Contacts of the helix formed by residues 3 - 34 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 1.3 75.3 - - - +
4B LYS* 1.3 59.6 + - - +
5B ASP* 4.2 4.5 + - - +
6B ILE* 3.2 26.3 + - - +
7B ILE* 2.9 28.9 + - - +
111B SER* 4.7 8.7 + - - -
113B ASP* 5.1 3.3 + - - +
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Residues in contact with LYS 4 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU 4.0 1.0 + - - -
3B SER* 1.3 72.3 - - - +
5B ASP* 1.3 62.0 + - - +
7B ILE* 3.5 12.8 + - + +
8B LYS* 3.0 27.9 + - - +
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Residues in contact with ASP 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B SER* 3.3 5.4 + - - +
4B LYS* 1.3 80.7 - - - +
6B ILE* 1.3 63.0 + - - +
8B LYS* 3.3 9.3 + - - +
9B LEU* 3.1 30.5 + - + +
107B HIS* 3.3 38.2 + - + +
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Residues in contact with ILE 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 4.0 11.9 - - + -
3B SER* 3.2 23.3 + - - +
5B ASP* 1.3 72.9 - - - +
7B ILE* 1.3 61.3 + - - +
9B LEU* 3.4 4.9 + - + +
10B LEU* 2.9 51.7 + - + +
104B ILE* 4.3 14.4 - - + +
107B HIS* 3.8 22.4 - - + -
108B ALA* 3.9 27.6 - - + +
111B SER* 4.1 9.4 - - - +
113B ASP* 3.9 22.7 - - + +
116B THR* 4.1 6.1 - - + +
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Residues in contact with ILE 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B PRO* 3.9 20.0 - - + -
2B LEU* 3.5 31.4 - - + +
3B SER 2.9 18.4 + - - +
4B LYS* 3.6 11.7 - - + +
5B ASP 3.3 0.2 - - - -
6B ILE* 1.3 76.5 - - - +
8B LYS* 1.3 62.5 + - - +
10B LEU* 3.9 3.8 - - - +
11B ASN* 3.0 34.6 + - - +
61B LEU* 5.2 1.8 - - - -
66B VAL* 3.6 35.4 - - + -
67B PRO* 5.0 3.1 - - + +
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Residues in contact with LYS 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B LYS 3.0 14.9 + - - +
5B ASP* 3.3 10.7 + - - +
7B ILE* 1.3 79.4 - - - +
9B LEU* 1.3 75.4 + - - +
11B ASN* 3.8 4.1 - - - +
12B GLU* 2.9 67.2 + - + +
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Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ASP* 3.1 21.2 + - + +
6B ILE* 3.9 5.4 - - + +
8B LYS* 1.3 90.2 - - - +
10B LEU* 1.3 60.7 + - - +
12B GLU* 3.6 21.0 + - - +
13B GLN* 3.1 27.0 + - - +
103B ASN* 3.8 19.7 - - - +
104B ILE* 3.8 33.6 - - + +
107B HIS* 3.8 37.5 - - + +
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Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LEU* 3.8 18.6 - - + -
6B ILE* 2.9 38.4 + - + +
7B ILE 4.1 0.4 - - - +
9B LEU* 1.3 74.3 - - - +
11B ASN* 1.3 61.2 + - - +
13B GLN* 3.4 4.2 + - + +
14B VAL* 3.0 32.3 + - - +
57B LEU* 4.3 18.6 - - + +
60B PHE* 4.0 21.3 - - + -
61B LEU* 4.0 18.8 - - + -
104B ILE* 4.2 20.2 - - + -
116B THR* 4.4 3.1 - - + -
120B LEU* 4.1 26.2 - - + -
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Residues in contact with ASN 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ILE* 3.0 38.2 + - - +
8B LYS* 3.8 4.5 - - - +
10B LEU* 1.3 74.7 - - - +
12B GLU* 1.3 64.0 + - - +
14B VAL* 3.3 4.9 + - - +
15B ASN* 2.8 31.5 + - - +
61B LEU* 3.9 8.6 - - - +
66B VAL* 4.3 4.2 - - - +
67B PRO 3.5 18.6 + - - -
68B VAL* 3.5 13.0 - - - +
69B GLN* 2.8 42.7 + - + +
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Residues in contact with GLU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LYS* 2.9 55.8 + - + +
