Contacts of the helix formed by residues 57 - 94 (chain A) in PDB entry 5GNA
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 57 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLY 3.3 8.2 + - - +
56A ILE* 1.3 79.5 - - - +
58A ARG* 1.3 59.9 + - - +
59A SER* 3.8 8.0 + - - -
60A ILE* 3.4 26.3 + - - +
61A GLN* 3.0 28.6 + - - +
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Residues in contact with ARG 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A THR* 1.3 74.7 - - - +
59A SER* 1.3 57.9 + - - +
61A GLN* 2.7 34.2 + - - +
62A ASP* 2.8 58.9 + - - +
464B MET 3.4 18.0 + - - -
465B ASN* 3.7 13.0 + - - +
466B LYS 2.6 27.6 + - - -
467B SER* 3.5 21.0 + - - -
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Residues in contact with SER 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A THR* 3.2 9.2 + - - -
58A ARG* 1.3 80.1 - - - +
60A ILE* 1.3 65.2 + - - +
62A ASP* 3.4 10.4 + - - +
63A MET* 3.0 26.2 + - - +
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Residues in contact with ILE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A THR* 4.2 15.5 - - + -
7A PHE* 4.1 6.7 - - + -
8A ILE* 3.7 39.3 - - + -
56A ILE* 3.6 24.2 - - + -
57A THR* 3.4 15.3 + - - +
58A ARG 3.3 0.2 - - - -
59A SER* 1.3 81.4 - - - +
61A GLN* 1.3 59.9 + - - +
63A MET* 3.1 16.0 + - + +
64A VAL* 2.9 28.8 + - - +
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Residues in contact with GLN 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 5.5 0.2 - - - -
52A THR* 5.7 3.4 - - + -
56A ILE* 3.0 37.5 + - + +
57A THR 3.0 17.3 + - - +
58A ARG* 2.7 42.3 + - - +
60A ILE* 1.3 77.3 - - - +
62A ASP* 1.3 56.3 + - - +
64A VAL* 3.4 0.4 + - - -
65A ALA* 2.8 31.3 + - - +
463B ALA 4.8 1.7 - - - +
464B MET* 3.1 37.2 - - - +
466B LYS* 3.5 4.0 - - - +
467B SER* 4.8 5.2 - - - -
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Residues in contact with ASP 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ARG* 2.8 56.6 + - - +
59A SER* 3.5 8.5 - - - +
61A GLN* 1.3 72.8 - - - +
63A MET* 1.3 63.9 + - - +
65A ALA* 3.4 7.4 + - - +
66A GLY* 3.1 18.2 + - - -
465B ASN* 4.9 4.5 - - - +
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Residues in contact with MET 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.3 23.1 - - + -
12A GLN* 3.5 16.4 - - - +
59A SER 3.0 14.1 + - - +
60A ILE* 3.1 20.1 + - + +
62A ASP* 1.3 75.0 - - - +
64A VAL* 1.3 63.9 + - + +
66A GLY* 3.3 10.7 + - - -
67A TYR* 3.2 47.0 + - + +
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Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 3.6 30.3 - - + -
8A ILE* 4.3 22.0 - - + -
11A TRP* 3.5 37.0 - - + -
60A ILE 2.9 14.3 + - - +
61A GLN 3.9 2.7 - - - +
63A MET* 1.3 73.3 - - + +
65A ALA* 1.3 65.0 + - - +
66A GLY 3.1 1.8 - - - -
67A TYR* 2.9 22.5 + - + +
68A ILE* 3.0 14.0 + - + +
464B MET* 3.8 20.6 - - + -
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Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLN 2.8 21.8 + - - +
62A ASP* 3.6 7.9 - - - +
64A VAL* 1.3 72.6 - - - +
66A GLY* 1.3 56.5 + - - +
68A ILE* 3.3 7.2 + - - -
69A LYS* 3.0 24.3 + - - +
461B PHE* 3.4 20.8 - - + -
464B MET* 3.8 15.0 - - + +
