Contacts of the helix formed by residues 3 - 34 (chain D) in PDB entry 3BVI
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 SER 3 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D LEU* 1.3 73.1 - - - +
4D LYS* 1.3 59.6 + - - +
5D ASP* 3.8 6.3 + - - +
6D ILE* 3.3 25.3 + - - +
7D ILE* 2.9 29.9 + - - +
111D SER* 4.8 9.2 + - - -
113D ASP* 5.1 3.3 + - - -
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Residues in contact with LYS 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D LEU 4.0 0.4 + - - -
3D SER* 1.3 72.9 - - - +
5D ASP* 1.3 61.2 + - - +
7D ILE* 3.4 15.4 + - + +
8D LYS* 3.0 27.5 + - - +
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Residues in contact with ASP 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D SER* 3.3 5.8 + - - +
4D LYS* 1.3 79.5 - - - +
6D ILE* 1.3 63.3 + - + +
8D LYS* 3.2 13.1 + - - +
9D LEU* 3.1 33.1 + - + +
107D HIS* 5.7 7.4 - - + -
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Residues in contact with ILE 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D LEU* 4.0 13.2 - - + -
3D SER* 3.3 19.7 + - - +
5D ASP* 1.3 75.5 - - + +
7D ILE* 1.3 60.9 + - - +
9D LEU* 3.4 3.5 + - + +
10D LEU* 2.9 50.3 + - + +
104D ILE* 4.2 19.3 - - + +
107D HIS* 4.4 8.1 - - + +
108D ALA* 4.0 34.8 - - + +
111D SER* 4.1 12.8 - - - +
113D ASP* 3.8 24.2 - - + +
116D THR* 4.2 5.2 - - + +
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Residues in contact with ILE 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0D PRO* 3.9 24.0 - - + -
2D LEU* 3.5 31.6 - - + +
3D SER 2.9 17.4 + - - +
4D LYS* 3.5 15.7 - - + +
6D ILE* 1.3 77.0 - - - +
8D LYS* 1.3 59.5 + - - +
10D LEU* 3.4 5.8 + - - +
11D ASN* 2.9 39.6 + - - +
61D LEU* 5.1 0.6 - - - +
66D VAL* 3.6 30.3 - - + -
67D PRO* 4.9 3.6 - - + +
69D GLN* 4.3 9.9 - - - +
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Residues in contact with LYS 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LYS 3.0 14.1 + - - +
5D ASP* 3.2 17.7 + - - +
7D ILE* 1.3 79.8 - - - +
9D LEU* 1.3 64.4 + - + +
11D ASN* 3.4 5.0 + - - +
12D GLU* 2.6 62.2 + - + +
69D GLN* 5.6 2.7 - - - +
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Residues in contact with LEU 9 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ASP* 3.1 25.1 + - + +
6D ILE* 3.9 5.8 - - + +
8D LYS* 1.3 83.4 - - + +
10D LEU* 1.3 58.5 + - - +
12D GLU* 3.5 22.7 + - - +
13D GLN* 3.0 27.7 + - - +
103D ASN* 4.0 18.2 - - - +
104D ILE* 3.9 33.2 - - + +
107D HIS* 3.8 42.4 - - + +
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Residues in contact with LEU 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D LEU* 3.8 19.1 - - + -
6D ILE* 2.9 41.1 + - + +
7D ILE 3.9 1.3 - - - +
9D LEU* 1.3 77.5 - - - +
11D ASN* 1.3 62.2 + - - +
13D GLN* 3.2 6.2 + - + +
14D VAL* 3.1 27.0 + - - +
57D LEU* 4.5 17.2 - - + +
60D PHE* 4.1 16.4 - - + -
61D LEU* 3.9 21.1 - - + -
104D ILE* 4.1 25.8 - - + -
116D THR* 4.4 5.6 - - + -
119D PHE* 5.8 0.4 - - + -
120D LEU* 4.3 18.6 - - + -
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Residues in contact with ASN 11 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D ILE* 2.9 29.9 + - - +
8D LYS* 3.8 4.5 - - - +
10D LEU* 1.3 73.1 - - - +
12D GLU* 1.3 64.9 + - - +
14D VAL* 3.2 8.1 + - - +
15D ASN* 2.9 28.9 + - - -
61D LEU* 3.6 11.3 - - - +
66D VAL* 4.4 3.6 - - - +
67D PRO 3.2 13.9 + - - -
68D VAL* 3.4 10.4 - - - +
69D GLN* 2.9 61.8 + - + +