9B LEU* 3.8 17.8 - - - +
11B ASN* 1.3 75.0 - - - +
13B GLN* 1.3 56.4 + - - +
15B ASN* 3.2 8.4 + - - +
16B LYS* 2.8 48.0 + - - +
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Residues in contact with GLN 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU 3.1 17.2 + - - +
10B LEU* 3.6 6.3 - - + +
11B ASN 3.2 0.2 - - - -
12B GLU* 1.3 74.3 - - - +
14B VAL* 1.3 66.9 + - - +
16B LYS* 3.6 17.3 + - - +
17B GLU* 3.0 25.5 + - - +
57B LEU* 3.9 13.0 - - + -
97B ILE* 4.2 9.1 - - - +
100B SER* 3.1 33.3 + - - +
101B ILE* 3.9 10.0 - - - +
104B ILE* 3.7 26.0 - - + +
123B TYR* 3.0 30.6 + - + +
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Residues in contact with VAL 14 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU 3.0 16.8 + - - +
11B ASN* 3.5 10.3 - - - +
13B GLN* 1.3 75.5 - - - +
15B ASN* 1.3 63.8 + - - +
17B GLU* 3.2 6.8 + - - +
18B MET* 3.1 27.5 + - + +
54B ALA* 4.2 5.7 - - + +
57B LEU* 3.8 30.1 - - + -
58B ILE* 4.0 23.1 - - + -
61B LEU* 4.0 19.1 - - + -
68B VAL* 4.7 1.8 - - + -
70B LEU* 3.9 27.8 - - + -
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Residues in contact with ASN 15 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASN 2.8 24.6 + - - +
12B GLU* 3.7 7.8 - - - +
14B VAL* 1.3 82.9 - - - +
16B LYS* 1.3 60.9 + - - +
18B MET* 3.5 5.5 + - - +
19B ASN* 2.9 34.6 + - - +
69B GLN 2.9 24.5 + - - -
70B LEU* 3.7 9.4 - - - +
71B THR* 3.0 43.7 + - + +
73B ILE* 3.9 11.1 - - + +
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Residues in contact with LYS 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLU* 2.8 39.3 + - - +
13B GLN* 3.6 27.7 + - - +
14B VAL 3.3 0.2 - - - -
15B ASN* 1.3 72.4 - - - +
17B GLU* 1.3 58.4 + - - +
19B ASN* 3.4 7.3 + - - +
20B SER* 2.9 30.3 + - - -
93B HIS* 5.4 0.7 - - - -
96B HIS* 3.4 37.2 - - + -
97B ILE* 4.4 11.2 - - + +
100B SER* 4.0 19.3 - - - +
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Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLN* 3.0 20.5 + - - +
14B VAL 3.2 4.5 + - - +
16B LYS* 1.3 77.9 - - - +
18B MET* 1.3 57.0 + - - +
20B SER* 3.6 4.5 - - - -
21B SER* 2.9 28.6 + - - -
50B GLU* 3.5 37.8 - - - +
53B HIS* 4.0 14.6 - - + -
54B ALA* 3.9 12.1 - - + +
57B LEU* 4.5 4.3 - - + -
97B ILE* 4.0 8.2 - - - +
123B TYR* 2.4 34.9 + - - +
1006B FE 2.5 28.2 - - - -
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Residues in contact with MET 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 3.1 20.3 + - + +
15B ASN* 3.9 2.5 - - - +
16B LYS 3.3 0.2 - - - -
17B GLU* 1.3 72.4 - - - +
19B ASN* 1.3 66.3 + - - +
21B SER* 3.4 2.6 + - - -
22B ASN 3.2 11.1 + - - -
51B TYR* 4.3 17.7 - - + -
54B ALA* 4.2 12.3 - - + -
55B LYS* 6.5 0.2 - - + -
58B ILE* 4.1 25.8 - - + -
70B LEU* 4.0 24.0 - - + -
73B ILE* 3.7 32.4 - - + +
22E ASN* 3.6 27.1 - - - +
25E MET* 5.0 4.0 - - + -
1009E GOL 2.9 33.2 + - - +
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Residues in contact with ASN 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASN* 2.9 29.1 + - - +
16B LYS* 3.6 6.0 - - - +
18B MET* 1.3 75.8 - - - +
20B SER* 1.3 63.4 + - - +
22B ASN* 3.3 4.5 + - - +
23B LEU* 3.1 21.7 + - - +
71B THR* 5.3 1.0 + - - -
72B SER 4.8 2.3 - - - +
73B ILE* 3.7 15.3 - - - +
74B SER* 2.7 55.8 + - - +
76B PRO* 5.4 1.2 - - - +
