Contacts of the helix formed by residues 2 - 37 (chain F) in PDB entry 2Q7M
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 2 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E GLU* 5.2 5.4 - - - +
5E THR* 6.0 2.1 - - - +
8E ASN* 5.5 2.8 - - - +
1F MET* 1.3 76.8 - - - +
3F GLN* 1.3 67.7 + - - +
4F GLU* 2.8 9.1 + - + +
5F THR* 2.5 50.8 + - - +
6F VAL* 2.8 7.7 - - - +
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Residues in contact with GLN 3 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E TYR* 2.9 47.9 + - - +
136E ILE* 3.5 33.6 + - + +
137E PHE* 3.5 32.3 - - - +
1F MET 3.0 6.4 + - - +
2F ASP* 1.3 69.6 - - - +
4F GLU* 1.3 65.8 + - - +
6F VAL* 3.4 10.3 - - - -
7F GLY* 3.2 12.5 + - - -
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Residues in contact with GLU 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ASP* 5.0 6.8 - - - +
2F ASP* 2.8 10.9 + - + +
3F GLN* 1.3 77.4 - - - +
5F THR* 1.3 83.6 + - - +
7F GLY* 2.8 18.5 + - - -
8F ASN* 2.8 37.6 + - - +
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Residues in contact with THR 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ASP* 5.8 2.9 - - - +
1F MET* 3.7 10.4 - - - -
2F ASP* 2.5 47.8 + - - +
4F GLU* 1.3 98.9 - - - +
6F VAL* 1.3 64.3 + - - -
7F GLY 2.8 1.8 - - - -
8F ASN* 2.8 26.9 + - - +
9F VAL* 2.8 13.3 - - - +
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Residues in contact with VAL 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E LEU* 3.9 29.6 - - + -
129E GLY 5.6 2.5 - - - +
130E ILE* 6.1 0.2 - - - -
133E TYR* 4.0 21.3 - - + -
1F MET* 3.4 26.8 - - + +
2F ASP 2.8 28.4 + - - +
3F GLN* 3.4 12.1 - - - +
5F THR* 1.3 72.5 - - - +
7F GLY* 1.3 58.5 + - - +
9F VAL* 2.9 20.7 - - - +
10F VAL* 2.8 30.9 + - + +
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Residues in contact with GLY 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E TYR* 3.1 31.2 + - - -
3F GLN 3.2 2.6 + - - -
4F GLU 2.8 13.6 + - - -
6F VAL* 1.3 80.6 - - - +
8F ASN* 1.3 56.0 + - - -
9F VAL 3.1 5.6 + - - -
10F VAL* 3.7 8.0 + - - +
11F LEU* 4.2 3.5 - - - +
80F GLN* 3.4 9.5 + - - +
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Residues in contact with ASN 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F GLU* 2.8 35.4 + - - +
5F THR* 2.8 25.5 + - - +
7F GLY* 1.3 71.0 - - - -
9F VAL* 1.3 61.0 + - - +
76F LEU* 4.4 12.0 - - - +
80F GLN* 2.8 29.8 + - + +
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Residues in contact with VAL 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E LEU* 5.6 4.0 - - + -
1F MET* 4.4 13.2 - - + -
5F THR 2.8 23.3 - - - +
6F VAL* 2.9 23.1 - - + +
8F ASN* 1.3 73.1 - - - +
10F VAL* 1.3 54.3 + - - +
11F LEU 2.7 1.4 + - - -
12F LEU* 2.7 28.4 + - - +
13F ALA* 2.9 11.9 + - + +
72F TRP* 3.6 29.8 - - + -
76F LEU* 5.6 4.7 - - + -
80F GLN* 2.4 21.5 - - - +
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Residues in contact with VAL 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E LEU* 6.0 1.8 - - + -
130E ILE* 3.6 14.3 - - + +
133E TYR* 3.8 29.8 - - + -
134E TYR* 3.3 33.7 - - + +
6F VAL* 2.8 34.3 + - + +
7F GLY 3.9 7.9 - - - +
9F VAL* 1.3 76.2 - - - +
11F LEU* 1.3 61.1 + - + +
13F ALA* 3.9 6.5 - - - -
14F ILE* 2.8 49.5 + - + +
80F GLN* 3.1 0.2 - - - +
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Residues in contact with LEU 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E TYR* 3.9 10.8 - - - +
7F GLY 4.2 6.7 - - - +
9F VAL 2.7 6.1 + - - -
10F VAL* 1.3 89.3 - - + +
12F LEU* 1.3 59.3 + - - +
14F ILE* 3.5 12.4 - - + +
15F VAL* 2.9 31.5 + - - +
80F GLN* 2.8 44.0 - - + +
