Contacts of the helix formed by residues 8 - 44 (chain C) in PDB entry 3GWK
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 THR 8 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LYS 3.5 4.5 + - - +
7C LEU* 1.3 74.6 - - - +
9C PRO* 1.4 76.2 - - + +
10C GLU* 3.4 6.9 + - - +
11C GLU* 3.0 36.9 + - - +
12C LEU* 2.9 22.1 + - - +
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Residues in contact with PRO 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C THR* 1.4 86.5 - - + +
10C GLU* 1.3 58.4 + - + +
12C LEU* 3.3 5.3 + - + +
13C ARG* 2.9 51.2 + - - +
81C ALA* 3.6 23.1 - - + +
84C ILE* 3.7 32.1 - - + -
85C GLU* 3.8 21.5 - - + +
88C ASP* 4.6 8.3 - - - +
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Residues in contact with GLU 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C THR* 3.2 6.7 + - - +
9C PRO* 1.3 80.7 - - + +
11C GLU* 1.3 57.2 + - - +
13C ARG* 2.8 41.4 + - - +
14C SER* 2.9 33.0 + - - +
85C GLU* 4.4 2.2 - - - +
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Residues in contact with GLU 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LYS 4.1 2.6 - - - +
7C LEU* 3.4 27.6 - - + +
8C THR* 3.0 45.2 + - - +
10C GLU* 1.3 76.5 - - + +
12C LEU* 1.3 65.1 + - - +
14C SER* 3.2 7.4 + - - -
15C SER* 3.0 27.8 + - - +
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Residues in contact with LEU 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C ILE* 4.5 7.9 - - + -
7C LEU* 3.9 32.1 - - + +
8C THR 2.9 19.1 + - - +
9C PRO 3.3 6.5 + - - +
11C GLU* 1.3 77.3 - - - +
13C ARG* 1.3 56.4 + - - +
15C SER* 3.4 5.2 + - - -
16C ALA* 2.9 29.0 + - - +
77C LEU* 3.9 35.9 - - + +
80C VAL* 4.1 8.5 - - + -
81C ALA* 3.9 27.1 - - + +
84C ILE* 3.9 27.8 - - + -
40E ILE* 6.5 0.2 - - + -
44E TRP* 5.7 5.2 - - + -
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Residues in contact with ARG 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C PRO* 2.9 22.7 + - - +
10C GLU* 2.8 40.7 + - - +
11C GLU 3.2 0.2 - - - -
12C LEU* 1.3 72.8 - - - +
14C SER* 1.3 66.0 + - - +
16C ALA* 3.3 8.0 + - - +
17C GLN* 3.1 22.7 + - - +
78C LEU* 4.1 19.6 + - + +
81C ALA* 3.7 18.5 + - + +
82C ASP* 2.8 38.6 + - - +
85C GLU* 2.9 40.6 + - - -
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Residues in contact with SER 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLU* 2.9 18.2 + - - -
11C GLU* 3.2 8.0 + - - -
13C ARG* 1.3 77.7 - - - +
15C SER* 1.3 63.1 + - - +
17C GLN* 3.4 13.9 + - - +
18C LYS* 3.6 25.5 + - - +
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Residues in contact with SER 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 4.7 10.4 - - - +
11C GLU* 3.0 18.1 + - - +
12C LEU* 3.7 6.5 - - - -
14C SER* 1.3 77.2 - - - +
16C ALA* 1.3 63.8 + - - +
18C LYS* 3.0 17.1 + - - +
19C TYR* 3.2 17.1 - - - -
77C LEU* 4.2 11.7 - - - -
36E GLU* 2.7 35.6 + - - +
39E VAL* 5.2 3.6 - - - +
40E ILE* 5.0 5.8 - - - +
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Residues in contact with ALA 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU 2.9 18.1 + - - +
13C ARG 3.3 6.3 + - - +
15C SER* 1.3 76.4 - - - +
17C GLN* 1.3 64.2 + - - +
19C TYR* 3.0 13.2 + - - +
20C THR 3.0 10.9 + - - -
74C ASN* 3.1 36.9 - - - +
77C LEU* 3.9 15.4 - - + +
78C LEU* 3.7 18.4 - - + -
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Residues in contact with GLN 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ARG 3.1 12.7 + - - +
