Contacts of the helix formed by residues 56 - 85 (chain F) in PDB entry 4MJI
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 GLY 56 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54F GLN 3.8 1.2 + - - -
55F GLU* 1.3 77.5 + - - +
57F PRO* 1.3 78.7 - - - +
58F GLU* 3.2 18.4 + - - +
59F TYR* 3.0 17.8 + - - +
60F TRP* 3.6 3.3 - - - -
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Residues in contact with PRO 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F GLY* 1.3 81.5 - - - +
58F GLU* 1.3 76.7 + - - +
60F TRP* 2.9 12.1 + - + +
61F ASP* 2.9 39.1 + - - +
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Residues in contact with GLU 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F GLY* 3.6 21.6 + - - +
57F PRO* 1.3 79.9 - - - +
59F TYR* 1.3 66.0 + - + +
61F ASP* 3.7 7.1 + - - +
62F ARG* 2.8 32.8 + - + +
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Residues in contact with TYR 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F TYR* 3.5 12.6 + - - -
33F PHE* 3.5 23.7 - - - -
34F VAL* 5.1 3.6 - - + +
45F THR* 4.9 4.5 - - + -
52F ILE* 3.8 19.7 - - + -
55F GLU* 3.6 21.1 - - + +
56F GLY 3.0 14.6 + - - +
58F GLU* 1.3 84.1 - - + +
60F TRP* 1.3 82.6 + + + +
62F ARG* 3.2 3.5 + - - +
63F ASN* 2.6 47.1 + - + +
167F TRP* 3.4 44.4 - + + -
171F HIS* 3.8 6.6 - - - -
1H THR* 3.6 18.9 - - + -
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Residues in contact with TRP 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34F VAL* 5.2 1.4 - - - +
45F THR* 3.0 47.2 + - + +
46F GLU 4.4 0.4 - - - -
47F PRO* 4.1 24.0 - - + +
52F ILE* 3.1 39.6 - - + +
53F GLU* 3.7 17.9 - - - -
55F GLU* 2.6 37.2 - - + -
56F GLY 3.6 10.3 - - - -
57F PRO* 2.9 11.4 + - + +
59F TYR* 1.3 88.1 - + + +
61F ASP* 1.3 57.1 - - - +
63F ASN* 3.3 1.7 + - - +
64F THR* 2.6 40.0 + - - +
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Residues in contact with ASP 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57F PRO* 2.9 34.1 + - - +
58F GLU* 3.7 6.4 + - - +
60F TRP* 1.3 73.7 - - - +
62F ARG* 1.3 65.1 + - - +
64F THR* 3.7 5.1 + - - -
65F GLN* 3.3 23.1 + - - +
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Residues in contact with ARG 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F GLU* 2.8 25.3 + - + +
59F TYR* 3.3 6.5 - - - +
61F ASP* 1.3 74.6 - - - +
63F ASN* 1.3 66.3 + - - +
65F GLN* 2.7 73.7 + - - +
66F ILE* 3.1 18.9 + - - +
1H THR* 4.9 9.2 - - + -
27I THR* 5.4 6.5 + - - -
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Residues in contact with ASN 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F TYR* 4.5 1.7 + - - -
34F VAL* 6.3 0.2 - - - -
45F THR* 3.5 22.0 - - + +
59F TYR* 2.6 48.2 + - - +
62F ARG* 1.3 77.5 - - - +
64F THR* 1.3 55.4 + - - +
66F ILE* 3.3 7.3 + - - +
67F PHE* 2.7 50.7 + - + -
1H THR* 3.1 38.3 - - - +
2H ALA* 3.2 22.3 + - - +
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Residues in contact with THR 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F PHE* 4.7 4.6 - - + -
43F PRO* 3.7 23.6 - - + +
44F ARG* 4.2 8.2 - - + +
45F THR* 3.2 22.7 + - - +
60F TRP* 2.6 23.4 + - - +
61F ASP* 4.0 5.8 - - - -
62F ARG 3.3 0.2 - - - -
63F ASN* 1.3 78.3 - - - +
65F GLN* 1.3 56.5 + - - +
67F PHE* 3.9 2.5 - - - +
68F LYS* 2.8 34.2 + - + +
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Residues in contact with GLN 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F ASP 3.3 13.8 + - - +
62F ARG* 2.7 67.0 + - - +
64F THR* 1.3 75.7 - - - +
66F ILE* 1.3 65.8 + - - +
68F LYS* 3.2 9.5 + - - +
69F THR* 2.6 44.6 + - - +
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Residues in contact with ILE 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F ARG* 3.1 26.4 + - - +
63F ASN* 3.6 15.0 - - - +
65F GLN* 1.3 95.4 - - - +
67F PHE* 1.3 59.5 + - + +
69F THR* 3.7 6.8 - - - -
70F ASN* 2.9 29.6 + - - +
163F LEU* 5.8 2.9 - - + -
1H THR* 5.0 5.6 - - - -
2H ALA* 3.5 29.6 - - + +
3H PHE 3.4 25.6 - - - +
4H THR* 3.4 19.2 - - + +