81F VAL* 5.7 2.9 - - - -
84F ALA* 3.4 24.4 - - + +
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Residues in contact with LEU 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 2.7 14.2 + - - +
11F LEU* 1.3 69.6 - - - +
13F ALA* 1.3 58.4 + - - +
15F VAL* 3.4 5.3 - - - +
16F THR* 2.7 37.4 + - - -
71F LEU* 3.7 13.0 - - + +
72F TRP* 3.0 65.3 - - + -
75F GLY* 3.8 15.3 - - - -
76F LEU* 4.2 6.7 - - + -
80F GLN* 3.8 20.0 - - + +
84F ALA* 3.6 30.7 - - + +
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Residues in contact with ALA 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E SER* 5.4 2.7 - - - -
77E LEU* 3.7 30.3 - - + -
130E ILE* 4.0 7.2 - - + -
9F VAL* 2.9 17.3 + - + +
10F VAL* 3.9 6.5 - - - +
12F LEU* 1.3 75.9 - - - +
14F ILE* 1.3 55.1 + - - +
16F THR* 3.0 5.3 + - - -
17F LEU* 2.6 45.2 + - + +
72F TRP* 3.7 11.4 - - + -
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Residues in contact with ILE 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E ILE* 3.1 32.7 - - + +
134E TYR* 4.5 11.4 - - + +
10F VAL* 2.8 42.8 + - + +
11F LEU* 3.5 14.1 - - + +
13F ALA* 1.3 77.0 - - - +
15F VAL* 1.3 70.9 + - + +
17F LEU* 3.0 5.1 + - - -
18F ILE* 2.8 40.0 + - + +
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Residues in contact with VAL 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F LEU 2.9 14.4 + - - +
12F LEU* 3.4 6.7 - - - +
14F ILE* 1.3 81.8 - - + +
16F THR* 1.3 62.7 + - - +
18F ILE* 3.0 12.2 - - + +
19F SER* 2.9 26.5 + - - -
67F PHE* 5.2 1.8 - - + -
71F LEU* 3.3 37.2 - - + -
84F ALA* 3.3 25.4 - - + +
87F GLY 3.7 2.9 - - - +
88F LEU* 3.6 28.0 - - + +
91F LEU* 3.6 12.3 - - + +
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Residues in contact with THR 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E ALA* 4.5 17.7 - - + -
73E SER* 6.0 2.5 - - - -
12F LEU 2.7 20.3 + - - -
13F ALA* 3.5 4.3 - - - -
15F VAL* 1.3 83.2 - - - +
17F LEU* 1.3 57.1 + - + +
19F SER* 2.7 21.8 + - - -
20F VAL* 2.7 21.3 + - - +
64F TYR* 4.1 11.9 - - - +
68F LEU* 3.7 11.5 - - + +
71F LEU* 3.4 9.4 - - - +
72F TRP* 3.3 28.3 + - + -
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Residues in contact with LEU 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E VAL* 4.5 6.7 - - + +
73E SER* 3.6 26.2 - - - +
77E LEU* 4.7 0.2 - - + -
123E PHE* 3.3 27.5 - - + -
126E SER* 3.9 27.8 - - - +
127E VAL* 4.9 3.6 - - + +
130E ILE* 4.2 14.4 - - + -
13F ALA* 2.6 43.4 + - + +
14F ILE* 3.5 6.5 - - - +
16F THR* 1.3 78.1 - - + +
18F ILE* 1.3 63.3 + - + +
20F VAL* 2.8 33.2 - - + +
21F VAL* 3.1 4.9 + - - +
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Residues in contact with ILE 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ILE* 2.8 41.0 + - + +
15F VAL* 3.0 15.7 - - + +
17F LEU* 1.3 78.2 - - + +
19F SER* 1.3 58.1 + - - +
21F VAL* 2.7 32.7 + - + +
22F GLN* 2.9 15.0 + - + +
88F LEU* 6.1 2.7 - - + -
91F LEU* 3.4 27.4 - - + -
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Residues in contact with SER 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F VAL 2.9 8.7 + - - -
16F THR* 2.7 23.0 + - - +
18F ILE* 1.3 80.0 - - - +
20F VAL* 1.3 53.7 + - - +
21F VAL 3.2 0.2 - - - -
22F GLN* 3.8 5.1 - - - +
23F ASN* 2.3 40.7 + - - +
64F TYR* 2.8 28.3 + - - -
67F PHE* 4.6 5.9 - - - -
91F LEU* 3.1 35.4 - - - -
94F ARG* 4.9 0.2 - - - -
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Residues in contact with VAL 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E THR* 3.0 49.6 - - + +
69E ALA* 3.8 18.6 - - + -
70E VAL* 4.0 7.6 - - + -
123E PHE* 3.6 24.0 - - + -
506E 2CS 4.8 5.0 - - + +