465B ASN* 3.3 26.7 - - - +
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Residues in contact with GLY 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ASP 3.1 12.8 + - - -
63A MET 3.3 5.4 + - - -
64A VAL 3.1 1.0 - - - -
65A ALA* 1.3 77.2 - - - +
67A TYR* 1.3 57.2 + - - +
69A LYS* 3.5 10.6 + - - +
70A GLN* 3.1 29.0 + - - +
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Residues in contact with TYR 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.9 2.0 - - + -
11A TRP* 4.1 20.9 - - + +
12A GLN* 2.9 50.9 + - + -
15A ALA* 3.7 16.9 - - + +
63A MET* 3.2 46.8 + - + +
64A VAL* 2.9 18.4 + - + +
66A GLY* 1.3 73.1 - - - +
68A ILE* 1.3 56.2 + - - +
70A GLN* 3.5 15.5 + - - +
71A THR* 2.7 37.0 + - - -
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Residues in contact with ILE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TRP* 3.4 46.2 - - + -
64A VAL* 3.0 18.4 + - + +
65A ALA* 3.3 6.7 + - - +
67A TYR* 1.3 74.1 - - - +
69A LYS* 1.3 65.1 + - - +
71A THR* 3.2 8.7 + - - -
72A LEU* 3.0 23.2 + - + +
457B LEU* 3.4 34.5 - - + +
460B GLN 4.0 10.3 - - - +
461B PHE* 3.7 14.1 - - + +
464B MET* 4.0 27.1 - - + -
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Residues in contact with LYS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA 3.0 16.4 + - - +
66A GLY* 3.8 9.2 - - - +
68A ILE* 1.3 77.9 - - - +
70A GLN* 1.3 58.7 + - - +
72A LEU* 3.2 13.9 + - + +
73A ASP* 2.9 52.9 + - - +
461B PHE* 3.8 21.3 - - + -
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Residues in contact with GLN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA* 4.5 9.2 - - + +
19A GLN* 6.1 3.8 - - - +
66A GLY 3.1 17.4 + - - +
67A TYR* 3.7 24.9 - - - +
68A ILE 3.3 0.2 - - - -
69A LYS* 1.3 78.7 - - - +
71A THR* 1.3 57.0 + - - +
73A ASP* 3.4 10.0 + - + +
74A ASN* 3.0 49.1 + - - +
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Residues in contact with THR 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TRP* 5.0 0.7 + - - -
14A ILE* 3.7 17.6 - - + +
15A ALA* 3.3 20.6 + - - +
18A SER* 3.6 17.7 + - - -
40A TYR* 3.4 25.4 - - - +
67A TYR 2.7 20.3 + - - -
68A ILE* 3.2 11.0 + - - -
70A GLN* 1.3 73.9 - - - +
72A LEU* 1.3 59.6 + - - +
74A ASN* 3.4 2.3 + - - +
75A GLU* 2.9 28.9 + - - +
457B LEU* 3.5 16.6 - - + -
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 3.0 21.2 + - + +
69A LYS* 3.5 13.9 - - + +
71A THR* 1.3 74.3 - - - +
73A ASP* 1.3 66.9 + - - +
75A GLU* 3.3 6.0 + - - +
76A GLN* 3.0 24.4 + - - +
454B SER* 3.5 40.4 + - - +
457B LEU* 3.5 31.6 - - + +
458B THR* 3.7 15.7 - - + +
461B PHE* 4.5 9.4 - - + -
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Residues in contact with ASP 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A LYS* 2.9 51.7 + - - +
70A GLN* 3.6 8.9 - - + +
72A LEU* 1.3 77.5 - - - +
74A ASN* 1.3 65.7 + - - +
76A GLN* 3.3 8.0 + - - +
77A LEU* 3.2 27.2 + - + +
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Residues in contact with ASN 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA 4.1 4.6 + - - -
18A SER* 2.9 39.9 + - - +
19A GLN* 3.5 23.0 - - - +
22A LEU* 3.7 26.9 - - + +
70A GLN* 3.0 33.1 + - - +