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Residues in contact with PHE 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7F TYR* 4.1 15.3 - + - -
9F TYR* 3.2 35.9 - + - -
22F PHE* 3.9 17.5 - + + -
24F ALA* 3.8 7.0 - - + -
34F VAL* 5.1 7.0 - - + -
36F PHE* 3.6 39.5 - + + -
45F THR* 3.3 24.7 - - + -
63F ASN* 2.7 37.5 + - + +
64F THR 4.2 0.2 - - - +
66F ILE* 1.3 72.6 - - + +
68F LYS* 1.3 54.5 + - - +
70F ASN* 3.3 5.8 - - - +
71F THR* 2.5 42.8 + - - -
2H ALA* 3.3 23.3 - - + -
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Residues in contact with LYS 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F PHE* 4.3 6.3 - - + -
43F PRO* 6.4 1.3 - - + -
64F THR* 2.8 22.5 + - + +
65F GLN* 3.2 10.1 - - - +
67F PHE* 1.3 73.6 - - - +
69F THR* 1.3 69.6 + - - +
71F THR* 3.5 9.4 + - - -
72F GLN* 3.4 19.1 + - + +
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Residues in contact with THR 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65F GLN* 2.6 30.9 + - - +
66F ILE* 3.7 6.5 - - - -
68F LYS* 1.3 75.3 - - - +
70F ASN* 1.3 52.7 + - - +
72F GLN* 2.9 19.0 + - - +
73F THR* 2.6 34.0 + - + +
4H THR* 3.5 25.8 - - + -
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Residues in contact with ASN 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F TYR* 3.1 20.8 + - - -
22F PHE* 3.9 15.5 - - + -
66F ILE* 2.9 26.8 + - - +
67F PHE* 3.4 7.8 - - - +
69F THR* 1.3 71.2 - - - +
71F THR* 1.3 66.0 + - - +
73F THR* 3.9 4.3 - - - -
74F TYR* 3.1 28.4 + - - -
3H PHE 2.6 26.5 + - - -
4H THR* 3.3 5.5 - - - +
5H ILE* 2.6 41.0 + - + +
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Residues in contact with THR 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20F PRO 5.6 3.1 - - - +
21F ARG 5.3 0.7 - - - -
22F PHE* 3.6 28.9 - - + +
36F PHE* 3.8 14.0 - - - -
38F SER* 3.9 17.7 - - - +
67F PHE 2.5 38.3 + - - -
68F LYS* 3.6 9.9 - - - -
69F THR 3.2 0.4 + - - -
70F ASN* 1.3 74.9 - - - +
72F GLN* 1.3 59.4 + - - +
74F TYR* 3.2 3.1 + - - +
75F ARG* 3.0 46.9 + - + +
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Residues in contact with GLN 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F LYS* 3.4 9.1 + - + +
69F THR* 2.9 9.4 + - - +
71F THR* 1.3 79.4 - - - +
73F THR* 1.3 61.5 + - + +
75F ARG* 2.5 44.2 + - - +
76F GLU* 3.0 36.5 + - + +
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Residues in contact with THR 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F THR* 2.6 49.1 + - + +
70F ASN* 3.8 5.4 - - - +
72F GLN* 1.3 80.2 - - + +
74F TYR* 1.4 55.7 + - - +
76F GLU* 3.3 9.1 - - - +
77F ASN* 3.0 33.9 + - - +
5H ILE* 3.4 27.4 + - - +
6H PRO 3.4 12.3 + - - -
7H SER* 4.8 6.7 + - - -
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Residues in contact with TYR 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F TYR* 3.1 27.0 - + + -
11F ALA* 3.7 21.1 - - + -
22F PHE* 3.4 32.3 - + + -
70F ASN* 3.1 22.5 + - + -
71F THR 3.6 6.5 - - - +
73F THR* 1.4 72.8 - - - +
75F ARG* 1.3 58.4 + - - +
76F GLU 3.0 1.3 + - - -
77F ASN* 3.7 7.5 - - + +
78F LEU* 2.8 38.7 + - + +
95F TRP* 4.0 31.9 - + + -
97F THR* 2.6 29.9 + - - -
116F TYR* 4.8 6.7 - + - -
5H ILE* 3.5 33.7 - - + +
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Residues in contact with ARG 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F ALA* 5.7 0.2 - - - +
19F GLU* 4.2 19.9 - - - +
20F PRO* 3.5 44.1 + - + +
71F THR* 3.0 27.7 + - + +
72F GLN* 2.5 69.3 + - - +
74F TYR* 1.3 74.3 - - - +
76F GLU* 1.3 62.0 + - - +
78F LEU* 3.6 5.4 - - - +
79F ARG* 3.4 25.6 + - - +
----------------------------------------------------------
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Residues in contact with GLU 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F GLN* 3.0 22.5 + - + +
73F THR* 3.3 15.9 - - - +
75F ARG* 1.3 76.3 - - - +
77F ASN* 1.3 53.9 + - - +
79F ARG* 3.0 30.6 + - - +
80F ILE* 2.8 50.8 + - + +
83F ARG* 4.0 10.0 + - - -
7H SER* 5.2 8.3 - - - +
