Contacts of the helix formed by residues 4 - 35 (chain G) in PDB entry 3BKN
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 4 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G GLN 3.9 1.0 + - - -
3G GLY* 1.3 71.7 - - - -
5G PRO* 1.3 76.4 - - - +
6G ASP* 2.7 35.3 + - - +
7G VAL* 3.1 25.9 + - + +
8G LEU* 3.0 20.8 + - - +
111G LYS* 3.3 36.1 + - + +
113G ASP* 5.3 5.5 + - + +
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Residues in contact with PRO 5 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G GLN* 5.4 5.2 - - - +
3G GLY 3.5 6.7 - - - +
4G ASP* 1.3 91.9 - - - +
6G ASP* 1.3 62.3 + - - +
8G LEU* 3.6 9.1 + - + +
9G LYS* 3.1 25.6 + - - +
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Residues in contact with ASP 6 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G ASP* 2.7 15.0 + - - +
5G PRO* 1.3 75.5 - - - +
7G VAL* 1.3 64.5 + - - +
9G LYS* 3.5 10.9 + - - +
10G LEU* 3.0 23.9 + - - +
107G LEU* 4.1 23.5 - - + +
111G LYS* 3.1 25.9 + - - -
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Residues in contact with VAL 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G ASP* 3.1 25.0 + - + +
6G ASP* 1.3 76.2 - - - +
8G LEU* 1.3 58.2 + - - +
10G LEU* 3.2 6.6 + - - +
11G LEU* 2.8 36.9 + - + +
65G LEU* 4.5 5.2 - - + -
107G LEU* 4.5 2.9 - - + -
108G CYS* 4.1 22.4 - - - -
111G LYS* 4.0 25.8 - - + -
113G ASP* 3.4 26.9 - - + +
116G SER* 3.9 17.9 - - - +
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Residues in contact with LEU 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G GLY* 4.5 14.6 - - - +
4G ASP 3.0 14.9 + - - +
5G PRO* 4.0 7.9 - - + +
6G ASP 3.3 0.2 - - - -
7G VAL* 1.3 74.5 - - - +
9G LYS* 1.3 65.2 + - - +
11G LEU* 3.9 4.2 - - + +
12G ASN* 2.9 31.8 + - - +
62G ILE* 3.9 33.9 - - + +
65G LEU* 3.9 38.8 - - + +
66G ASP 4.7 1.1 - - - +
67G GLY* 3.7 20.4 - - - -
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Residues in contact with LYS 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G PRO 3.1 18.7 + - - +
6G ASP* 3.8 12.6 - - - +
7G VAL 3.3 0.2 - - - -
8G LEU* 1.3 75.6 - - - +
10G LEU* 1.3 57.3 + - - +
12G ASN* 3.4 4.9 + - - +
13G GLU* 3.0 36.1 + - + +
73G ARG* 5.6 0.2 + - - -
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Residues in contact with LEU 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G ASP 3.0 18.5 + - - +
7G VAL 3.6 3.4 - - - +
9G LYS* 1.3 76.7 - - - +
11G LEU* 1.3 63.8 + - + +
13G GLU* 3.0 9.6 + - - +
14G GLN* 3.0 21.2 + - - +
100G ARG* 3.8 29.6 - - + +
101G LEU* 4.4 7.6 - - + -
104G GLY* 3.4 44.6 - - - +
107G LEU* 4.9 10.8 - - + -
108G CYS* 3.6 19.7 - - - -
120G LEU* 3.8 12.3 - - + -
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Residues in contact with LEU 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G VAL* 2.8 32.0 + - + +
8G LEU* 4.0 5.6 - - + +
10G LEU* 1.3 71.7 - - + +
12G ASN* 1.3 58.3 + - - +
14G GLN* 3.4 3.9 + - - +
15G LEU* 2.9 23.6 + - - +
58G ILE* 3.2 22.2 - - + +
61G ARG* 3.9 27.8 - - + -
62G ILE* 3.9 24.9 - - + +
65G LEU* 4.2 8.7 - - + -
116G SER* 4.0 17.9 - - - +
119G LEU* 5.2 4.3 - - + -
120G LEU* 3.8 36.6 - - + -
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Residues in contact with ASN 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G LEU* 2.9 21.2 + - - +
9G LYS* 3.9 5.2 - - - +
11G LEU* 1.3 74.9 - - - +
13G GLU* 1.3 64.3 + - - +
15G LEU* 3.4 8.0 + - - +
16G THR* 3.1 25.1 + - - -
62G ILE* 3.3 21.2 - - - +
68G LEU 2.6 29.6 + - - +
70G ASN* 2.9 30.4 + - + +