71A THR 3.7 0.2 - - - +
73A ASP* 1.3 74.6 - - - +
75A GLU* 1.3 58.7 + - - +
77A LEU* 3.2 8.1 + - - +
78A LEU* 2.9 29.9 + - - +
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Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER* 5.2 2.7 - - - +
40A TYR* 2.5 36.3 + - + +
71A THR* 2.9 21.3 + - + +
72A LEU* 3.6 5.3 - - - +
74A ASN* 1.3 75.6 - - - +
76A GLN* 1.3 62.4 - - - +
78A LEU* 3.2 12.6 + - + +
79A LYS* 3.0 31.0 + - - +
450B LEU* 3.5 18.1 - - + +
453B THR* 2.6 28.1 + - - -
454B SER* 2.5 39.7 + - - +
457B LEU* 3.9 7.8 - - - +
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Residues in contact with GLN 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU 3.0 13.7 + - - +
73A ASP* 3.5 11.4 - - - +
74A ASN 3.2 0.2 - - - -
75A GLU* 1.3 75.9 - - - +
77A LEU* 1.3 64.9 + - + +
79A LYS* 3.3 34.2 + - - +
80A GLY* 3.6 7.3 + - - -
454B SER* 5.3 1.1 + - - -
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Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.7 32.1 - - + -
26A GLN* 5.4 4.0 - - - +
73A ASP* 3.2 14.6 + - + +
74A ASN* 3.6 9.2 - - - +
76A GLN* 1.3 80.0 - - + +
78A LEU* 1.3 62.3 + - - +
80A GLY* 3.3 11.0 + - - -
81A LEU* 3.4 16.6 + - + +
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER* 5.1 3.1 - - - +
21A LEU* 3.9 31.6 - - + +
22A LEU* 4.0 13.0 - - + +
25A ALA* 3.7 29.8 - - + -
33A LEU* 4.3 6.5 - - + -
74A ASN 2.9 16.7 + - - +
75A GLU* 3.4 11.0 - - + +
76A GLN 3.2 0.2 - - - -
77A LEU* 1.3 74.9 - - - +
79A LYS* 1.3 59.2 + - - +
81A LEU* 3.1 4.6 + - - +
82A LEU* 2.9 42.5 + - + +
446B MET* 3.8 15.9 - - + -
450B LEU* 3.7 26.0 - - + -
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Residues in contact with LYS 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A GLU 3.0 19.2 + - - +
76A GLN* 3.3 28.4 + - - +
78A LEU* 1.3 76.3 - - - +
80A GLY* 1.3 56.3 + - - +
82A LEU* 3.4 7.1 + - - -
83A GLN* 3.0 26.7 + - - +
447B MET* 3.5 22.2 - - + +
450B LEU* 3.3 48.0 + - + -
451B ASN* 3.8 12.8 - - - +
454B SER* 3.2 28.3 + - - -
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Residues in contact with GLY 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A GLN 3.6 5.1 + - - -
77A LEU* 3.3 7.7 + - - -
78A LEU 3.2 0.6 - - - -
79A LYS* 1.3 76.5 - - - +
81A LEU* 1.3 63.8 + - - +
83A GLN* 3.4 6.1 + - - +
84A GLN* 3.1 23.4 + - - +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.8 21.8 - - + -
25A ALA* 3.8 26.2 - - + +
26A GLN* 3.8 33.9 - - + +
30A TRP* 3.9 8.6 - - + -
77A LEU* 3.4 9.3 + - + +
78A LEU* 3.1 7.2 + - - +
80A GLY* 1.3 73.0 - - - +
82A LEU* 1.3 65.3 + - - +
84A GLN* 3.5 23.2 + - - +
85A ARG* 3.1 22.7 + - - +
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP* 4.3 6.5 - - + -
33A LEU* 4.0 15.5 - - + -
78A LEU* 2.9 24.4 + - + +
79A LYS* 3.6 1.6 - - - +
81A LEU* 1.3 74.5 - - - +
83A GLN* 1.3 59.2 + - - +
85A ARG* 3.1 5.7 + - - +
86A LEU* 2.8 32.4 + - + +
443B LEU* 3.7 38.1 - - + +
446B MET* 3.9 10.1 - - + -
447B MET* 3.3 48.2 - - + +
450B LEU* 3.8 21.5 - - + -
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Residues in contact with GLN 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LYS 3.0 10.1 + - - +
