Contacts of the helix formed by residues 13 - 47 (chain T) in PDB entry 1N34
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 LEU 13 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A G 5.9 10.1 - - - +
9T ASN* 5.3 8.1 - - + -
10T LEU* 2.5 32.5 + - + +
11T SER* 2.9 8.7 - - - +
12T ALA* 1.3 69.5 - - - +
14T LYS* 1.3 58.2 + - - +
15T ARG* 3.0 2.0 - - - -
16T HIS* 2.5 43.2 + - + +
17T ARG* 3.2 32.1 - - + +
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Residues in contact with LYS 14 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A G 3.5 6.2 + - - -
62A U 3.3 26.6 + - - -
102A G 5.4 4.7 - - - +
103A C 4.3 9.2 - - - +
104A G 4.8 12.3 - - - +
106A C 3.8 20.9 - - - +
107A G 4.6 2.4 + - - -
11T SER 3.2 9.8 + - - +
12T ALA* 2.7 47.2 + - - +
13T LEU* 1.3 79.3 - - - +
15T ARG* 1.3 57.4 + - + +
16T HIS 2.5 1.7 + - - -
17T ARG* 2.4 63.1 + - - +
18T GLN* 2.6 23.6 + - + +
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Residues in contact with ARG 15 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A C 2.9 37.0 + - - +
107A G 2.9 53.8 + - - +
108A G 3.5 53.2 - - + +
323A U 5.8 2.0 + - - -
324A G 5.8 2.6 + - - -
12T ALA 3.7 10.1 - - - +
13T LEU* 4.3 1.1 - - - +
14T LYS* 1.3 84.3 - - + +
16T HIS* 1.3 51.8 + - - +
18T GLN* 2.8 23.7 - - - +
19T SER* 2.5 37.6 + - - -
----------------------------------------------------------
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Residues in contact with HIS 16 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A G 3.4 12.8 - - - +
333A G 2.9 59.0 + - - -
13T LEU* 2.5 21.7 + - + +
14T LYS 2.5 4.9 + - - -
15T ARG* 1.3 69.1 - - - +
17T ARG* 1.3 71.0 + - + +
18T GLN 2.8 2.1 + - - -
19T SER* 2.4 30.2 + - - -
20T LEU* 3.0 31.3 + - + +
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Residues in contact with ARG 17 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A G 2.7 31.6 + - - -
103A C 2.6 47.5 + - - +
11T SER* 3.6 20.2 + - - +
13T LEU* 3.2 27.6 - - + +
14T LYS* 2.4 29.8 + - - +
16T HIS* 1.3 77.5 - - + +
18T GLN* 1.3 64.0 + - + +
20T LEU* 3.4 13.9 - - - +
21T LYS* 3.2 29.3 + - - +
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Residues in contact with GLN 18 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A G 3.1 40.0 + - - +
105A G 3.8 25.7 + - - -
106A C 5.6 5.1 - - - +
14T LYS* 2.6 31.2 + - + +
15T ARG* 2.8 39.4 - - - +
17T ARG* 1.3 70.1 - - + +
19T SER* 1.3 66.8 + - - +
21T LYS* 3.1 12.9 + - - +
22T ARG* 3.1 28.4 + - - +
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Residues in contact with SER 19 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A C 4.4 9.4 - - - -
323A U 3.6 37.2 - - - -
329A A 6.3 0.2 - - - -
15T ARG 2.5 15.1 + - - -
16T HIS* 2.4 40.7 + - - -
18T GLN* 1.3 67.7 - - - +
20T LEU* 1.3 70.5 + - - +
22T ARG* 2.6 18.7 + - - +
23T ARG* 2.7 14.7 + - - -
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Residues in contact with LEU 20 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A C 5.5 0.2 + - - -
16T HIS* 3.0 39.9 + - + +
17T ARG* 3.4 12.1 - - - +
19T SER* 1.3 83.1 + - - +
21T LYS* 1.3 68.9 + - + +
23T ARG* 3.0 32.1 + - - +
24T LEU* 3.2 25.0 + - + +
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Residues in contact with LYS 21 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A C 3.4 40.9 + - - -
104A G 3.8 16.6 + - - +
150A C 4.7 20.7 + - - -
151A A 5.6 1.2 - - - -
17T ARG* 3.2 17.6 + - - +
18T GLN* 3.1 12.4 + - - +
20T LEU* 1.3 80.0 - - + +
22T ARG* 1.3 63.4 + - - +
24T LEU* 3.5 10.5 + - - +
25T ARG* 3.0 43.2 + - - +
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Residues in contact with ARG 22 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A G 4.5 16.4 + - - -