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Residues in contact with GLU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LYS* 2.6 62.5 + - + +
9D LEU* 3.7 21.8 - - - +
11D ASN* 1.3 74.8 - - + +
13D GLN* 1.3 57.1 + - - +
15D ASN* 3.2 9.2 + - - +
16D LYS* 2.9 43.8 + - + +
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Residues in contact with GLN 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D LEU 3.0 13.9 + - - +
10D LEU* 3.4 11.0 - - + +
11D ASN 3.2 0.2 - - - -
12D GLU* 1.3 74.2 - - - +
14D VAL* 1.3 65.1 + - - +
16D LYS* 3.3 16.4 + - - +
17D GLU* 3.0 24.2 + - - +
57D LEU* 3.9 13.5 - - + -
97D ILE* 4.0 8.7 - - - +
100D SER* 3.2 32.9 + - - -
101D ILE* 3.7 11.1 - - - +
104D ILE* 3.6 27.6 - - + +
123D TYR* 2.9 31.5 + - + +
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Residues in contact with VAL 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D LEU 3.1 19.6 + - - +
11D ASN* 3.2 11.2 + - - +
13D GLN* 1.3 74.9 - - - +
15D ASN* 1.3 58.4 + - - +
17D GLU* 3.2 5.9 + - - +
18D MET* 3.0 32.6 + - + +
54D ALA* 4.3 4.8 - - + +
57D LEU* 3.9 28.2 - - + +
58D ILE* 3.9 24.2 - - + -
61D LEU* 4.0 19.7 - - + -
68D VAL* 4.8 1.3 - - + -
70D LEU* 3.7 28.7 - - + -
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Residues in contact with ASN 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASN 2.9 24.2 + - - -
12D GLU* 3.2 8.8 + - - +
14D VAL* 1.3 79.4 - - - +
16D LYS* 1.3 55.5 + - - +
18D MET* 3.4 8.8 + - - +
19D ASN* 3.0 28.6 + - - +
69D GLN 3.0 23.0 + - - -
70D LEU* 3.5 12.1 - - - +
71D THR* 2.9 46.1 + - - +
73D ILE* 4.2 12.1 - - + +
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Residues in contact with LYS 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D GLU* 2.9 31.5 + - - +
13D GLN* 3.3 28.5 + - - +
15D ASN* 1.3 76.7 - - - +
17D GLU* 1.3 55.5 + - - +
19D ASN* 3.4 7.9 + - - +
20D SER* 2.9 31.7 + - - -
93D HIS* 5.1 0.5 + - - -
96D HIS* 3.3 29.3 + - + -
97D ILE* 4.1 18.4 - - + +
100D SER* 3.9 22.9 - - - +
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Residues in contact with GLU 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D GLN* 3.0 16.5 + - - +
14D VAL 3.7 7.6 - - - +
16D LYS* 1.3 74.6 - - - +
18D MET* 1.3 61.0 + - - +
20D SER* 3.3 7.6 + - - -
21D SER* 3.0 28.6 + - - -
50D GLU* 3.5 46.6 - - - +
53D HIS* 4.0 14.8 - - + -
54D ALA* 3.8 13.2 - - + +
57D LEU* 4.4 5.6 - - + -
97D ILE* 3.9 9.9 - - - +
123D TYR* 2.4 33.6 + - - +
1006D FE 2.7 20.2 - - - -
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Residues in contact with MET 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C SER* 5.7 0.4 - - - +
22C ASN* 4.6 10.5 - - - +
25C MET* 5.1 5.4 - - + -
14D VAL* 3.0 24.0 + - + +
15D ASN* 3.5 11.0 - - - +
17D GLU* 1.3 76.1 - - - +
19D ASN* 1.3 59.8 + - - +
21D SER* 3.4 4.7 + - - -
22D ASN* 3.2 27.7 + - - -
51D TYR* 3.8 25.8 - - + -
54D ALA* 3.8 20.4 - - + -
55D LYS 5.5 0.2 - - - +
58D ILE* 4.0 21.8 - - + -
70D LEU* 4.5 13.0 - - + -
73D ILE* 3.9 16.2 - - + -
1008D GOL 3.6 30.3 - - - +
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Residues in contact with ASN 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ASN 3.0 18.0 + - - +
16D LYS* 3.6 8.3 - - - +
18D MET* 1.3 72.1 - - - +
20D SER* 1.3 61.1 + - - +
22D ASN* 3.3 11.6 + - - +
23D LEU* 2.9 30.9 + - - +
73D ILE* 3.3 30.5 - - + +
74D SER* 4.1 8.5 + - - -
76D PRO* 5.4 6.7 - - - +
93D HIS* 4.4 14.2 - - - -
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Residues in contact with SER 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LYS 2.9 17.8 + - - -
