Contacts of the helix formed by residues 3 - 34 (chain J) in PDB entry 2X17
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 3 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1J MET 4.1 0.6 + - - -
2J LEU* 1.3 75.4 - - - +
4J GLU* 1.3 65.7 + - - +
5J ARG* 3.8 3.2 + - - -
6J MET* 3.0 18.0 + - - +
7J LEU* 3.0 22.8 + - - +
111J GLU* 2.7 35.4 + - - -
113J ASP* 5.6 0.8 + - - -
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Residues in contact with GLU 4 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J LEU 3.9 0.8 + - - -
3J SER* 1.3 71.9 - - - +
5J ARG* 1.3 61.1 + - - +
7J LEU* 3.8 9.5 + - + +
8J LYS* 3.4 24.4 + - + +
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Residues in contact with ARG 5 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J SER* 3.1 2.4 - - - +
4J GLU* 1.3 78.9 - - - +
6J MET* 1.3 58.9 + - - +
8J LYS* 3.4 6.8 + - + +
9J ALA* 3.0 28.1 + - - +
107J LEU* 4.8 19.7 - - + -
111J GLU* 4.0 20.4 - - - +
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Residues in contact with MET 6 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J LEU* 3.8 14.8 - - + -
3J SER* 3.0 25.8 + - - +
5J ARG* 1.3 76.1 - - - +
7J LEU* 1.3 56.3 + - - +
9J ALA* 3.1 4.5 + - - +
10J LEU* 2.8 39.7 + - + +
104J LEU* 4.2 17.9 - - - +
107J LEU* 3.8 20.2 - - + +
108J ALA* 3.7 36.8 - - + +
111J GLU* 4.0 11.0 + - - +
113J ASP* 3.8 23.1 - - + +
116J THR* 3.8 17.7 - - - +
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Residues in contact with LEU 7 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J LEU* 4.3 17.4 - - + +
3J SER 3.0 15.1 + - - +
4J GLU* 3.9 8.5 - - - +
6J MET* 1.3 75.9 - - - +
8J LYS* 1.3 54.4 + - - +
10J LEU* 3.5 5.0 + - - +
11J ASN* 2.8 48.8 + - - +
61J ILE* 3.8 16.2 - - + -
66J GLY* 4.2 7.0 - - - -
67J ARG* 3.6 42.6 - - + +
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Residues in contact with LYS 8 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J GLU* 3.4 17.0 + - + +
5J ARG* 3.7 6.5 - - - +
6J MET 3.3 0.6 - - - -
7J LEU* 1.3 77.8 - - - +
9J ALA* 1.3 58.7 + - - +
11J ASN* 3.5 6.9 + - + +
12J ASP* 3.0 54.1 + - - +
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Residues in contact with ALA 9 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5J ARG 3.0 17.3 + - - +
6J MET 3.1 5.4 + - - +
8J LYS* 1.3 78.1 - - - +
10J LEU* 1.3 58.8 + - - +
12J ASP* 3.6 8.6 + - - +
13J GLN* 3.3 21.7 + - - +
16J ARG* 4.4 2.4 + - - -
104J LEU* 3.7 18.9 - - + +
107J LEU* 3.7 24.9 - - + -
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Residues in contact with LEU 10 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J LEU* 3.8 28.3 - - + -
6J MET* 2.8 36.8 + - + +
7J LEU* 3.9 3.4 - - - +
9J ALA* 1.3 70.5 - - - +
11J ASN* 1.3 59.6 + - - +
13J GLN* 3.5 4.4 + - - +
14J LEU* 3.0 27.5 + - - +
57J PHE* 3.7 32.3 - - + -
60J TYR* 4.0 18.6 - - + -
61J ILE* 4.0 18.0 - - + +
104J LEU* 4.1 10.1 - - + -
116J THR* 4.0 18.2 - - + -
119J PHE* 4.3 8.3 - - + -
120J LEU* 5.1 0.9 - - + -
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Residues in contact with ASN 11 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7J LEU* 2.8 38.6 + - - +
8J LYS* 3.8 7.7 - - + +
9J ALA 3.4 0.2 - - - -
10J LEU* 1.3 75.0 - - - +
12J ASP* 1.3 62.0 + - - +
14J LEU* 3.4 8.7 - - - +
15J ASN* 3.1 26.0 + - - +
61J ILE* 3.9 9.3 - - - +
67J ARG 3.5 17.8 + - - -
68J VAL* 3.4 11.1 - - - +
69J GLU* 3.1 43.6 + - + +
71J ASP* 4.5 5.5 - - - +