73G ARG* 3.4 9.7 + - - +
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Residues in contact with GLU 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G LYS* 3.0 22.3 + - + +
10G LEU* 3.0 12.1 + - - +
12G ASN* 1.3 74.4 - - - +
14G GLN* 1.3 64.3 + - - +
16G THR* 3.1 6.2 + - - -
17G SER* 3.0 19.9 + - - -
73G ARG* 4.0 13.6 - - - +
75G PHE* 4.3 17.2 - - + -
100G ARG* 2.8 46.2 + - - +
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Residues in contact with GLN 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G LEU 3.0 14.1 + - - +
11G LEU 3.8 4.5 - - - +
13G GLU* 1.3 79.3 - - - +
15G LEU* 1.3 56.9 + - - +
17G SER* 3.0 6.6 + - - -
18G GLU* 2.6 55.6 + - - +
58G ILE* 3.4 20.4 - - + -
97G VAL* 3.6 26.6 - - - +
100G ARG* 3.0 35.1 + - - +
101G LEU* 3.7 20.0 - - + +
120G LEU* 4.2 18.4 - - + -
123G ILE* 4.0 5.1 - - + +
127G GLU* 3.9 2.0 + - - -
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Residues in contact with LEU 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G LEU 2.9 17.9 + - - +
12G ASN* 3.4 20.0 - - - +
13G GLU 3.3 0.2 - - - -
14G GLN* 1.3 76.8 - - - +
16G THR* 1.3 56.3 + - - +
18G GLU* 3.1 4.4 + - - +
19G LEU* 2.9 40.0 + - + +
55G ALA* 3.5 27.1 - - + +
58G ILE* 3.7 17.4 - - + +
59G THR* 3.4 22.0 - - - +
62G ILE* 4.3 5.2 - - + -
69G PRO* 4.1 6.7 - - + -
70G ASN 3.4 31.6 - - - +
71G TYR* 4.1 15.0 - - + +
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Residues in contact with THR 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G ASN 3.1 7.2 + - - -
13G GLU 3.5 8.3 - - - -
15G LEU* 1.3 73.6 - - - +
17G SER* 1.3 62.8 + - - +
19G LEU* 3.2 6.5 + - - +
20G THR* 2.9 29.3 + - - -
70G ASN* 4.5 7.3 + - - +
73G ARG* 2.9 72.6 + - + +
75G PHE* 3.7 29.2 - - + +
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Residues in contact with SER 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G GLU 3.0 7.2 + - - -
14G GLN* 3.0 15.8 + - - -
16G THR* 1.3 78.3 - - - +
18G GLU* 1.3 54.9 + - - +
20G THR* 3.3 2.8 + - - -
21G ALA* 2.8 29.7 + - - +
75G PHE* 3.7 13.2 - - - -
93G ILE* 4.6 11.1 + - - +
96G GLU* 5.4 1.6 + - - +
97G VAL* 3.4 18.0 + - - +
100G ARG* 3.1 37.5 + - - -
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Residues in contact with GLU 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G GLN* 2.6 50.9 + - - +
15G LEU* 3.7 5.2 - - - +
17G SER* 1.3 69.9 - - - +
19G LEU* 1.3 61.1 + - - +
21G ALA* 3.2 4.3 + - - +
22G ILE* 2.8 35.5 + - - +
51G GLU* 2.5 12.1 - - - +
54G HIS* 3.3 20.0 - - + +
55G ALA* 3.9 22.4 - - + +
58G ILE* 4.0 10.8 - - + +
97G VAL* 5.8 0.4 - - - -
123G ILE* 3.6 5.2 - - - +
127G GLU* 3.2 1.1 - - - +
201G ZN 2.0 37.0 - - - -
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Residues in contact with LEU 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G LEU* 2.9 28.8 + - + +
16G THR* 3.8 4.5 - - - +
18G GLU* 1.3 76.3 - - - +
20G THR* 1.3 62.4 + - - +
22G ILE* 3.4 10.8 + - + +
23G ASN* 3.3 25.8 + - - +
55G ALA* 4.2 10.3 - - + -
70G ASN 3.7 23.8 - - - +
71G TYR* 3.9 29.8 - - + +
73G ARG 4.4 10.1 - - - +
74G LEU* 3.6 16.6 - - + +
23H ASN* 4.8 4.3 - - - +
301H HEM 3.4 32.4 - - + +
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Residues in contact with THR 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G THR 2.9 17.9 + - - -
17G SER* 3.6 5.6 - - - -
19G LEU* 1.3 74.1 - - - +
21G ALA* 1.3 60.5 + - - +
23G ASN 3.2 2.6 + - - -
24G GLN* 2.9 26.3 + - - +
74G LEU* 3.7 9.8 - - + +
75G PHE* 2.9 47.9 + - + +