16F THR 2.7 18.1 + - - +
17F LEU* 2.8 30.1 - - + +
18F ILE 3.0 0.2 - - - -
19F SER* 1.3 74.0 + - - +
21F VAL* 1.3 61.3 + - - +
23F ASN* 3.3 3.8 - - - +
24F GLY* 3.2 17.3 + - - -
64F TYR* 3.7 3.1 - - - +
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Residues in contact with VAL 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123E PHE* 3.5 31.6 - - + -
506E 2CS 3.2 48.7 - - + -
17F LEU 3.4 3.6 - - - +
18F ILE* 2.7 14.9 + - - +
20F VAL* 1.3 78.4 - - - +
22F GLN* 1.3 70.9 + - + +
23F ASN 3.0 1.6 - - - -
24F GLY* 3.2 10.2 + - - -
25F PHE* 4.1 0.2 - - - +
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Residues in contact with GLN 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506E 2CS 5.6 0.4 - - - -
18F ILE* 2.9 10.8 + - + +
19F SER* 3.8 7.2 - - - +
21F VAL* 1.3 85.3 - - + +
23F ASN* 1.3 63.2 + - - +
25F PHE* 3.2 12.1 + - + +
26F PHE* 3.2 44.5 + - + -
91F LEU* 3.4 27.9 + - + +
94F ARG* 2.7 51.2 + - - +
95F GLN* 3.5 14.1 + - - +
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Residues in contact with ASN 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E THR* 3.4 19.7 + - + -
506E 2CS 2.8 26.7 - - + -
19F SER 2.3 26.5 + - - +
20F VAL 3.3 8.3 - - - +
22F GLN* 1.3 74.6 - - - +
24F GLY* 1.3 64.5 + - - +
25F PHE 3.0 2.4 + - - -
26F PHE* 3.2 6.8 + - - +
27F ALA 3.1 9.4 + - - -
60F CYS* 5.8 0.8 - - - +
61F VAL* 3.9 24.2 - - - +
64F TYR* 3.9 17.6 - - - -
94F ARG* 2.3 40.2 + - - +
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Residues in contact with GLY 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506E 2CS 3.0 57.2 - - - -
20F VAL 3.2 7.0 + - - -
21F VAL 3.2 5.1 + - - -
23F ASN* 1.3 78.8 - - - +
25F PHE* 1.3 56.8 + - - +
27F ALA* 3.5 4.8 + - - +
28F HIS* 3.1 20.8 + - - +
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Residues in contact with PHE 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506E 2CS 2.8 40.6 - - + -
21F VAL 4.1 1.1 - - - +
22F GLN* 3.2 11.6 + - + +
23F ASN 3.0 0.8 - - - -
24F GLY* 1.3 75.5 - - - +
26F PHE* 1.3 84.6 + + - +
27F ALA 2.9 1.8 - - - -
28F HIS* 2.5 35.2 + + - +
29F LYS* 2.8 41.1 + - + -
95F GLN* 3.9 16.8 - - - -
98F PHE* 4.5 6.7 - + - -
99F VAL* 6.4 1.3 - - + -
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Residues in contact with PHE 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506E 2CS 5.2 0.4 - - + -
22F GLN* 3.2 42.0 + - + -
23F ASN* 3.2 7.4 + - - +
25F PHE* 1.3 87.9 - + - +
27F ALA* 1.3 59.0 + - - +
28F HIS 3.3 0.5 + - - -
29F LYS 3.5 0.5 + - - -
30F VAL* 3.5 14.2 + - - +
57F ASN* 2.9 31.1 + - - +
60F CYS* 4.0 24.7 - - + -
94F ARG* 3.7 24.5 - - - -
95F GLN* 2.8 30.3 - - - -
98F PHE* 3.0 50.0 - + + -
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Residues in contact with ALA 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E TYR* 4.1 3.4 - - + -
113E ILE* 2.8 35.3 - - + +
506E 2CS 3.0 53.2 - - + -
23F ASN 3.1 4.0 + - - +
24F GLY* 3.5 5.8 - - - +
25F PHE 2.9 0.6 - - - -
26F PHE* 1.3 78.3 - - - +
28F HIS* 1.3 57.4 + - - +
30F VAL* 3.8 11.0 - - - +
31F GLU 3.9 1.6 + - - -
57F ASN* 3.7 7.8 - - - +
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Residues in contact with HIS 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E ILE* 4.9 1.8 - - - -
116E LYS* 5.9 2.4 + - - -
506E 2CS 4.3 24.3 - + + -
24F GLY 3.1 12.4 + - - +
25F PHE* 2.5 33.0 + + - +
27F ALA* 1.3 71.5 - - - +
29F LYS* 1.3 74.2 + - + +
30F VAL 2.8 4.7 - - - -
31F GLU* 2.8 28.2 + - - +
32F HIS* 3.2 40.6 + + - +
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Residues in contact with LYS 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F PHE* 2.8 36.6 + - + +