175A C 5.0 8.3 + - - -
323A U 3.4 33.3 + - - +
324A G 2.8 37.8 + - - -
18T GLN* 3.1 16.5 + - - +
19T SER* 2.6 18.3 + - - +
21T LYS* 1.3 72.0 - - + +
23T ARG* 1.3 50.1 + - - +
25T ARG* 2.5 26.2 + - + +
26T ASN* 2.4 41.2 + - - +
70T SER* 4.2 6.3 + - - -
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Residues in contact with ARG 23 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A C 3.0 50.3 - - - +
323A U 3.7 14.0 - - - +
1436A U 4.7 12.7 + - - -
1460A A 5.2 2.4 + - - -
19T SER 2.7 12.2 + - - +
20T LEU* 3.0 24.9 + - - +
22T ARG* 1.3 74.0 - - - +
24T LEU* 1.3 90.8 + - - +
26T ASN 2.8 0.2 + - - -
27T LYS* 2.6 63.3 + - + +
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Residues in contact with LEU 24 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1459A C 4.7 9.3 - - - +
1460A A 4.4 16.6 - - - +
20T LEU* 3.2 26.6 + - + +
21T LYS* 3.6 9.0 - - - +
23T ARG* 1.3 106.4 - - - +
25T ARG* 1.3 64.5 + - - +
27T LYS* 4.2 10.0 - - - +
28T ALA* 3.1 23.4 + - - +
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Residues in contact with ARG 25 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A G 4.4 7.3 + - - -
174A C 4.2 17.5 + - - -
175A C 4.7 29.2 + - - +
21T LYS* 3.0 45.7 + - - +
22T ARG* 2.5 32.2 + - + +
24T LEU* 1.3 75.9 - - - +
26T ASN* 1.3 66.0 + - - +
28T ALA* 3.8 2.0 - - - +
29T LYS* 3.0 21.5 + - + +
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Residues in contact with ASN 26 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A U 3.0 36.9 + - - +
324A G 2.8 26.7 + - - -
22T ARG* 2.4 32.7 + - - +
23T ARG 2.8 1.5 + - - +
25T ARG* 1.3 70.3 - - - +
27T LYS* 1.3 66.5 + - - +
29T LYS* 2.8 16.8 + - - +
30T LYS* 2.9 19.6 + - - +
70T SER* 3.9 1.0 - - - -
71T THR* 3.0 49.5 + - + +
----------------------------------------------------------
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Residues in contact with LYS 27 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A U 4.6 0.6 + - - -
1436A U 5.7 2.7 - - - +
1437A C 5.3 9.6 - - - +
1459A C 3.6 21.8 + - - +
1460A A 3.1 37.3 + - - -
23T ARG* 2.6 50.3 + - + +
24T LEU* 3.8 11.2 - - - +
26T ASN* 1.3 74.4 - - - +
28T ALA* 1.3 64.5 + - - +
30T LYS* 3.0 6.4 + - - +
31T SER* 2.8 29.6 + - - +
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Residues in contact with ALA 28 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1455A G 3.5 35.5 - - - +
1459A C 3.6 9.0 - - - +
24T LEU 3.1 16.0 + - - +
25T ARG* 3.8 2.2 - - - +
27T LYS* 1.3 79.2 - - - +
29T LYS* 1.3 58.7 + - - +
31T SER* 3.0 8.8 + - - -
32T ALA* 2.8 32.4 + - - +
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Residues in contact with LYS 29 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A C 3.8 27.6 + - - +
25T ARG* 3.0 16.0 + - + +
26T ASN* 2.8 17.3 + - - +
28T ALA* 1.3 71.5 - - - +
30T LYS* 1.3 55.8 + - - +
32T ALA* 2.9 21.6 - - - +
33T ILE* 3.6 10.4 + - - +
62T LEU* 4.0 8.6 - - + +
65T LYS* 4.0 5.5 + - - -
66T ALA* 3.1 45.4 + - + +
68T LYS* 5.1 0.8 - - - +
69T GLY* 3.5 20.2 + - - +
71T THR* 3.5 17.2 - - + +
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Residues in contact with LYS 30 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A U 5.7 2.4 + - - -
323A U 5.3 6.9 + - - -
1437A C 5.1 8.5 + - - +
26T ASN* 2.9 14.8 + - - +
27T LYS* 3.0 9.8 + - - +
29T LYS* 1.3 72.9 - - - +
31T SER* 1.3 59.0 + - - +
32T ALA 2.8 0.9 - - - -
33T ILE* 2.5 44.0 + - + +
34T LYS* 3.3 22.7 + - - +
66T ALA* 6.0 0.7 - - - -
71T THR* 4.4 17.9 + - - +
72T LEU* 3.4 29.3 - - + +
80T ARG* 3.2 28.6 - - - +