76G SER 4.3 5.8 - - - +
77G LEU* 3.6 24.9 - - + +
93G ILE* 4.9 16.2 - - + -
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Residues in contact with ALA 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G SER 2.8 21.0 + - - +
18G GLU* 3.7 4.0 - - - +
20G THR* 1.3 71.3 - - - +
22G ILE* 1.3 65.9 + - - +
25G TYR* 3.0 37.5 + - + -
51G GLU* 3.8 26.9 - - + +
93G ILE* 3.9 26.4 - - + +
94G GLU* 5.1 2.7 - - - +
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Residues in contact with ILE 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G GLU 2.8 24.1 + - - +
19G LEU* 3.6 10.8 - - + +
20G THR 3.3 0.4 - - - -
21G ALA* 1.3 70.9 - - - +
23G ASN* 1.3 64.5 + - - +
26G PHE* 2.9 27.8 + - + +
48G SER* 3.4 5.0 + - - +
51G GLU* 3.7 7.3 - - + +
52G MET* 3.6 54.5 - - + +
55G ALA* 3.9 15.0 - - + -
301H HEM 3.6 62.6 - - + -
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Residues in contact with ASN 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G LEU 3.3 12.3 + - - +
20G THR 3.2 7.3 + - - +
22G ILE* 1.3 78.5 - - - +
24G GLN* 1.3 63.9 + - - +
26G PHE* 4.6 0.2 - - - -
27G LEU* 3.0 29.3 + - - +
74G LEU* 3.7 20.8 - - - +
77G LEU* 4.0 8.7 - - + -
19H LEU* 4.6 7.3 - - - +
71H TYR* 3.0 44.7 + - + +
74H LEU* 5.9 2.2 - - - +
301H HEM 2.9 30.3 - - - +
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Residues in contact with GLN 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G THR* 2.9 16.6 + - - +
21G ALA 4.0 2.9 - - - +
23G ASN* 1.3 76.8 - - - +
25G TYR* 1.3 58.0 + - + +
27G LEU* 4.0 4.0 - - + +
28G HIS* 2.9 38.4 + - + +
76G SER 4.4 1.9 - - - +
77G LEU* 3.7 15.9 - - + +
78G ARG* 2.7 51.0 + - - +
79G VAL* 6.2 0.2 - - + -
89G ALA* 3.1 29.1 + - - +
90G ASP* 2.8 23.7 + - - +
93G ILE* 3.4 24.7 - - + +
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Residues in contact with TYR 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G ALA* 3.0 30.3 + - + +
24G GLN* 1.3 74.0 - - + +
26G PHE* 1.3 66.6 + - - +
28G HIS* 3.2 2.1 + - - -
29G SER* 2.9 21.7 + - - -
44G THR* 3.4 23.6 - - + +
47G GLU* 3.9 24.0 - - + +
48G SER* 3.9 22.0 - - - +
51G GLU* 3.6 26.0 - - + -
90G ASP* 3.5 35.8 - - + +
93G ILE* 5.5 3.4 - - + -
94G GLU* 2.5 42.4 + - - +
130G HIS* 3.9 7.6 - - - +
134G LEU* 3.7 17.3 - - + +
202G ZN 4.5 0.4 - - - -
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Residues in contact with PHE 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G ILE 2.9 19.7 + - - +
23G ASN* 4.0 3.8 - - - +
25G TYR* 1.3 77.9 - - - +
27G LEU* 1.3 57.6 + - - +
29G SER* 2.9 25.2 + - - -
30G LYS* 3.0 30.1 + - + +
45G ARG* 3.7 24.5 - - + -
48G SER* 3.3 22.1 + - - +
49G PHE* 4.3 5.6 - + - -
52G MET* 4.3 8.5 - - + -
56H GLU* 3.7 31.9 - - + -
71H TYR* 3.4 30.5 - + + -
301H HEM 3.5 35.9 - + + -
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Residues in contact with LEU 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G ASN 3.0 17.7 + - - +
24G GLN* 4.0 3.8 - - + +
26G PHE* 1.3 76.0 - - - +
28G HIS* 1.3 66.2 + - + +
30G LYS* 3.3 5.7 + - - +
31G MET* 2.9 42.9 + - + +
77G LEU* 4.7 5.2 - - + -
79G VAL* 3.9 36.3 - - + -
59H THR* 4.7 3.8 - - + -
63H LEU* 5.0 1.3 - - + -
69H PRO* 3.9 35.2 - - + +
71H TYR* 3.9 39.7 - - + -
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Residues in contact with HIS 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G GLN* 2.9 24.6 + - + +
25G TYR 3.2 4.2 + - - +
27G LEU* 1.3 76.6 - - + +
29G SER* 1.3 57.6 + - - +
31G MET* 3.2 7.0 + - - +
32G GLN* 2.8 38.2 + - - +