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Residues in contact with SER 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LYS 2.9 17.2 + - - -
17B GLU* 3.6 9.0 - - - -
19B ASN* 1.3 75.7 - - - +
21B SER* 1.3 66.6 + - - +
23B LEU* 3.1 5.6 + - - +
24B TYR* 3.0 31.5 + - - -
50B GLU* 3.1 23.5 + - - -
93B HIS* 2.8 37.6 + - - -
97B ILE* 4.9 3.8 - - - -
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Residues in contact with SER 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLU 2.9 18.0 + - - -
18B MET* 3.6 7.2 - - - -
19B ASN 3.4 0.2 - - - -
20B SER* 1.3 77.0 - - - +
22B ASN* 1.3 63.1 + - - +
24B TYR 3.2 0.7 + - - -
25B MET* 3.1 19.8 + - - +
47B ALA* 2.8 34.5 + - - +
50B GLU* 4.0 11.6 - - - +
51B TYR* 3.9 8.9 - - - +
51E TYR* 3.2 18.2 + - - -
1009E GOL 3.8 9.1 + - - -
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Residues in contact with ASN 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B MET 3.2 5.4 + - - +
19B ASN 3.9 5.8 - - - +
20B SER 3.3 0.2 - - - -
21B SER* 1.3 75.5 + - - +
23B LEU* 1.3 65.0 + - - +
25B MET* 3.3 5.9 + - - +
26B SER 3.0 18.0 + - - -
73B ILE* 3.8 13.3 - - + +
74B SER 4.9 3.3 + - - +
76B PRO* 3.6 20.8 - - + +
18E MET* 3.5 25.3 - - - +
51E TYR* 5.4 0.3 + - - -
70E LEU* 3.8 18.8 - - + +
71E THR 5.0 3.2 + - - -
73E ILE* 3.6 30.3 - - - +
1009E GOL 3.1 18.7 + - - -
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ASN 3.1 14.4 + - - +
20B SER* 3.1 8.9 + - - +
22B ASN* 1.3 74.5 - - - +
24B TYR* 1.3 59.9 + - + +
26B SER* 3.1 4.9 + - - -
27B MET* 2.9 57.1 + - + +
76B PRO* 3.7 11.1 - - + +
77B GLU* 4.3 30.1 - - + +
80B PHE* 4.4 6.1 - - + -
93B HIS* 4.1 35.4 - - + +
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Residues in contact with TYR 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B SER* 3.0 39.2 + - - -
21B SER 3.7 1.8 - - - +
23B LEU* 1.3 78.9 - - + +
25B MET* 1.3 56.7 + - - +
27B MET* 3.7 15.1 - - - +
28B SER* 2.8 30.0 + - - -
43B LEU* 3.8 25.0 - - + +
46B HIS* 3.3 25.6 - + - -
47B ALA* 3.6 23.1 - - + -
50B GLU* 4.0 4.3 - - + -
90B ALA* 3.4 31.7 + - + +
93B HIS* 3.6 13.0 - + - -
94B GLU* 2.6 41.5 + - - +
134B PHE* 3.8 8.4 - + - -
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Residues in contact with MET 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B SER* 3.1 18.2 + - - +
22B ASN* 3.6 14.8 - - - +
23B LEU 3.3 0.2 - - - -
24B TYR* 1.3 75.0 - - - +
26B SER* 1.3 59.0 + - - +
28B SER* 3.3 4.5 + - - -
29B SER* 2.9 30.3 + - - -
44B PHE* 3.6 43.5 - - + +
47B ALA* 3.7 17.5 - - + +
48B ALA 4.5 2.0 - - - +
18E MET* 4.8 1.3 - - + -
51E TYR* 3.7 22.9 - - + +
55E LYS* 4.1 13.5 - - + -
58E ILE* 4.1 28.4 - - + +
68E VAL* 5.2 5.2 - - + +
70E LEU* 3.8 16.2 - - + -
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Residues in contact with SER 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASN 3.0 13.8 + - - -
23B LEU 3.4 7.6 - - - -
25B MET* 1.3 76.3 - - - +
27B MET* 1.3 61.4 + - - +
29B SER* 3.4 7.1 + - - -
30B TRP* 3.1 22.3 + - - +
76B PRO* 3.8 15.2 - - - +
77B GLU 2.5 30.8 + - - -
78B HIS* 3.6 11.1 - - - +
80B PHE* 3.8 2.9 - - - -
68E VAL 4.9 10.0 + - - +
70E LEU* 4.7 4.6 - - - +
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Residues in contact with MET 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B LEU* 2.9 39.4 + - + +
24B TYR* 3.7 32.5 - - - +
26B SER* 1.3 73.2 - - - +
28B SER* 1.3 66.0 + - - +
30B TRP* 3.2 6.0 + - - +