17D GLU* 3.3 12.1 + - - -
19D ASN* 1.3 73.4 + - - +
21D SER* 1.3 66.0 + - - +
23D LEU* 3.1 3.5 + - - +
24D TYR* 2.9 32.7 + - - -
50D GLU* 3.8 23.1 + - - -
93D HIS* 2.7 32.9 + - - -
97D ILE* 4.0 11.1 - - - +
----------------------------------------------------------
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Residues in contact with SER 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C TYR* 2.7 27.9 + - - -
17D GLU 3.0 13.1 + - - -
18D MET* 3.5 5.4 - - - -
19D ASN 3.4 0.2 - - - -
20D SER* 1.3 74.1 - - - +
22D ASN* 1.3 62.9 + - - +
24D TYR 3.5 0.2 + - - -
25D MET* 3.1 28.3 + - - +
47D ALA* 3.5 23.6 + - - +
50D GLU* 4.0 2.1 - - - +
51D TYR* 4.3 9.0 - - - -
1008D GOL 2.9 21.9 + - - -
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Residues in contact with ASN 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C MET* 4.5 7.8 - - - +
70C LEU* 3.4 31.2 - - + +
71C THR 5.7 1.4 + - - -
73C ILE* 4.1 14.3 - - - +
18D MET 3.2 10.1 + - - -
19D ASN* 3.5 12.6 - - - +
20D SER 3.2 0.2 - - - -
21D SER* 1.3 78.0 - - - +
23D LEU* 1.3 60.4 + - - +
25D MET* 3.4 1.1 + - - -
26D SER 3.1 17.8 + - - -
73D ILE* 4.6 8.5 - - - +
74D SER 5.2 1.8 + - - -
76D PRO* 3.5 20.3 - - + +
1008D GOL 2.8 42.2 + - - -
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Residues in contact with LEU 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D ASN* 2.9 20.3 + - - +
20D SER* 3.1 5.6 + - - +
22D ASN* 1.3 75.4 - - - +
24D TYR* 1.3 61.1 + - + +
26D SER* 3.3 2.8 + - - -
27D MET* 3.0 58.0 + - + +
76D PRO* 3.7 19.4 - - + +
77D GLU* 4.5 13.7 - - + +
80D PHE* 4.5 8.1 - - + -
89D LYS* 5.6 1.8 - - + +
93D HIS* 4.0 38.8 - - + +
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Residues in contact with TYR 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D SER* 2.9 26.5 + - - +
23D LEU* 1.3 76.1 - - + +
25D MET* 1.3 59.9 + - - +
27D MET* 3.8 11.4 - - - -
28D SER* 2.9 30.1 + - - -
43D LEU* 3.7 26.4 - - + +
46D HIS* 3.3 26.6 + + - -
47D ALA* 3.5 21.1 - - + -
50D GLU* 4.0 11.0 - - + -
90D ALA* 3.4 33.2 + - + +
93D HIS* 3.6 20.8 - + - -
94D GLU* 2.4 43.7 + - - +
134D PHE* 4.0 6.4 - + - -
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Residues in contact with MET 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C MET* 4.9 4.5 - - + -
51C TYR* 3.6 22.9 - - + +
55C LYS* 3.9 15.9 - - + -
58C ILE* 4.2 27.4 - - + +
68C VAL* 5.1 5.1 - - + +
70C LEU* 4.0 15.9 - - + -
21D SER* 3.1 24.0 + - - +
22D ASN* 3.7 5.2 - - - +
23D LEU 3.3 0.2 - - - -
24D TYR* 1.3 75.1 - - - +
26D SER* 1.3 58.5 + - - +
28D SER* 3.5 3.7 - - - -
29D SER* 2.9 29.1 + - - -
44D PHE* 3.5 46.4 - - + +
47D ALA* 3.7 15.9 - - + +
48D ALA 4.4 0.7 - - - +
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Residues in contact with SER 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C VAL* 5.0 9.3 + - - -
70C LEU* 4.6 4.9 - - - +
22D ASN 3.1 14.3 + - - -
23D LEU 3.3 7.6 + - - -
25D MET* 1.3 76.9 - - - +
27D MET* 1.3 57.5 + - - +
29D SER* 3.3 7.9 + - - -
30D TRP* 3.0 26.0 + - - +
76D PRO* 3.9 13.5 - - - +
77D GLU 2.6 27.9 + - - -
78D HIS* 3.4 17.3 - - - +
80D PHE* 4.2 2.2 - - - -
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Residues in contact with MET 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LEU* 3.0 36.4 + - + +
24D TYR* 3.8 32.3 - - - +
25D MET 3.4 0.2 - - - -
26D SER* 1.3 71.9 - - - +
28D SER* 1.3 66.1 + - - +
30D TRP* 3.2 5.0 + - - +
31D CYS* 3.1 26.0 + - - -