44G THR* 4.1 10.5 - - + -
78G ARG 3.2 20.0 + - - -
79G VAL* 3.7 6.1 - - + -
80G GLY 3.1 22.7 + - - -
86G GLN* 3.5 43.5 + - + +
89G ALA* 3.9 5.6 - - + -
90G ASP* 2.8 37.9 + - - +
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Residues in contact with SER 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G TYR 2.9 13.4 + - - -
26G PHE* 2.9 12.3 + - - -
28G HIS* 1.3 77.0 - - - +
30G LYS* 1.3 64.4 + - - +
32G GLN* 3.3 4.1 + - - -
33G ASP* 2.9 26.7 + - - +
41G ALA* 3.4 18.6 - - - +
44G THR* 3.6 10.0 - - - +
45G ARG* 3.4 42.1 + - - +
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Residues in contact with LYS 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G PHE* 3.0 31.2 + - + +
27G LEU* 3.7 7.0 - - - +
29G SER* 1.3 86.4 + - - +
31G MET* 1.3 57.0 + - - +
33G ASP* 3.3 19.6 + - - +
34G ASN* 3.1 29.6 + - - +
45G ARG* 4.1 4.8 - - - +
56H GLU* 2.6 40.1 + - - +
59H THR* 3.9 13.5 - - + -
60H ASP* 2.7 40.1 + - - +
63H LEU* 3.6 20.4 - - + +
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Residues in contact with MET 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G LEU* 2.9 30.2 + - + +
28G HIS* 3.4 9.2 - - - +
30G LYS* 1.3 74.3 - - - +
32G GLN* 1.3 65.4 + - - +
34G ASN* 3.3 6.9 + - - +
35G TRP* 3.1 50.1 + - + +
79G VAL* 3.9 23.6 - - + -
80G GLY 3.6 20.2 - - - +
81G GLN* 4.1 13.0 - - - +
86G GLN* 3.7 16.2 - - - +
63H LEU* 4.4 21.5 - - + -
68H LEU* 6.4 2.7 - - + -
69H PRO* 6.2 0.4 - - - -
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Residues in contact with GLN 32 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G HIS* 2.8 27.4 + - - +
29G SER 3.5 3.8 - - - +
31G MET* 1.3 71.6 - - - +
33G ASP* 1.3 61.9 + - - +
35G TRP* 3.1 14.9 + - - +
37G PHE* 2.9 38.9 + - + +
40G LEU* 3.5 26.6 - - - +
41G ALA* 3.7 8.5 - - + -
44G THR* 2.5 34.3 + - - +
83G LEU* 4.0 11.9 - - + +
86G GLN* 2.9 34.6 + - - +
87G PHE* 5.1 7.1 - - - -
90G ASP* 5.6 0.8 + - - -
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Residues in contact with ASP 33 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G SER 2.9 12.1 + - - +
30G LYS* 3.3 29.1 + - + +
32G GLN* 1.3 75.6 - - - +
34G ASN* 1.3 57.4 - - - +
36G GLY* 3.1 19.2 + - - -
37G PHE 4.7 1.3 - - - -
38G THR* 3.5 27.6 - - - +
41G ALA* 3.6 13.6 - - - +
160G SER* 4.0 5.5 - - - +
161G ALA* 3.7 29.7 + - + +
60H ASP* 5.2 1.1 - - - +
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Residues in contact with ASN 34 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G LYS 3.1 12.1 + - - +
31G MET* 3.3 9.2 + - - +
33G ASP* 1.3 78.3 - - - +
35G TRP* 1.3 64.3 + - + +
36G GLY 3.3 0.2 - - - -
161G ALA* 3.5 23.7 - - - +
60H ASP* 4.1 10.5 + - - -
63H LEU* 3.6 45.7 - - + +
64H LEU* 4.1 2.7 + - - +
401H MG 3.8 11.3 - - - -
132I ASP* 3.9 12.3 + - - +
136I THR* 3.5 21.6 + - - +
139I GLN* 5.1 4.0 - - - +
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Residues in contact with TRP 35 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G MET* 3.1 40.0 + - + +
32G GLN* 3.1 6.0 + - - +
34G ASN* 1.3 82.1 - - + +
36G GLY* 1.3 57.4 + - - +
37G PHE* 3.4 34.7 - + + -
81G GLN* 3.4 33.4 - - - -
82G THR* 3.9 13.2 - - - -
83G LEU* 4.1 6.3 - - + -
86G GLN* 3.5 39.0 - - - -
136I THR* 3.7 6.3 - - - +
139I GLN* 5.5 6.6 - - - +
140I LEU* 3.3 24.8 - - - +
143I LYS* 3.9 27.1 + - - +
----------------------------------------------------------
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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