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Residues in contact with SER 31 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1455A G 3.6 5.6 + - - -
1459A C 3.1 25.5 + - - -
27T LYS* 2.8 24.8 + - - -
28T ALA* 3.0 5.9 + - - -
30T LYS* 1.3 74.3 - - - +
32T ALA* 1.3 72.2 + - - +
34T LYS* 3.2 20.0 + - - +
35T THR* 2.8 25.8 + - - +
----------------------------------------------------------
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Residues in contact with ALA 32 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1454A G 4.3 6.9 - - - +
1455A G 3.7 23.3 - - - -
28T ALA 2.8 16.1 + - - +
29T LYS* 2.9 20.2 - - - +
30T LYS 2.7 2.8 + - - -
31T SER* 1.3 71.5 + - - +
33T ILE* 1.3 67.0 + - - +
35T THR* 2.7 17.4 + - - -
36T LEU* 3.2 9.8 + - - +
62T LEU* 4.7 12.6 - - + -
----------------------------------------------------------
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Residues in contact with ILE 33 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29T LYS 3.9 3.6 - - - +
30T LYS* 2.5 20.0 + - + +
32T ALA* 1.3 72.2 - - - +
34T LYS* 1.3 56.0 + - + +
36T LEU* 2.6 17.1 + - - +
37T SER* 2.5 47.1 + - - +
59T ALA* 5.9 1.6 - - + +
62T LEU* 3.3 24.9 - - + -
63T ILE* 3.1 52.7 - - + +
66T ALA* 3.8 17.0 - - + -
72T LEU* 4.7 10.1 - - + -
80T ARG* 5.3 11.0 - - + +
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Residues in contact with LYS 34 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A G 5.9 1.8 + - - -
1437A C 4.2 16.6 + - - -
1438A G 3.6 36.4 + - - +
30T LYS* 3.7 35.2 - - - +
31T SER* 3.3 18.4 - - - +
33T ILE* 1.3 77.1 - - + +
35T THR* 1.3 54.4 + - + +
37T SER* 2.5 15.9 + - - -
38T LYS* 2.5 52.6 + - - +
80T ARG* 3.7 28.4 - - - +
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Residues in contact with THR 35 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1441A G 3.7 20.0 - - - +
1454A G 3.4 12.4 + - - +
1455A G 2.5 31.6 + - - +
31T SER* 2.8 6.6 + - - +
32T ALA 2.7 16.3 + - - -
34T LYS* 1.3 76.6 - - + +
36T LEU* 1.3 59.5 + - - +
38T LYS* 3.5 31.3 - - + +
39T LYS* 3.3 18.9 + - - +
----------------------------------------------------------
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Residues in contact with LEU 36 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1453A G 3.4 25.4 - - - +
1454A G 4.5 13.4 - - - -
32T ALA 3.2 11.4 + - - +
33T ILE* 2.6 20.7 + - - +
35T THR* 1.3 73.0 - - - +
37T SER* 1.3 48.7 + - - -
39T LYS* 3.0 15.9 - - + +
40T ALA 2.8 30.7 + - - -
55T ILE* 3.5 22.2 - - + +
58T LYS* 4.6 9.2 - - + -
59T ALA* 3.4 41.3 - - + +
62T LEU* 4.7 12.3 - - + -
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Residues in contact with SER 37 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33T ILE* 2.5 42.9 + - - +
34T LYS* 2.5 12.5 + - - -
36T LEU* 1.3 70.7 - - - +
38T LYS* 1.3 67.8 + - - +
40T ALA* 3.1 11.6 - - - +
41T ILE* 3.0 22.3 + - - +
59T ALA* 4.9 6.8 - - - +
63T ILE* 5.2 2.2 - - - +
84T LEU* 4.7 14.1 - - - -
87T LYS* 6.0 2.9 - - - -
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Residues in contact with LYS 38 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1438A G 6.0 0.7 - - - -
1439A C 2.8 39.1 + - - +
1440A C 5.1 8.2 + - - +
1441A G 5.2 1.8 + - - -
34T LYS* 2.5 28.2 + - + +
35T THR* 3.5 43.3 - - + +
37T SER* 1.3 75.4 - - - +
39T LYS* 1.3 68.8 + - - +
41T ILE* 2.8 12.7 + - - +
42T GLN* 2.9 16.6 + - + +
----------------------------------------------------------
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Residues in contact with LYS 39 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1453A G 3.0 39.7 + - - +
1454A G 3.2 17.4 + - - +
35T THR 3.3 10.6 + - - +
36T LEU* 3.0 20.8 + - + +
38T LYS* 1.3 78.6 - - - +