43D LEU* 3.9 14.1 - - + -
80D PHE* 3.5 36.6 - - + -
86D ILE* 3.5 36.9 - - + +
89D LYS* 3.8 21.1 - - + -
90D ALA* 3.9 8.7 - - + +
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Residues in contact with SER 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C ILE* 5.9 0.2 - - - +
62C ASN* 4.4 2.9 + - - -
24D TYR 2.9 19.6 + - - -
25D MET* 3.5 8.3 - - - -
27D MET* 1.3 76.2 - - - +
29D SER* 1.3 63.8 + - - +
31D CYS* 3.1 4.3 + - - +
32D TYR* 2.9 32.8 + - - -
40D GLY* 2.8 26.2 + - - -
43D LEU* 3.7 10.7 - - - +
44D PHE* 3.4 24.7 - - - +
----------------------------------------------------------
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Residues in contact with SER 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ASN* 3.9 12.9 + - - -
66C VAL 4.0 2.6 + - - -
67C PRO* 3.6 8.0 - - - +
68C VAL* 2.9 49.9 + - - +
25D MET 2.9 17.9 + - - -
26D SER 3.5 5.8 - - - -
28D SER* 1.3 75.3 + - - +
30D TRP* 1.3 62.4 + - - +
32D TYR* 3.3 0.7 + - - +
33D THR* 3.0 27.5 + - - +
----------------------------------------------------------
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Residues in contact with TRP 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D SER 3.0 10.9 + - - +
27D MET 3.2 9.2 + - - +
29D SER* 1.3 75.1 - - - +
31D CYS* 1.3 69.0 + - - +
33D THR* 3.0 7.5 + - - -
34D HIS* 2.7 68.8 + + + -
36D LEU* 3.8 24.5 - - + -
78D HIS 3.9 13.0 - - - +
79D LYS* 4.8 0.6 - - - +
80D PHE* 3.4 59.1 + + + +
81D GLU 4.2 3.4 - - - -
82D GLY* 3.5 32.1 - - - -
83D LEU 4.4 0.2 - - - -
86D ILE* 3.4 17.5 - - + -
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Residues in contact with CYS 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D MET 3.1 17.7 + - - -
28D SER 3.1 6.2 + - - +
30D TRP* 1.3 82.6 - - - +
32D TYR* 1.3 61.5 + - - +
34D HIS 3.0 7.1 + - - -
36D LEU* 2.9 50.3 + - + +
39D ALA* 3.8 18.8 - - - -
40D GLY* 3.7 8.3 - - - +
43D LEU* 3.8 14.1 - - - -
83D LEU* 4.4 9.9 - - - -
86D ILE* 3.9 17.0 - - - -
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Residues in contact with TYR 32 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ASP* 5.2 0.3 - - - +
62C ASN* 3.3 59.6 - - + +
63C GLU* 6.2 0.4 - - - -
65C ASN* 3.8 15.1 + - - +
28D SER* 2.9 27.3 + - - +
29D SER 3.3 4.2 + - - +
31D CYS* 1.3 77.1 - - - +
33D THR* 1.3 61.4 + - + +
34D HIS 3.4 0.5 + - - -
35D SER* 3.7 9.0 + - - -
36D LEU 4.0 3.1 + - - -
37D ASP* 3.7 31.0 - - + +
40D GLY* 3.3 20.2 - - - -
41D LEU* 3.3 33.4 + - - +
44D PHE* 4.6 4.8 - + + +
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Residues in contact with THR 33 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ASN* 5.8 1.1 - - - +
65C ASN* 3.9 28.5 + - - +
66C VAL 3.9 5.2 - - - +
67C PRO* 3.8 38.0 - - + +
1002C GLN 4.9 1.2 - - - +
1003C SER* 3.4 18.3 - - - -
29D SER* 3.0 17.8 + - - +
30D TRP* 3.0 14.6 + - - -
31D CYS 3.2 0.2 - - - -
32D TYR* 1.3 77.7 - - + +
34D HIS* 1.3 73.7 + - - +
35D SER 3.5 0.9 - - - -
----------------------------------------------------------
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Residues in contact with HIS 34 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003C SER* 3.4 11.2 + - - +
1005C HIS* 3.0 19.4 + - + +
30D TRP* 2.7 82.9 + + + +
31D CYS 3.0 3.7 + - - +
33D THR* 1.3 96.3 + - - +
35D SER* 1.3 71.2 + - - +
36D LEU* 3.2 11.7 + - + +
----------------------------------------------------------
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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