26F PHE 3.5 5.4 + - - +
28F HIS* 1.3 90.8 + - + +
30F VAL* 1.3 57.0 + - - +
31F GLU 3.5 0.2 - - - -
32F HIS* 3.0 36.3 + - - +
33F GLU* 4.0 26.9 + - - +
53F VAL* 3.2 23.5 - - + +
98F PHE* 4.2 16.6 - - + -
102F LEU* 5.5 9.9 - - + -
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Residues in contact with VAL 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E TYR* 2.9 36.6 - - + -
26F PHE 3.5 8.3 + - - +
27F ALA 3.8 4.5 - - - +
28F HIS 2.8 0.4 - - - -
29F LYS* 1.3 79.2 - - - +
31F GLU* 1.3 70.0 + - - +
32F HIS 3.4 0.7 - - - -
33F GLU* 3.7 3.1 + - - +
34F SER* 3.3 20.9 + - - -
50F PHE* 5.2 2.1 - - - -
53F VAL* 3.4 23.6 - - + -
54F TYR* 3.8 23.8 - - + +
57F ASN* 3.5 25.6 - - + +
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Residues in contact with GLU 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E PRO 4.4 1.9 - - - +
111E GLY 2.8 22.6 - - - +
112E TYR* 3.3 27.9 - - - +
113E ILE* 4.1 10.9 - - + +
27F ALA 3.9 5.6 + - - +
28F HIS* 2.8 14.5 + - - +
30F VAL* 1.3 84.4 - - - +
32F HIS* 1.3 61.7 + - + +
34F SER* 3.1 8.5 + - - -
35F ARG* 2.8 64.0 + - + +
40F ARG* 4.7 0.9 + - - -
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Residues in contact with HIS 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F HIS* 3.2 35.6 + + - +
29F LYS* 3.0 35.8 + - - +
30F VAL 3.4 0.2 - - - -
31F GLU* 1.3 79.1 - - + +
33F GLU* 1.3 61.4 + - - +
35F ARG* 3.5 8.7 + - + +
36F THR* 3.1 38.5 + - + +
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Residues in contact with GLU 33 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F LYS* 4.0 26.4 + - - +
30F VAL 3.7 4.9 + - - +
31F GLU 3.2 0.4 - - - -
32F HIS* 1.3 85.7 - - - +
34F SER* 1.3 62.3 + - - +
35F ARG 3.2 2.2 + - - -
36F THR* 3.2 20.1 + - - +
37F GLN* 3.7 17.2 + - + +
47F THR* 5.6 0.4 - - - +
49F ALA* 3.3 37.8 - - + +
50F PHE* 3.3 38.1 - - + +
53F VAL* 4.6 7.0 - - + +
102F LEU* 5.8 1.8 - - - +
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Residues in contact with SER 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E THR* 3.5 2.8 - - - +
112E TYR* 6.5 0.2 - - - -
30F VAL* 3.3 16.7 + - - -
31F GLU* 3.1 11.9 + - - -
33F GLU* 1.3 78.0 - - - +
35F ARG* 1.3 62.6 - - - +
37F GLN 4.6 1.8 - - - -
38F ASN* 3.1 31.4 - - - +
39F GLY 4.0 2.4 + - - -
40F ARG* 2.7 42.5 + - - -
50F PHE* 3.8 13.6 - - - -
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Residues in contact with ARG 35 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E THR* 2.8 35.6 + - - +
110E PRO* 4.9 1.4 - - - +
31F GLU* 2.8 45.4 + - + +
32F HIS* 3.7 11.7 - - + +
33F GLU 3.2 0.2 - - - -
34F SER* 1.3 80.3 - - - +
36F THR* 1.3 66.7 + - + +
37F GLN 3.1 2.1 + - - -
38F ASN* 2.3 62.9 + - - +
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Residues in contact with THR 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F HIS* 3.1 17.5 + - + +
33F GLU* 3.2 23.7 + - - +
35F ARG* 1.3 77.7 - - + +
37F GLN* 1.3 85.1 + - - +
38F ASN 3.7 0.4 - - - -
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Residues in contact with GLN 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F GLU* 3.7 11.5 + - - +
34F SER* 3.8 6.5 - - - +
36F THR* 1.3 101.3 + - - +
38F ASN* 1.3 64.7 + - - +
39F GLY 3.4 8.0 + - - +
41F SER* 5.2 1.4 + - - -
46F GLY* 6.1 0.7 - - - -
47F THR* 2.9 43.2 - - + +
50F PHE* 5.1 3.2 - - + -
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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) + - + + + + + -
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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