40T ALA* 1.3 65.9 + - - +
41T ILE 3.1 0.3 + - - -
42T GLN* 3.2 9.9 + - - +
43T LEU* 3.0 30.1 - - + +
55T ILE* 3.3 27.4 - - + -
----------------------------------------------------------
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Residues in contact with ALA 40 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36T LEU* 2.8 12.7 + - + +
37T SER* 3.1 19.7 - - - +
39T LYS* 1.3 74.8 - - - +
41T ILE* 1.3 58.7 + - - +
43T LEU* 3.4 14.9 - - - +
44T ALA* 3.9 2.8 + - - +
52T ALA* 3.7 10.8 - - - +
55T ILE* 3.3 35.0 - - + -
56T MET* 4.0 15.7 - - + +
59T ALA* 4.9 0.7 - - + -
84T LEU* 4.8 8.1 - - + -
88T VAL* 4.9 4.6 - - + +
----------------------------------------------------------
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Residues in contact with ILE 41 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37T SER 3.0 7.0 + - - +
38T LYS* 2.8 13.3 + - - +
40T ALA* 1.3 68.9 - - - +
42T GLN* 1.3 55.9 + - - +
43T LEU 2.8 4.9 - - - -
44T ALA* 2.4 40.1 + - + +
45T GLN* 3.6 6.1 + - - +
84T LEU* 3.2 34.8 - - + -
87T LYS* 3.3 45.3 - - + +
88T VAL* 3.4 11.9 - - + -
91T LEU* 4.2 23.6 - - + -
----------------------------------------------------------
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Residues in contact with GLN 42 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38T LYS* 2.9 14.9 + - + +
39T LYS* 3.6 11.7 - - - +
41T ILE* 1.3 77.6 - - - +
43T LEU* 1.3 66.1 + - + +
44T ALA 3.5 0.2 + - - -
45T GLN* 3.7 28.4 + - - +
46T GLU* 3.0 30.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 43 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39T LYS* 3.0 28.3 - - + +
40T ALA 3.4 11.0 - - - +
41T ILE 2.7 0.6 + - - -
42T GLN* 1.3 82.0 - - + +
44T ALA* 1.3 65.8 + - - +
46T GLU* 2.8 15.9 + - + +
47T GLY 2.7 20.3 + - - -
48T LYS* 3.5 33.1 + - + -
51T GLU* 3.9 15.5 - - + +
52T ALA* 3.7 14.8 - - + -
55T ILE* 3.7 22.9 - - + -
----------------------------------------------------------
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Residues in contact with ALA 44 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40T ALA 3.9 2.0 + - - +
41T ILE* 2.4 32.4 + - + +
43T LEU* 1.3 71.7 - - - +
45T GLN* 1.3 65.6 + - - +
47T GLY* 2.7 18.6 + - - -
52T ALA* 4.5 4.0 - - - +
88T VAL* 3.8 14.1 - - + +
91T LEU* 3.3 32.3 - - + +
92T LEU* 3.6 24.0 - - + +
----------------------------------------------------------
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Residues in contact with GLN 45 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41T ILE* 3.6 6.5 + - - +
42T GLN* 3.8 29.1 + - - +
44T ALA* 1.3 72.0 - - - +
46T GLU* 1.3 70.1 + - - +
91T LEU* 2.8 36.2 - - + +
94T ALA* 5.3 8.3 - - - +
----------------------------------------------------------
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Residues in contact with GLU 46 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42T GLN* 3.0 35.1 + - - +
43T LEU* 2.8 15.2 + - + +
44T ALA 2.8 2.6 + - - -
45T GLN* 1.3 81.2 - - - +
47T GLY* 1.3 56.4 + - - +
48T LYS* 3.2 42.6 + - + +
94T ALA* 5.6 3.6 - - - +
----------------------------------------------------------
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Residues in contact with GLY 47 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43T LEU 2.7 1.2 + - - -
44T ALA 2.7 17.5 + - - -
45T GLN 4.4 0.2 - - - -
46T GLU* 1.3 76.5 - - - +
48T LYS* 1.3 56.1 + - - +
49T ALA* 2.5 23.3 + - - +
92T LEU* 4.7 9.9 - - - -
94T ALA* 6.1 3.8 - - - -
96T GLY* 5.8 10.3 - - - -
----------------------------------------------------------
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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