - - +
50B THR 3.1 0.8 - - - -
51B ILE* 1.3 82.7 - - + +
53B VAL* 1.3 57.9 + - - +
55B GLY* 3.6 3.1 - - - +
56B ILE* 2.7 47.5 + - + +
97B LEU* 3.9 23.1 - - + -
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ILE 3.6 11.7 - - - +
50B THR* 3.0 16.8 + - + +
52B LEU* 1.3 80.5 - - - +
54B PRO* 1.3 72.1 - - + +
57B ALA* 3.0 19.2 + - - +
94B THR* 3.5 28.7 + - + -
97B LEU* 3.8 24.2 - - + +
98B LEU* 4.0 24.7 - - + +
101B ASP* 5.3 0.4 - - - +
221B LYS* 3.5 30.7 - - + +
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Residues in contact with PRO 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B MET* 3.3 33.4 - - + +
28B THR* 3.2 23.5 + - - +
31B PHE* 3.9 27.1 - - + -
50B THR 2.8 25.6 - - - +
51B ILE 3.4 6.3 - - - +
53B VAL* 1.3 83.7 - - + +
55B GLY* 1.3 63.5 + - - +
57B ALA* 3.9 2.0 - - + -
58B SER* 2.9 21.0 + - - -
221B LYS* 4.7 7.0 - - + +
222B VAL* 4.3 10.1 - - + -
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Residues in contact with GLY 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B THR* 3.2 18.5 + - - -
51B ILE 3.1 15.9 + - - -
52B LEU* 3.6 4.5 - - - -
53B VAL 3.0 1.4 - - - -
54B PRO* 1.3 76.5 - - - +
56B ILE* 1.3 61.4 + - - +
58B SER* 2.8 22.8 + - - -
59B ALA* 3.4 8.2 + - - +
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Residues in contact with ILE 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LEU* 2.7 35.1 + - + +
53B VAL 4.0 2.2 - - - +
55B GLY* 1.3 71.5 - - - -
57B ALA* 1.3 61.8 + - - +
59B ALA* 3.3 9.2 + - + +
60B ALA* 3.1 20.3 + - + +
90B ASP* 4.7 12.8 - - - -
93B PHE* 4.0 31.0 - - + -
94B THR* 4.2 9.9 - - - +
97B LEU* 3.8 24.7 - - + -
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B MET* 3.4 35.7 - - + -
53B VAL 3.0 17.4 + - - +
55B GLY 3.1 0.2 - - - -
56B ILE* 1.3 79.9 - - - +
58B SER* 1.3 57.3 + - - +
60B ALA* 3.2 1.7 + - - +
61B TYR* 3.0 34.5 + - - -
90B ASP* 3.6 14.6 - - - +
94B THR* 4.5 0.2 + - - -
221B LYS* 3.6 16.6 - - + -
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Residues in contact with SER 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B THR* 3.7 19.3 - - - +
24B MET* 3.6 20.4 - - - +
25B LEU* 4.0 23.5 - - - +
28B THR* 4.5 1.0 + - - -
54B PRO 2.9 13.0 + - - -
55B GLY* 2.8 22.0 + - - -
57B ALA* 1.3 75.4 - - - +
59B ALA* 1.3 57.5 + - - +
61B TYR* 3.8 5.3 - - - +
62B LEU* 3.1 27.0 + - - +
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLY 3.4 6.5 + - - +
56B ILE* 3.3 12.7 + - + +
57B ALA 3.2 0.6 - - - -
58B SER* 1.3 79.6 + - - +
60B ALA* 1.3 63.5 + - - +
62B LEU* 3.8 8.5 + - - +
63B ALA* 3.5 20.1 + - - +
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Residues in contact with ALA 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ILE* 3.1 11.1 + - + +
57B ALA 3.2 6.9 + - - +
59B ALA* 1.3 77.1 - - - +
61B TYR* 1.3 58.9 + - - +
62B LEU 3.4 0.2 - - - -
63B ALA* 3.5 1.2 + - - -
64B MET* 3.0 35.7 + - + +
86B ALA* 3.5 20.7 - - + +
90B ASP* 3.6 34.1 - - + +
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Residues in contact with TYR 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B LEU* 3.4 34.5 - - + +
20B GLY* 3.7 25.1 - - - -
21B THR* 3.4 17.8 + - - +
24B MET* 4.5 11.0 - - + -
57B ALA 3.0 25.4 + - - +
58B SER* 3.8 4.3 - - - +
59B ALA 3.3 0.2 - - - -
60B ALA* 1.3 76.9 - - - +
62B LEU* 1.3 58.9 + - - +
64B MET* 3.4 28.0 + - + +
65B PHE* 2.8 30.0 + - - +
87B ARG* 5.6 2.8 + - - -
90B ASP* 4.2 10.1 - - - -
210B THR* 6.2 0.9 - - + -
213B PHE* 4.2 1.7 - - - +
214B MET* 3.3 32.0 + - + +
217B ASP* 2.7 32.2 + - + +
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B THR* 3.7 20.1 + - + -
58B SER 3.1 17.4 + - - +
59B ALA* 4.0 8.5 - - - +
61B TYR* 1.3 76.0 - - - +
63B ALA* 1.3 63.7 + - - +
65B PHE* 3.2 9.4 - - + +
66B PHE* 3.1 58.7 + - + -
68B ILE* 6.0 0.9 - - + -
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Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ALA 3.5 11.9 + - - +
60B ALA* 3.7 8.7 - - - +
61B TYR 3.2 0.2 - - - -
62B LEU* 1.3 78.3 - - - +
64B MET* 1.3 60.3 + - - +
66B PHE 3.2 2.3 + - - -
67B GLY 3.0 4.2 + - - -
68B ILE* 2.7 57.9 + - + +
69B GLY 4.9 1.8 - - - +
86B ALA* 4.3 11.9 - - + -
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Residues in contact with MET 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ARG* 2.7 32.4 + - - -
17B LEU* 3.1 29.8 - - + +
60B ALA* 3.0 21.8 + - + +
61B TYR* 3.4 46.2 - - + +
63B ALA* 1.3 75.7 - - - +
65B PHE* 1.3 51.7 + - - +
67B GLY* 3.0 3.5 + - - -
68B ILE 4.7 0.7 - - - +
69B GLY 5.4 1.3 - - - +
84B TYR* 3.8 30.4 - - + -
86B ALA* 3.6 15.3 - - + -
87B ARG* 3.8 42.0 - - + +
90B ASP* 5.3 0.4 - - - +
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Residues in contact with PHE 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LEU* 3.9 20.4 - - + -
7B LEU* 3.2 45.4 - - + +
11B ARG* 3.2 11.4 + - - -
14B THR* 3.3 40.2 - - - +
17B LEU* 3.8 8.7 - - + -
18B GLY* 3.9 17.0 - - - -
21B THR* 4.5 3.8 - - - +
61B TYR 2.8 19.4 + - - +
62B LEU* 3.2 13.9 - - + +
63B ALA 3.1 0.2 - - - -
64B MET* 1.3 72.4 - - - +
66B PHE* 1.3 84.2 + + - +
67B GLY 2.9 7.9 + - - -
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Residues in contact with PHE 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.9 19.3 - - + +
11B ARG* 4.1 3.7 + - - -
62B LEU* 3.1 53.9 + - + -
65B PHE* 1.3 96.3 - + - +
67B GLY* 1.3 63.5 + - - +
68B ILE* 3.2 28.3 + - + +
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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