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Residues in contact with ASP 12 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J LYS* 3.0 49.4 + - - +
9J ALA* 3.8 8.6 - - - +
10J LEU 3.3 0.2 - - - -
11J ASN* 1.3 78.9 - - - +
13J GLN* 1.3 56.8 + - - +
15J ASN* 3.2 9.2 + - - +
16J ARG* 2.8 48.9 + - - +
71J ASP* 3.6 16.3 - - - +
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Residues in contact with GLN 13 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J ALA 3.3 6.9 + - - +
10J LEU 3.9 4.0 - - - +
11J ASN 3.3 0.2 - - - -
12J ASP* 1.3 76.1 - - - +
14J LEU* 1.3 60.4 + - - +
15J ASN 3.1 0.2 - - - -
16J ARG* 3.0 27.0 + - - +
17J GLU* 2.9 60.0 + - - +
57J PHE* 3.4 28.9 - - + -
97J ILE* 4.0 8.5 - - - +
100J SER* 2.9 33.0 + - - +
101J ILE* 3.7 13.7 - - + +
104J LEU* 3.6 21.5 - - + -
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Residues in contact with LEU 14 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251 PHE* 4.5 8.1 - - + -
10J LEU 3.0 12.0 + - - +
11J ASN* 3.4 13.2 - - - +
13J GLN* 1.3 76.1 - - - +
15J ASN* 1.3 57.2 + - - +
17J GLU* 3.6 1.9 + - - -
18J LEU* 3.2 43.4 + - + +
54J ALA* 3.6 21.8 - - + +
57J PHE* 4.0 12.5 - - + -
58J TYR* 3.6 31.4 - - + +
61J ILE* 3.8 19.5 - - + -
68J VAL* 4.0 15.0 - - + -
69J GLU 5.9 0.7 - - - +
70J LEU* 3.8 18.6 - - + -
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Residues in contact with ASN 15 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221 TYR* 3.6 9.3 + - - -
11J ASN 3.1 13.4 + - - +
12J ASP* 3.3 12.1 - - - +
13J GLN 3.1 0.2 - - - -
14J LEU* 1.3 76.3 - - - +
16J ARG* 1.3 59.3 + - - +
18J LEU* 3.3 7.6 + - - +
19J TYR* 3.0 27.9 + - - +
70J LEU* 5.5 0.6 - - - +
71J ASP* 3.0 47.2 + - - +
72J GLU 3.4 17.9 + - - +
73J ILE* 4.2 5.2 - - - +
74J PRO* 4.9 6.8 - - - +
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Residues in contact with ARG 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9J ALA 4.4 3.2 + - - -
12J ASP* 2.8 32.3 + - - +
13J GLN* 3.0 58.5 + - - +
15J ASN* 1.3 78.3 - - + +
17J GLU* 1.3 56.2 + - - +
19J TYR* 3.3 9.3 + - - +
20J SER* 2.9 31.0 + - - -
93J HIS* 5.5 0.2 - - - -
96J PHE* 4.1 27.8 - - + -
97J ILE* 4.1 8.7 - - + +
100J SER* 3.7 25.5 + - - -
103J GLU* 5.6 3.2 + - - -
104J LEU* 5.2 1.2 - - - +
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Residues in contact with GLU 17 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J GLN* 2.9 38.1 + - - +
14J LEU 3.9 4.7 - - - +
16J ARG* 1.3 75.8 - - - +
18J LEU* 1.3 61.5 + - - +
20J SER* 3.3 8.5 + - - -
21J ALA* 3.2 17.7 + - - +
50J GLU* 2.9 47.9 - - - +
53J HIS* 3.7 16.8 + - + +
54J ALA* 4.0 7.6 - - + +
57J PHE* 4.0 13.2 - - + -
97J ILE* 4.1 14.2 - - - +
101J ILE* 4.5 2.1 - - - +
123J PHE* 3.9 21.7 - - - -
127J GLN* 4.7 3.6 + - - -
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Residues in contact with LEU 18 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221 TYR* 3.5 40.4 - - + +
251 PHE* 4.3 10.5 - - + -
14J LEU* 3.2 37.2 + - + +
15J ASN* 3.6 9.9 - - - +
16J ARG 3.3 0.2 - - - -
17J GLU* 1.3 75.0 - - - +
19J TYR* 1.3 59.6 + - - +
21J ALA* 3.4 7.4 - - + +
22J TYR* 3.1 24.1 + - - +
50J GLU 5.2 0.2 - - - -
51J ILE* 4.9 20.0 - - + -
54J ALA* 3.8 16.8 - - + -
70J LEU* 4.0 3.8 - - + -
73J ILE* 4.3 16.5 - - + +
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Residues in contact with TYR 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J ASN* 3.0 17.8 + - - +
16J ARG* 3.3 7.4 + - - +
18J LEU* 1.3 73.0 - - - +
20J SER* 1.3 56.1 + - - +
22J TYR* 3.0 3.6 + - + -