14C SER* 3.7 11.4 - - - +
15C SER 3.2 0.4 - - - -
16C ALA* 1.3 76.2 - - - +
18C LYS* 1.3 59.5 - - + +
20C THR* 3.3 16.6 - - - +
21C ALA* 2.9 43.4 + - + +
24C GLN* 5.9 0.4 - - - +
74C ASN* 4.6 0.4 - - - -
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Residues in contact with LYS 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C SER* 3.6 26.1 - - - +
15C SER* 3.0 8.2 + - - +
17C GLN* 1.3 79.0 - - + +
19C TYR* 1.4 57.5 + - + +
21C ALA* 4.0 4.0 - - - +
22C GLY* 3.0 24.8 + - - -
32E LEU* 4.3 27.1 - - + +
33E LEU* 3.8 21.0 - - + +
36E GLU* 2.8 41.6 + - + +
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Residues in contact with TYR 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C SER 3.2 23.1 - - - -
16C ALA 3.0 7.1 + - - +
18C LYS* 1.4 76.2 - - - +
20C THR* 1.3 60.7 + - - +
22C GLY 3.3 0.7 + - - -
23C SER* 2.9 29.5 + - - -
70C LEU* 3.4 39.7 - - + +
73C ILE* 3.7 31.0 - - + -
74C ASN 4.1 5.8 - - - +
77C LEU* 4.2 5.4 - - + -
33E LEU* 4.0 20.4 - - + -
36E GLU* 3.6 25.9 - - + -
37E GLN* 2.6 47.1 + - + +
40E ILE* 3.4 23.3 - - + +
56E PHE* 4.8 0.4 - + - -
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Residues in contact with THR 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ALA 3.0 12.5 + - - +
17C GLN* 3.3 30.1 - - - +
19C TYR* 1.3 79.2 - - - +
21C ALA* 1.3 66.0 + - - +
23C SER* 3.3 2.2 + - - -
24C GLN* 3.0 47.3 + - - +
71C GLU* 2.7 28.5 + - - -
74C ASN* 3.6 19.8 + - - +
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Residues in contact with ALA 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLN* 2.9 32.0 + - + +
18C LYS* 4.0 5.6 - - - +
20C THR* 1.3 78.1 - - - +
22C GLY* 1.3 62.7 + - - +
24C GLN* 3.3 11.2 + - - +
25C GLN* 3.0 35.4 + - + +
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Residues in contact with GLY 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C LYS 3.0 18.2 + - - -
19C TYR 3.8 0.7 - - - -
21C ALA* 1.3 74.8 - - - +
23C SER* 1.3 64.7 + - - +
25C GLN* 3.2 13.2 + - - +
26C VAL* 3.0 28.9 + - - +
70C LEU* 3.9 7.9 - - - -
29E VAL* 3.7 17.9 - - - -
33E LEU* 4.5 0.4 - - - -
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Residues in contact with SER 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C TYR 2.9 18.2 + - - -
20C THR* 3.3 6.5 + - - -
22C GLY* 1.3 74.5 - - - +
24C GLN* 1.3 66.5 + - - +
26C VAL* 3.8 2.0 - - - +
27C THR* 3.0 29.0 + - - -
67C ALA* 2.7 34.4 + - - +
70C LEU* 3.8 14.6 - - - +
71C GLU* 3.7 18.1 + - - +
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Residues in contact with GLN 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLN* 5.9 0.6 - - - +
20C THR* 3.0 45.8 + - - +
21C ALA* 3.7 8.4 - - - +
23C SER* 1.3 79.1 - - - +
25C GLN* 1.3 58.2 + - + +
27C THR* 3.4 5.9 + - - -
28C GLU* 3.0 46.2 + - + +
71C GLU* 5.5 1.3 - - - +
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Residues in contact with GLN 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ALA* 3.0 27.7 + - + +
22C GLY* 3.2 7.7 + - - +
24C GLN* 1.3 78.4 - - + +
26C VAL* 1.3 62.4 + - - +
28C GLU* 3.3 11.8 + - - +
29C VAL* 3.0 28.9 + - - +
25E GLN* 2.6 47.7 + - - +
29E VAL* 3.6 16.3 - - + +
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Residues in contact with VAL 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLY 3.0 21.3 + - - +
23C SER 3.8 3.8 - - - +
25C GLN* 1.3 74.0 - - - +
27C THR* 1.3 65.1 + - - +
29C VAL* 3.3 6.7 + - - +
30C LEU* 2.9 23.0 + - - +
63C ILE* 3.3 40.7 - - + +
