Contacts of the helix formed by residues 4 - 42 (chain D) in PDB entry 5JRE
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 ASN 4 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C SER* 4.8 5.7 - - - -
102C GLU* 4.3 15.4 - - - +
2D LEU 3.8 0.4 + - - -
3D PRO* 1.3 81.1 - - - +
5D LEU* 1.3 60.3 + - - +
6D ASP 3.3 2.7 - - - -
7D ASN* 3.2 25.0 + - + +
8D LEU* 2.8 25.9 + - + +
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Residues in contact with LEU 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C ASP* 3.1 57.0 - - + +
154C TYR* 3.9 25.1 - - + -
155C ILE* 4.3 13.2 - - + -
0D SER* 4.1 7.9 - - - +
2D LEU* 3.9 22.4 + - + +
3D PRO 3.2 4.4 - - - -
4D ASN* 1.3 75.5 - - - +
6D ASP* 1.3 59.0 + - - +
8D LEU* 3.2 6.2 + - + +
9D LYS* 2.9 27.7 + - - +
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Residues in contact with ASP 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C TYR* 2.5 38.6 + - - -
4D ASN 3.3 0.6 - - - -
5D LEU* 1.3 78.4 - - - +
7D ASN* 1.3 67.2 + - - +
9D LYS* 3.5 3.3 + - - +
10D GLU* 3.1 22.5 + - - +
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Residues in contact with ASN 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ASN* 3.2 25.9 + - + +
6D ASP* 1.3 76.9 - - - +
8D LEU* 1.3 61.4 + - - +
10D GLU* 3.3 6.1 + - - +
11D GLU* 2.8 45.6 + - - +
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Residues in contact with LEU 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C LYS* 4.5 8.3 - - + -
108C THR* 3.8 25.8 - - + -
111C TYR* 4.2 26.7 - - + -
112C LEU* 3.7 16.6 - - + -
155C ILE* 3.3 33.9 - - + -
2D LEU* 5.3 5.2 - - + -
3D PRO 4.7 5.2 - - - +
4D ASN* 2.8 17.4 + - - +
5D LEU* 3.5 10.5 - - + +
7D ASN* 1.3 76.9 - - - +
9D LYS* 1.3 56.6 - - - +
11D GLU* 3.3 11.2 + - - +
12D TYR* 2.8 27.4 + - - +
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Residues in contact with LYS 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C TYR* 2.7 63.3 + - + +
155C ILE* 3.9 28.3 - - + +
156C GLU* 3.5 26.7 + - - +
5D LEU 2.9 16.5 + - - +
6D ASP 3.6 5.6 - - - +
8D LEU* 1.3 77.3 - - - +
10D GLU* 1.3 59.6 + - - +
12D TYR* 3.3 1.4 + - - +
13D GLN* 2.9 38.4 + - + +
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Residues in contact with GLU 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ASP 3.1 14.0 + - - +
7D ASN* 3.6 8.1 - - - +
8D LEU 3.3 0.2 - - - -
9D LYS* 1.3 82.7 - - - +
11D GLU* 1.3 57.9 + - + +
13D GLN* 3.4 6.5 + - - +
14D LYS* 2.9 29.3 + - - +
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Residues in contact with GLU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C LYS* 4.5 6.8 - - - +
102C GLU* 4.4 12.1 - - - +
108C THR* 3.9 23.1 + - + +
7D ASN* 2.8 37.2 + - - +
8D LEU* 3.7 11.9 - - - +
10D GLU* 1.3 73.4 - - + +
12D TYR* 1.3 64.5 + - - +
14D LYS* 3.2 18.9 + - - +
15D LEU* 3.0 28.8 + - + +
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Residues in contact with TYR 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C THR* 4.1 7.9 - - + +
109C TRP* 3.7 23.6 - + - -
112C LEU* 3.4 29.4 - - + -
155C ILE* 3.5 20.0 - - + -
156C GLU 3.8 11.0 - - - -
157C LEU* 3.8 10.2 - - + -
158C LYS* 2.8 21.0 + - + -
159C ASN* 3.1 6.2 + - - +
162C LEU* 3.7 13.9 - - + +
8D LEU 2.8 20.1 + - - +
9D LYS 3.7 2.7 - - - +
11D GLU* 1.3 74.2 - - - +
13D GLN* 1.3 83.6 + - - +
15D LEU* 3.1 6.7 + - - +
16D GLU* 2.6 57.8 + - + +
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Residues in contact with GLN 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C ILE 2.7 28.6 + - - +
156C GLU* 3.0 22.8 + - - +
158C LYS* 2.9 24.1 + - - +
9D LYS* 2.9 31.6 + - + +
10D GLU* 3.9 5.4 - - - +
12D TYR* 1.3 85.2 - - - +
14D LYS* 1.3 62.1 + - - +