23J LEU* 2.7 47.6 + - + +
73J ILE* 3.9 17.2 - - + +
74J PRO* 3.5 48.9 - - + -
75J LYS 4.6 1.9 + - - -
76J PRO* 3.7 14.6 - - + +
77J PRO* 3.5 26.0 - - - +
93J HIS* 3.7 31.6 - + - -
96J PHE* 6.2 0.2 - + - -
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Residues in contact with SER 20 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J ARG 2.9 21.8 + - - -
17J GLU* 3.3 11.4 - - - -
19J TYR* 1.3 76.1 - - - +
21J ALA* 1.3 61.5 + - - +
23J LEU* 3.2 3.2 + - - +
24J TYR* 2.9 39.6 + - - -
50J GLU* 3.4 24.1 + - - -
93J HIS* 3.5 15.3 + - - -
94J GLU* 5.8 0.7 - - - -
97J ILE* 3.4 24.1 - - - +
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Residues in contact with ALA 21 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J GLU 3.2 5.7 + - - +
18J LEU* 3.4 12.3 - - + +
20J SER* 1.3 78.8 - - - +
22J TYR* 1.3 57.1 + - - +
25J PHE* 3.1 24.3 + - - +
47J ALA* 3.3 35.4 - - - +
50J GLU* 3.5 16.0 - - + +
51J ILE* 3.7 20.0 - - + +
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Residues in contact with TYR 22 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151 ASN* 3.9 6.2 + - - +
181 LEU* 3.7 30.3 - - + +
701 LEU* 3.4 33.7 - - + +
711 ASP 2.7 30.6 + - - -
731 ILE* 3.6 22.7 - - + -
18J LEU 3.1 12.5 + - - +
19J TYR* 3.0 9.7 + + + +
21J ALA* 1.3 75.0 - - - +
23J LEU* 1.3 60.6 + - - +
25J PHE* 3.5 10.2 + + + +
26J ALA* 3.1 24.4 + - - +
73J ILE* 3.7 25.8 - - + -
74J PRO 3.9 4.9 - - - -
76J PRO* 3.6 28.0 - - + +
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Residues in contact with LEU 23 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J TYR* 2.7 32.5 + - + +
20J SER 3.7 5.2 - - - +
22J TYR* 1.3 73.4 - - - +
24J TYR* 1.3 63.2 + - + +
26J ALA* 3.0 5.9 + - - +
27J MET* 3.0 53.0 + - + +
76J PRO* 4.2 7.3 - - + +
77J PRO* 3.8 29.2 - - + -
80J TRP* 4.1 9.0 - - + -
89J ALA 5.1 0.9 - - - +
90J ALA* 5.4 0.2 - - - -
93J HIS* 3.6 46.4 - - + +
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Residues in contact with TYR 24 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J SER* 2.9 37.6 + - - +
23J LEU* 1.3 78.4 - - + +
25J PHE* 1.3 57.9 + - - +
27J MET* 3.9 8.7 - - + +
28J ALA* 3.1 20.8 + - - +
42J TRP* 5.7 0.9 - + - -
43J MET* 3.4 54.2 - - + +
46J GLN* 4.2 15.3 - - + -
47J ALA* 4.1 9.2 - - + -
50J GLU* 3.8 30.1 - - + -
90J ALA* 3.7 29.3 + - + -
93J HIS* 4.7 10.7 - + - -
94J GLU* 2.6 36.2 + - - +
134J VAL* 4.7 6.0 - - + +
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Residues in contact with PHE 25 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141 LEU* 4.4 5.4 - - + -
181 LEU* 4.2 19.5 - - + -
541 ALA* 5.1 3.6 - - + -
551 LEU* 3.9 27.6 - - + -
581 TYR* 3.7 38.8 - + + -
701 LEU* 3.7 36.4 - - + +
21J ALA 3.1 17.8 + - - +
22J TYR* 3.6 16.2 - + - +
23J LEU 3.2 0.2 - - - -
24J TYR* 1.3 77.1 - - - +
26J ALA* 1.3 58.6 + - - +
28J ALA* 3.5 7.7 - - + +
29J ALA* 3.2 24.9 + - - +
43J MET 5.4 0.2 - - - -
44J LYS* 4.8 8.7 - - + -
47J ALA* 4.3 8.0 - - + +
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Residues in contact with ALA 26 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671 ARG* 5.1 0.5 + - - -
701 LEU* 3.7 11.9 - - + +
22J TYR 3.1 13.2 + - - +
23J LEU 3.0 10.2 + - - +
25J PHE* 1.3 75.4 - - - +
27J MET* 1.3 59.3 + - - +
29J ALA* 3.5 6.4 + - - +
30J TYR* 3.1 23.7 + - - +
76J PRO* 3.8 18.8 - - + -
77J PRO 3.7 21.3 - - - +
78J LYS* 4.4 4.7 - - - +
80J TRP* 4.0 6.2 - - + -
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Residues in contact with MET 27 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23J LEU* 3.0 35.4 + - + +