66C PHE* 4.2 21.5 - - + -
67C ALA* 4.1 8.5 - - + -
70C LEU* 4.6 0.9 - - + -
25E GLN* 6.1 0.2 - - - -
26E VAL* 5.1 17.0 - - + -
29E VAL* 3.9 25.6 - - + -
63E ILE* 6.4 0.4 - - + -
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Residues in contact with THR 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C SER* 3.0 19.2 + - - -
24C GLN* 3.7 6.3 - - - -
26C VAL* 1.3 76.2 - - - +
28C GLU* 1.3 61.0 + - + +
30C LEU* 3.3 6.4 + - - +
31C ASN* 2.9 56.9 + - - +
67C ALA* 3.3 16.7 - - - +
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Residues in contact with GLU 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLN* 3.0 32.2 + - - +
25C GLN* 3.6 11.5 - - - +
27C THR* 1.3 76.2 - - + +
29C VAL* 1.3 68.0 + - + +
31C ASN* 3.3 7.4 + - - +
32C LEU* 3.0 25.1 + - - +
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Residues in contact with VAL 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLN 3.0 18.6 + - - +
26C VAL 3.3 6.3 + - - +
28C GLU* 1.3 75.4 - - + +
30C LEU* 1.3 65.8 + - - +
32C LEU* 3.3 6.8 + - + +
33C LEU* 3.0 37.9 + - + +
22E GLY* 3.7 30.1 - - - +
25E GLN* 3.7 31.0 - - + -
26E VAL* 3.9 16.6 - - + -
66E PHE* 4.8 3.6 - - + -
70E LEU* 4.4 3.4 - - + -
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C VAL 2.9 17.6 + - - +
27C THR* 3.7 6.7 - - - +
29C VAL* 1.3 80.2 - - - +
31C ASN* 1.3 65.2 + - - +
33C LEU* 5.0 1.3 - - - -
34C THR* 2.8 42.6 + - - +
56C PHE* 4.1 7.2 - - + -
60C SER* 3.6 34.5 - - - +
63C ILE* 4.1 12.3 - - + -
64C THR* 3.3 33.2 - - - +
66E PHE* 3.8 26.5 - - + -
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Residues in contact with ASN 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C THR* 2.9 46.4 + - - +
28C GLU* 3.9 6.2 - - - +
30C LEU* 1.3 87.3 - - - +
32C LEU* 1.3 62.8 + - - +
34C THR* 3.4 6.5 + - - -
35C GLN* 3.2 30.6 + - - +
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Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C GLU 3.0 18.1 + - - +
29C VAL* 3.7 6.1 - - - +
31C ASN* 1.3 76.5 - - - +
33C LEU* 1.3 65.2 + - + +
35C GLN* 3.2 20.4 + - - +
36C GLU* 3.0 27.4 + - - +
18E LYS* 4.1 44.0 - - + +
22E GLY* 6.5 0.7 - - - -
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Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C VAL* 3.0 30.2 + - + +
30C LEU* 4.3 0.7 - - - +
32C LEU* 1.3 79.3 - - + +
34C THR* 1.3 60.6 + - - +
35C GLN 3.2 0.2 - - - -
36C GLU* 3.7 12.0 - - + +
37C GLN* 2.8 32.7 + - - +
56C PHE* 3.9 17.7 - - + -
18E LYS* 3.7 43.3 - - + +
19E TYR* 3.8 19.2 + - + +
22E GLY* 4.5 0.9 - - - -
66E PHE* 5.3 0.9 - - + -
70E LEU* 3.5 39.5 - - + -
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Residues in contact with THR 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 2.8 31.1 + - - +
31C ASN* 3.6 7.4 - - - -
33C LEU* 1.3 76.0 - - - +
35C GLN* 1.3 64.1 + - - +
37C GLN* 3.4 5.2 + - + +
38C ALA* 3.2 21.5 + - + +
56C PHE* 3.8 22.1 - - + -
60C SER* 4.6 3.1 + - - -
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Residues in contact with GLN 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ASN* 3.2 19.0 + - - +
32C LEU* 3.4 17.8 - - - +
33C LEU 3.2 0.2 - - - -
34C THR* 1.3 79.3 - - + +
36C GLU* 1.3 68.8 + - - +
38C ALA* 3.1 8.1 + - - +
39C VAL* 3.0 28.3 + - + +
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Residues in contact with GLU 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 3.0 22.1 + - - +
33C LEU* 3.3 15.4 + - + +