16D GLU* 3.4 7.1 + - - +
17D GLU* 3.1 22.7 + - - +
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Residues in contact with LYS 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D GLU 2.9 18.8 + - - +
11D GLU* 3.5 17.5 - - - +
13D GLN* 1.3 75.6 - - - +
15D LEU* 1.3 60.6 + - - +
17D GLU* 3.2 7.8 + - + +
18D LYS* 2.9 43.9 + - + +
69D TYR* 2.8 39.1 + - - +
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Residues in contact with LEU 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C THR* 3.7 32.1 - - + -
109C TRP* 3.9 33.4 - - + +
11D GLU* 3.0 16.2 + - + +
12D TYR* 3.1 8.5 + - - +
14D LYS* 1.3 80.6 - - - +
16D GLU* 1.3 57.3 + - - +
18D LYS* 3.2 2.8 + - - +
19D LYS 2.9 24.9 + - - -
69D TYR* 3.6 36.6 - - + -
71D MET* 4.3 12.8 - - + -
72D PHE* 3.3 24.9 - - + -
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Residues in contact with GLU 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C TRP* 3.4 23.1 - - + -
158C LYS* 3.9 19.5 - - + +
159C ASN* 3.5 11.5 + - - +
12D TYR* 2.6 55.4 + - + +
13D GLN* 3.9 12.3 - - - +
15D LEU* 1.3 75.0 - - - +
17D GLU* 1.3 61.7 + - - +
19D LYS* 3.5 17.2 + - - +
20D GLN* 3.2 22.2 + - - +
72D PHE* 5.3 0.4 - - - -
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Residues in contact with GLU 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D GLN 3.1 13.8 + - - +
14D LYS* 3.2 11.9 + - + +
16D GLU* 1.3 78.3 - - - +
18D LYS* 1.3 60.4 + - + +
20D GLN* 3.4 7.1 + - + +
21D GLU* 3.0 43.7 + - + +
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Residues in contact with LYS 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D LYS* 2.9 31.2 + - + +
15D LEU* 3.2 6.7 + - - +
17D GLU* 1.3 75.6 - - + +
19D LYS* 1.3 60.4 + - - +
21D GLU* 3.2 27.5 + - + +
22D ILE* 2.8 37.4 + - + +
65D GLU* 3.3 28.3 - - - +
69D TYR* 3.5 48.5 - - + +
72D PHE* 4.8 1.3 - - + -
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Residues in contact with LYS 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C TRP* 5.2 6.8 - - + -
159C ASN* 5.0 12.1 - - - +
15D LEU 2.9 16.1 + - - +
16D GLU* 3.6 19.7 + - - +
17D GLU 3.3 0.2 - - - -
18D LYS* 1.3 76.0 - - - +
20D GLN* 1.3 57.5 + - - +
22D ILE* 3.1 5.5 + - - +
23D VAL* 2.9 38.3 + - + +
72D PHE* 3.8 40.0 - - + -
75D ASN* 3.7 29.4 - - - +
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Residues in contact with GLN 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D GLU 3.2 10.8 + - - +
17D GLU* 3.7 9.4 - - + +
19D LYS* 1.3 80.8 - - - +
21D GLU* 1.3 57.1 + - + +
23D VAL* 3.4 14.2 + - - +
24D ASP* 2.9 66.8 + - - +
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Residues in contact with GLU 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLU* 3.0 32.5 + - + +
18D LYS* 3.2 40.3 + - + +
20D GLN* 1.3 76.1 - - + +
22D ILE* 1.3 58.6 + - + +
24D ASP* 3.4 8.0 + - - +
25D ARG* 2.9 48.7 + - - +
65D GLU* 4.4 3.7 - - - +
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Residues in contact with ILE 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D LYS* 2.8 26.2 + - + +
19D LYS* 3.5 4.9 - - - +
21D GLU* 1.3 72.2 - - + +
23D VAL* 1.3 58.1 + - - +
25D ARG* 3.3 7.5 + - - +
26D SER* 2.9 25.8 + - - -
62D GLN* 3.1 32.7 + - - +
65D GLU* 4.4 15.0 - - + +
66D LEU* 3.8 20.0 - - + -
69D TYR* 4.4 15.3 - - + -
72D PHE* 3.9 29.8 - - + +
75D ASN* 3.9 5.2 - - + -
76D GLY 3.7 25.4 - - - +
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Residues in contact with VAL 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LYS* 2.9 26.4 + - + +
20D GLN* 3.8 16.6 - - - +
22D ILE* 1.3 76.4 - - - +
24D ASP* 1.3 66.1 + - - +
26D SER* 3.2 3.9 + - - -
27D ILE* 3.1 38.6 + - + +
75D ASN* 3.8 38.6 - - + +