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Residues in contact with ASN 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F THR 3.0 18.4 + - - +
74F TYR* 3.1 11.1 + - + +
76F GLU* 1.3 77.4 - - - +
78F LEU* 1.3 69.5 + - - +
80F ILE* 3.7 10.2 - - - +
81F ALA* 2.9 23.0 + - - +
95F TRP* 3.3 18.3 + - + +
116F TYR* 5.7 2.3 - - - -
5H ILE* 3.7 11.8 - - - +
6H PRO 3.6 15.9 - - - +
7H SER* 3.5 4.3 - - - +
8H ILE* 2.5 47.4 + - - +
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Residues in contact with LEU 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F ALA* 4.4 9.0 - - + +
12F MET* 3.8 6.7 - - - +
13F SER* 3.4 34.3 - - - +
20F PRO* 3.7 25.1 - - + -
74F TYR 2.8 23.9 + - - +
75F ARG* 3.6 6.5 - - - +
77F ASN* 1.3 75.3 - - - +
79F ARG* 1.3 58.6 + - + +
81F ALA* 3.1 17.2 - - - +
82F LEU* 3.1 17.2 + - + +
93F HIS* 3.7 31.9 - - + +
94F THR 4.3 1.6 - - - +
95F TRP* 3.6 23.2 - - + +
118F TYR* 4.6 1.7 + - + -
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Residues in contact with ARG 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F ARG* 3.4 12.2 + - - +
76F GLU* 3.0 31.3 + - - +
78F LEU* 1.3 74.8 - - - +
80F ILE* 1.3 69.2 + - - +
81F ALA 3.1 0.2 + - - -
82F LEU* 3.3 16.8 + - + +
83F ARG* 3.3 43.2 + - - +
89F GLU* 6.1 1.1 - - - +
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Residues in contact with ILE 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F GLU* 2.8 34.2 + - + +
77F ASN* 3.3 12.5 + - - +
79F ARG* 1.3 71.3 - - - +
81F ALA* 1.3 53.8 + - - +
83F ARG* 2.7 56.6 + - - +
84F TYR* 3.0 45.2 + - + -
7H SER* 4.7 3.1 - - - -
8H ILE* 3.3 44.6 - - + +
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Residues in contact with ALA 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F ASN 2.9 12.5 + - - +
78F LEU 3.1 11.0 - - - +
79F ARG 3.1 0.2 - - - -
80F ILE* 1.3 73.0 - - - +
82F LEU* 1.3 66.6 + - - +
83F ARG 3.0 2.8 + - - -
84F TYR* 3.2 10.3 + - - +
85F TYR* 3.2 32.0 + - + +
87F GLN* 4.2 0.2 - - - +
95F TRP* 3.8 12.8 - - + +
118F TYR* 3.6 34.5 - - + +
8H ILE 5.5 0.7 - - - -
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Residues in contact with LEU 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F SER* 5.9 1.8 - - - +
78F LEU* 3.1 17.1 + - + +
79F ARG* 3.7 14.8 - - + +
81F ALA* 1.3 79.4 - - - +
83F ARG* 1.3 58.6 + - + +
85F TYR 2.6 19.0 - - - +
86F ASN* 4.0 2.1 - - - +
87F GLN* 3.1 41.7 + - + +
88F SER 3.8 6.1 - - - +
89F GLU* 3.7 38.8 - - + +
91F GLY 5.1 1.1 - - - +
93F HIS* 4.0 18.2 - - + -
118F TYR* 3.8 7.9 - - - +
----------------------------------------------------------
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Residues in contact with ARG 83 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F GLU* 4.0 9.3 + - - -
79F ARG* 3.3 37.1 + - - +
80F ILE* 2.7 57.4 + - - +
82F LEU* 1.3 75.5 - - + +
84F TYR* 1.3 67.0 + - + +
85F TYR 3.3 5.0 + - - +
86F ASN* 3.7 12.3 - - - +
----------------------------------------------------------
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Residues in contact with TYR 84 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F ILE* 3.0 33.4 + - + +
81F ALA* 3.2 10.3 + - - +
83F ARG* 1.3 76.4 - - + +
85F TYR* 1.3 61.9 + + + +
86F ASN 4.3 0.3 + - - -
123F TYR* 3.7 13.9 - - - -
139F ALA* 3.7 30.6 - - + +
142F ILE* 3.4 38.0 - - + +
143F THR* 3.5 20.8 - - - -
146F LYS* 4.0 7.7 + - - -
8H ILE* 2.6 33.0 - - + +
----------------------------------------------------------
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Residues in contact with TYR 85 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F ALA* 3.2 16.5 + - + +
82F LEU 2.6 18.0 - - - +
83F ARG 3.7 1.3 - - - -
84F TYR* 1.3 79.4 - - + +
86F ASN* 1.3 51.2 + - - +
87F GLN* 2.5 40.7 + - - +
118F TYR* 3.7 33.4 - + - -
121F LYS* 3.5 9.1 + - - -
123F TYR* 3.2 27.6 - + - -
137F ASP* 2.3 34.6 + - - -
139F ALA* 3.4 21.5 - - + -
----------------------------------------------------------
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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