35C GLN* 1.3 82.6 - - - +
37C GLN* 1.3 62.6 + - - +
39C VAL* 3.2 15.6 + - - +
40C ILE* 2.9 27.2 + - - +
15E SER* 2.7 33.0 + - - +
18E LYS* 3.6 37.9 + - + +
19E TYR* 3.3 23.8 - - + +
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Residues in contact with GLN 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU 2.8 23.9 + - - +
34C THR* 3.5 7.9 - - + +
36C GLU* 1.3 73.4 - - - +
38C ALA* 1.3 57.2 + - - +
40C ILE* 3.4 9.3 + - - +
41C ASP* 2.9 29.0 + - - +
49C PHE* 5.7 3.0 - - - -
52C PHE* 3.9 3.6 - - - +
53C GLU* 3.9 18.7 + - - +
56C PHE* 3.4 47.4 - - + +
57C ASN* 5.5 1.0 - - - +
19E TYR* 2.7 31.9 + - - -
73E ILE* 3.8 12.7 - - - +
----------------------------------------------------------
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Residues in contact with ALA 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C THR* 3.2 9.4 + - + +
35C GLN* 3.1 11.7 + - - +
37C GLN* 1.3 75.9 - - - +
39C VAL* 1.3 66.7 + - + +
41C ASP* 3.2 7.0 + - - +
42C GLU* 3.0 46.2 + - - +
----------------------------------------------------------
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Residues in contact with VAL 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C GLN* 3.0 18.4 + - + +
36C GLU* 3.2 19.3 + - - +
38C ALA* 1.3 75.3 - - + +
40C ILE* 1.3 62.5 + - + +
42C GLU* 3.3 5.5 + - - +
43C ASN* 3.1 47.2 + - - +
7E LEU* 4.0 21.1 - - + -
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Residues in contact with ILE 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C GLU 2.9 14.0 + - - +
37C GLN* 3.7 8.5 - - - +
39C VAL* 1.3 76.3 - - + +
41C ASP* 1.3 66.7 + - - +
44C TRP* 3.2 41.0 + - + +
49C PHE* 4.0 30.5 - - + -
7E LEU* 4.1 19.3 - - + -
15E SER* 3.8 20.0 - - - +
19E TYR* 3.5 30.1 - - + +
73E ILE* 5.1 0.2 - - + -
77E LEU* 4.1 21.8 - - + -
----------------------------------------------------------
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Residues in contact with ASP 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C GLN 2.9 17.5 + - - +
38C ALA* 3.2 9.1 + - - +
40C ILE* 1.3 81.6 - - - +
42C GLU* 1.3 65.5 + - - +
44C TRP 3.7 12.6 + - - +
45C ASP* 5.1 1.9 - - - -
46C GLY 5.7 0.7 - - - +
53C GLU* 3.6 26.4 - - - +
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Residues in contact with GLU 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ALA* 3.0 32.9 + - - +
39C VAL* 4.7 3.3 - - - +
41C ASP* 1.3 84.8 - - - +
43C ASN* 1.3 76.1 + - - +
44C TRP 3.4 2.9 + - - -
45C ASP* 5.2 1.4 + - - +
6E LYS* 4.7 10.2 + - - +
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Residues in contact with ASN 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C VAL* 3.1 38.4 + - - +
40C ILE 3.9 0.7 - - - -
42C GLU* 1.3 93.2 + - - +
44C TRP* 1.3 62.2 + - - +
45C ASP 4.0 1.1 - - - -
5E ILE* 4.0 0.5 - - - +
6E LYS* 2.9 53.5 + - + +
7E LEU* 3.4 27.2 + - + +
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Residues in contact with TRP 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ILE* 3.2 31.4 + - + +
41C ASP* 3.7 12.6 - - - +
42C GLU 3.4 0.6 - - - -
43C ASN* 1.3 82.3 - - - +
45C ASP* 1.3 77.2 + - - +
46C GLY 3.7 5.2 + - - +
48C THR* 3.4 45.8 + - + -
49C PHE* 3.7 37.9 - + + -
5E ILE* 3.7 42.1 - - + +
6E LYS 4.8 0.7 - - - +
7E LEU* 5.2 4.3 - - + -
12E LEU* 5.0 10.5 - - + -
77E LEU* 4.6 6.5 - - + -
80E VAL* 3.8 31.9 - - + -
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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