24J TYR* 4.0 15.0 - - + +
26J ALA* 1.3 73.2 - - - +
28J ALA* 1.3 59.8 + - - +
30J TYR* 3.1 3.0 + - + +
31J PHE* 2.9 42.9 + - + -
43J MET* 3.8 29.8 - - + -
80J TRP* 3.5 40.6 - - + -
86J ALA* 3.6 27.8 - - + +
89J ALA* 4.3 2.9 - - + -
90J ALA* 3.8 22.9 - - + +
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Residues in contact with ALA 28 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581 TYR* 3.0 13.8 + - - +
24J TYR 3.1 18.8 + - - +
25J PHE* 3.5 11.9 - - + +
27J MET* 1.3 77.3 - - - +
29J ALA* 1.3 55.8 + - - +
31J PHE 3.5 0.2 + - - -
32J GLU* 3.0 23.7 + - - +
40J ALA* 3.4 30.5 - - - +
43J MET* 3.8 8.9 - - + +
44J LYS* 3.8 16.6 - - + +
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Residues in contact with ALA 29 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581 TYR* 3.5 20.3 + - + -
621 TYR* 2.5 30.7 + - - +
671 ARG* 3.8 10.5 + - - +
681 VAL* 4.2 15.0 - - + +
701 LEU* 5.6 2.2 - - + -
25J PHE 3.2 10.4 + - - +
26J ALA* 3.6 11.7 - - - +
27J MET 3.2 0.2 - - - -
28J ALA* 1.3 76.7 - - - +
30J TYR* 1.3 63.4 + - - +
32J GLU 3.4 0.2 + - - -
33J ASP* 3.1 14.0 + - - +
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Residues in contact with TYR 30 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671 ARG* 3.9 19.7 - - - +
26J ALA 3.1 13.9 + - - +
27J MET* 3.1 11.3 + - - +
29J ALA* 1.3 76.6 - - - +
31J PHE* 1.3 74.3 + + - +
33J ASP* 3.4 13.5 + - + +
34J LEU* 3.4 42.7 + - + +
78J LYS 4.1 9.4 - - - +
79J GLU* 4.4 5.6 - - + -
80J TRP* 2.9 53.7 + + + -
81J GLU 3.8 1.9 + - - -
82J SER* 3.3 23.2 - - - -
83J PRO* 3.6 1.2 - - - +
86J ALA* 4.0 24.9 - - + -
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Residues in contact with PHE 31 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J MET* 2.9 34.4 + - + +
28J ALA 4.0 1.6 - - - +
30J TYR* 1.3 81.3 - + - +
32J GLU* 1.3 62.4 + - - +
34J LEU* 3.4 4.1 + - + +
35J GLY 3.3 3.6 + - - -
36J LEU* 2.8 56.2 + - + +
39J PHE* 3.5 32.1 - + + -
40J ALA 3.8 5.6 - - - +
43J MET* 4.1 29.8 - - + -
83J PRO* 3.7 26.2 - - + -
86J ALA* 3.9 22.4 - - + -
87J PHE* 3.7 22.2 - + - -
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Residues in contact with GLU 32 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581 TYR* 2.9 19.7 + - - +
591 ASN* 5.9 0.4 - - - -
621 TYR* 3.7 35.2 - - + -
28J ALA 3.0 15.5 + - - +
29J ALA 3.6 6.1 - - - +
31J PHE* 1.3 77.1 - - - +
33J ASP* 1.3 61.1 + - - +
35J GLY* 3.2 12.9 + - - +
36J LEU 4.7 2.5 - - - +
37J GLU* 3.6 29.3 - - - +
40J ALA* 3.4 11.9 - - - +
44J LYS* 2.9 29.8 + - - -
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Residues in contact with ASP 33 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621 TYR* 3.7 8.2 - - + -
661 GLY 4.4 8.8 - - - +
671 ARG* 3.5 37.2 + - - +
29J ALA 3.1 13.0 + - - +
30J TYR* 3.5 12.9 - - - +
31J PHE 3.2 0.2 - - - -
32J GLU* 1.3 76.0 - - - +
34J LEU* 1.3 62.2 + - - +
35J GLY* 3.1 2.5 + - - -
79J GLU* 5.7 0.7 - - - +
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Residues in contact with LEU 34 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1395 ASP* 6.0 1.3 - - - +
1435 PHE* 5.1 15.8 - - + -
30J TYR* 3.4 50.6 + - + +
31J PHE* 3.4 9.5 + - + +
32J GLU 3.3 0.4 - - - -
33J ASP* 1.3 79.0 - - + +
35J GLY* 1.3 60.4 + - - +
36J LEU* 3.7 28.2 + - + +
83J PRO* 4.3 11.2 - - + -
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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