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Residues in contact with ASP 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D GLN* 2.9 51.0 + - - +
21D GLU* 3.7 7.3 - - - +
23D VAL* 1.3 80.3 - - - +
25D ARG* 1.3 57.6 + - - +
27D ILE* 3.3 13.4 + - - +
28D ARG* 3.0 27.9 + - - +
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Residues in contact with ARG 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D GLU* 2.9 43.6 + - - +
22D ILE* 3.7 8.8 - - - +
24D ASP* 1.3 75.8 - - - +
26D SER* 1.3 57.9 + - - +
28D ARG* 3.2 8.3 + - - +
29D MET* 2.8 41.2 + - + +
58D LEU* 3.7 41.4 - - + +
61D THR* 3.8 25.0 - - - +
62D GLN* 2.8 42.2 + - - +
65D GLU* 3.8 22.4 + - - +
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Residues in contact with SER 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ILE 2.9 18.3 + - - -
23D VAL* 3.4 5.8 - - - -
25D ARG* 1.3 76.7 - - - +
27D ILE* 1.3 57.1 + - - +
29D MET* 3.3 5.0 + - - +
30D SER* 2.9 32.3 + - - -
62D GLN* 3.5 10.5 - - - +
75D ASN 3.7 19.7 + - - -
76D GLY* 3.9 2.0 + - - -
78D ILE* 4.0 4.9 + - - +
79D GLY* 2.9 31.0 + - - -
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Residues in contact with ILE 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D VAL* 3.1 30.4 + - + +
24D ASP* 3.6 14.4 - - - +
26D SER* 1.3 76.2 - - - +
28D ARG* 1.3 63.6 + - - +
30D SER* 3.3 6.8 + - - -
31D LYS* 3.0 52.8 + - + +
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Residues in contact with ARG 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D ASP 3.0 14.2 + - - +
25D ARG* 3.2 9.6 + - - +
27D ILE* 1.3 78.2 - - - +
29D MET* 1.3 57.4 + - - +
31D LYS* 3.4 7.9 + - + +
32D LEU* 2.9 38.3 + - + +
54D GLU* 4.5 14.1 + - - +
58D LEU* 3.5 37.4 - - + +
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Residues in contact with MET 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D ARG* 2.8 22.5 + - + +
26D SER 3.6 4.7 - - - +
28D ARG* 1.3 75.7 - - - +
30D SER* 1.3 58.2 + - - +
33D SER* 2.8 35.2 + - - -
55D LEU* 3.6 14.4 - - + +
58D LEU* 3.8 24.0 - - + +
59D ALA* 3.7 25.6 - - + +
62D GLN* 3.9 31.4 - - - -
79D GLY* 3.4 32.8 - - - +
80D LEU* 3.8 8.3 - - + -
83D TYR* 3.7 19.3 - - + -
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Residues in contact with SER 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D SER 2.9 16.3 + - - -
27D ILE* 3.6 11.2 - - - -
28D ARG 3.2 0.2 - - - -
29D MET* 1.3 75.6 - - - +
31D LYS* 1.3 62.6 + - - +
33D SER* 3.3 4.6 + - - -
34D LYS* 3.2 35.2 + - - +
78D ILE* 4.1 9.4 - - - +
79D GLY* 4.0 7.1 - - - -
82D GLU* 3.1 32.3 + - - +
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Residues in contact with LYS 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D ILE* 3.0 37.5 + - + +
28D ARG* 3.8 7.2 - - + +
30D SER* 1.3 76.3 - - - +
32D LEU* 1.3 62.1 + - - +
34D LYS* 3.2 8.1 + - - +
35D SER* 3.0 24.7 + - - -
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Residues in contact with LEU 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D ARG* 2.9 29.0 + - + +
29D MET 3.9 3.4 - - - +
31D LYS* 1.3 72.3 - - + +
33D SER* 1.3 57.2 + - - +
35D SER* 3.6 6.1 - - - +
36D LEU* 2.9 30.3 + - - +
51D TYR* 3.8 34.5 - - + +
54D GLU* 4.0 37.2 - - + +
55D LEU* 4.1 21.4 - - + +
58D LEU* 3.7 29.4 - - + -
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Residues in contact with SER 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D MET 2.8 22.2 + - - -
30D SER 3.4 6.3 - - - -
31D LYS 3.2 0.2 - - - -
32D LEU* 1.3 76.6 - - - +
34D LYS* 1.3 60.1 + - - +
36D LEU* 3.4 1.9 + - - +
37D ILE* 3.0 36.9 + - - +
55D LEU* 3.5 12.7 - - - +
82D GLU* 3.0 44.3 + - - +
83D TYR* 3.5 2.4 + - - -
86D ALA* 3.9 9.1 - - - +