31B CYS* 3.1 24.9 + - - -
43B LEU* 3.9 14.6 - - + -
80B PHE* 3.7 36.8 - - + -
86B ILE* 3.8 36.2 - - + +
89B LYS* 4.1 15.5 - - + -
90B ALA* 4.2 7.0 - - - +
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Residues in contact with SER 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR 2.8 21.2 + - - -
25B MET* 3.3 8.5 + - - -
27B MET* 1.3 74.0 - - - +
29B SER* 1.3 56.8 + - - +
31B CYS* 3.2 4.9 + - - +
32B TYR* 3.0 40.2 + - - -
40B GLY* 2.6 27.4 + - - -
43B LEU* 3.8 10.5 - - - +
44B PHE* 3.5 21.7 - - - +
58E ILE* 6.5 0.4 - - - -
62E ASN* 4.4 2.9 + - - -
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Residues in contact with SER 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B MET 2.9 17.1 + - - -
26B SER 3.7 4.9 - - - -
28B SER* 1.3 72.7 + - - +
30B TRP* 1.3 65.5 + - - +
32B TYR* 3.9 0.8 - - - +
33B THR* 2.9 28.0 + - - +
58E ILE* 6.2 0.2 - - - -
62E ASN* 4.0 16.6 + - - -
66E VAL 4.1 2.1 + - - -
67E PRO* 3.5 8.8 - - - +
68E VAL* 2.9 45.8 + - - +
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Residues in contact with TRP 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B SER 3.1 14.8 + - - +
27B MET 3.2 9.4 + - - +
29B SER* 1.3 74.8 - - - +
31B CYS* 1.3 66.5 + - - +
33B THR* 3.0 8.7 + - - -
34B HIS* 2.8 73.3 + + + -
36B LEU* 4.0 17.7 - - + -
78B HIS 4.0 9.9 - - - +
80B PHE* 3.2 58.6 + + + +
81B GLU 4.1 3.8 - - - -
82B GLY* 3.5 33.0 - - - -
83B LEU 4.3 0.2 - - - -
86B ILE* 3.5 17.3 - - + -
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Residues in contact with CYS 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B MET 3.1 14.0 + - - +
28B SER 3.2 7.8 + - - +
30B TRP* 1.3 85.6 - - - +
32B TYR* 1.3 54.1 + - - +
34B HIS 3.1 11.3 + - - -
35B SER 3.4 0.2 + - - -
36B LEU* 2.8 52.4 + - + +
39B ALA* 3.9 19.1 - - - -
40B GLY* 3.6 7.6 - - - +
43B LEU* 3.9 10.3 - - - -
83B LEU* 4.5 9.6 - - - -
86B ILE* 3.8 20.2 - - - -
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Residues in contact with TYR 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B SER* 3.0 32.7 + - - +
29B SER 3.9 4.0 - - - +
30B TRP 3.4 0.2 - - - -
31B CYS* 1.3 75.1 - - - +
33B THR* 1.3 60.7 + - + +
34B HIS 3.2 1.2 + - - -
35B SER* 3.9 8.2 + - - -
36B LEU 4.5 3.4 - - - -
37B ASP* 3.8 31.8 - - + +
40B GLY* 3.3 17.3 - - - -
41B LEU* 3.3 32.6 - - - +
44B PHE* 4.7 4.7 - + + +
139D ASP* 5.1 0.3 - - - +
62E ASN* 3.4 57.2 - - + +
63E GLU* 5.7 0.4 - - - -
65E ASN* 3.4 18.2 + - - +
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Residues in contact with THR 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B SER* 2.9 18.6 + - - +
30B TRP* 3.0 9.5 + - - -
32B TYR* 1.3 79.2 - - + +
34B HIS* 1.3 74.3 + - - +
35B SER 3.6 1.1 - - - -
62E ASN* 5.9 1.1 - - - +
65E ASN* 4.0 23.9 + - - +
66E VAL 3.9 7.9 - - - +
67E PRO* 3.8 39.8 - - + +
1002E GLN 5.0 1.2 - - - +
1003E SER* 3.5 16.4 - - - -
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Residues in contact with HIS 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TRP* 2.8 81.6 + + + +
31B CYS 3.1 4.1 + - - +
33B THR* 1.3 98.4 + - - +
35B SER* 1.3 69.2 + - - +
36B LEU* 3.3 11.6 + - + +
1003E SER* 3.3 8.8 + - - -
1005E HIS* 3.1 19.6 - - + +
----------------------------------------------------------
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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