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Residues in contact with LYS 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D SER* 3.2 24.0 + - - +
31D LYS* 3.2 9.6 + - - +
33D SER* 1.3 78.1 - - - +
35D SER* 1.3 61.0 + - - +
37D ILE* 3.7 12.3 - - + +
38D TYR* 2.8 55.0 + - + -
82D GLU* 2.7 37.3 + - - +
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Residues in contact with SER 35 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D LYS 3.0 14.6 + - - -
32D LEU* 3.6 11.3 - - - +
33D SER 3.3 0.2 - - - -
34D LYS* 1.3 77.5 - - - +
36D LEU* 1.3 61.5 + - - +
38D TYR* 3.9 3.7 - - - +
39D SER* 3.0 29.5 + - - -
42D ARG* 5.0 0.3 + - - -
51D TYR* 3.8 33.6 + - - -
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Residues in contact with LEU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU 2.9 17.7 + - - +
33D SER 3.6 4.0 - - - +
35D SER* 1.3 76.5 - - - +
37D ILE* 1.3 63.2 + - - +
39D SER* 3.6 0.9 - - - -
40D MET* 2.9 31.0 + - + +
48D ALA* 3.2 38.8 - - + +
51D TYR* 3.9 13.2 - - + -
52D LYS* 3.9 22.2 - - + +
55D LEU* 4.0 5.2 - - + -
86D ALA* 4.0 20.6 - - + +
87D LEU* 4.0 23.8 - - + -
90D TYR* 4.1 11.7 - - + -
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Residues in contact with ILE 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D SER* 3.0 27.1 + - - +
34D LYS* 3.3 13.9 + - + +
36D LEU* 1.3 76.8 - - - +
38D TYR* 1.3 72.1 + - + +
40D MET* 3.2 4.4 + - - +
41D ILE* 3.0 33.1 + - + +
82D GLU* 6.1 0.7 - - - +
85D GLU* 3.9 23.3 - - - +
86D ALA* 3.9 27.4 - - + +
89D LEU* 3.7 27.4 - - + -
121D GLU* 3.3 28.0 - - + +
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Residues in contact with TYR 38 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D LYS* 2.8 47.6 + - + +
35D SER* 4.1 4.0 - - - +
37D ILE* 1.3 77.6 - - + +
39D SER* 1.3 62.4 - - - +
41D ILE* 3.3 16.5 + - + +
42D ARG* 3.1 35.8 + - - +
121D GLU* 5.9 0.2 - - - -
124D ARG* 4.2 29.8 + - - -
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Residues in contact with SER 39 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D SER 3.0 18.8 + - - -
36D LEU 3.6 4.3 - - - -
38D TYR* 1.3 77.7 - - - +
40D MET* 1.3 59.4 + - - +
42D ARG* 3.5 23.6 + - - +
43D GLU 3.1 3.3 + - - -
44D ASP 2.9 34.2 + - - +
47D SER* 3.6 6.7 - - - -
48D ALA* 3.8 25.1 - - - -
51D TYR* 3.3 18.1 - - - -
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Residues in contact with MET 40 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D LEU* 2.9 23.9 + - + +
37D ILE* 3.2 7.4 + - - +
39D SER* 1.3 76.5 - - - +
41D ILE* 1.3 64.5 + - - +
43D GLU* 3.1 14.7 + - - +
45D TYR* 3.6 36.5 + - + -
48D ALA* 3.5 24.5 - - + -
89D LEU* 4.7 2.9 - - + -
90D TYR* 3.6 55.2 - - + +
93D ILE* 3.8 35.4 - - + +
94D LYS* 4.4 8.1 - - + +
125D LYS* 4.6 2.3 + - - -
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Residues in contact with ILE 41 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ILE* 3.0 38.5 + - + +
38D TYR* 3.7 15.7 - - + +
40D MET* 1.3 77.6 - - - +
42D ARG* 1.3 57.9 + - + +
43D GLU* 3.1 6.1 + - - +
89D LEU* 4.5 7.4 - - + -
93D ILE* 5.0 0.9 - - + -
121D GLU 4.5 3.6 - - - +
124D ARG* 3.8 36.6 - - + +
125D LYS* 3.9 23.0 + - + +
128D GLU* 3.4 45.8 - - + +
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Residues in contact with ARG 42 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D SER 5.0 0.6 + - - -
38D TYR* 3.1 20.0 + - - +
39D SER* 3.5 45.1 + - - +
41D ILE* 1.3 75.9 - - + +
43D GLU* 1.3 68.5 + - - +
44D ASP* 3.1 32.0 + - + +
47D SER* 4.0 5.1 + - - -
51D TYR* 5.4 2.8 + - - -
128D GLU* 5.3 4.5 - - - -
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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