80A GLY* 3.8 7.0 - - - +
81A LEU 3.4 0.2 - - - -
82A LEU* 1.3 74.6 - - - +
84A GLN* 1.3 59.0 + - - +
86A LEU* 3.2 13.9 + - - +
87A ASP* 2.9 54.8 + - - +
447B MET* 2.9 30.7 - - + +
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Residues in contact with GLN 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLY 3.1 14.3 + - - +
81A LEU* 3.5 25.3 - - - +
83A GLN* 1.3 79.0 - - - +
85A ARG* 1.3 57.1 + - - +
87A ASP* 3.3 9.6 + - - +
88A GLU* 2.9 30.4 + - + +
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Residues in contact with ARG 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP* 3.3 48.3 - - + +
81A LEU 3.1 14.1 + - - +
82A LEU 3.1 7.8 + - - +
84A GLN* 1.3 73.8 - - - +
86A LEU* 1.3 60.2 + - - +
88A GLU* 2.9 39.9 + - - +
89A LEU* 2.8 46.1 + - + +
92A LEU* 4.7 6.1 - - - +
436B TYR* 5.1 8.3 - - - -
439B GLN* 2.8 30.3 + - - +
443B LEU* 3.5 24.9 - - + -
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU 2.8 12.7 + - - +
83A GLN* 3.5 19.3 - - - +
85A ARG* 1.3 77.5 - - - +
87A ASP* 1.3 57.3 + - - +
89A LEU* 3.3 2.0 + - + -
90A SER* 2.9 25.5 + - - -
440B PHE* 3.4 61.6 - - + +
443B LEU* 3.9 13.2 - - + -
444B ASP* 3.7 33.4 - - + +
447B MET* 3.4 31.4 - - + -
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Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLN* 2.9 43.1 + - - +
84A GLN* 3.6 9.8 - - - +
86A LEU* 1.3 73.0 - - - +
88A GLU* 1.3 65.6 + - - +
90A SER* 3.3 8.8 + - - -
91A SER* 3.2 22.2 + - - -
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Residues in contact with GLU 88 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP* 4.8 3.8 + - - -
84A GLN* 2.9 16.7 + - + +
85A ARG* 2.9 46.8 + - - +
87A ASP* 1.3 75.9 - - - +
89A LEU* 1.3 62.9 + - - +
91A SER* 3.3 7.0 + - - -
92A LEU* 3.1 30.0 + - + +
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ARG* 2.8 52.0 + - + +
86A LEU* 3.7 5.8 - - - +
88A GLU* 1.3 72.0 - - - +
90A SER* 1.3 54.6 + - - +
92A LEU* 3.2 9.0 + - + +
93A ILE* 2.7 42.5 + - + +
436B TYR* 3.9 35.9 - - + +
439B GLN* 3.7 17.5 - - - +
440B PHE* 3.7 38.6 - - + +
443B LEU* 3.9 11.7 - - + -
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Residues in contact with SER 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU 2.9 10.0 + - - -
87A ASP* 3.3 11.7 + - - -
89A LEU* 1.3 74.3 - - - +
91A SER* 1.3 58.6 + - - +
93A ILE* 3.8 8.9 - - - +
94A GLY* 2.9 28.9 + - - +
440B PHE* 3.5 23.3 - - - -
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Residues in contact with SER 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASP 3.2 9.7 + - - -
88A GLU* 3.5 11.4 - - - -
89A LEU 3.2 0.4 - - - -
90A SER* 1.3 78.0 - - - +
92A LEU* 1.3 67.9 + - - +
94A GLY* 3.5 9.6 + - - -
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ARG* 4.7 6.1 - - - +
88A GLU* 3.1 28.9 + - + +
89A LEU* 3.6 17.7 - - + +
91A SER* 1.3 83.1 - - - +
93A ILE* 1.3 62.1 + - - +
94A GLY* 4.5 0.3 - - - -
433B VAL* 5.1 5.7 - - - +
436B TYR* 3.9 43.3 - - + +
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Residues in contact with ILE 93 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 2.7 30.0 + - + +
90A SER* 3.8 7.0 - - - +
91A SER 3.3 0.2 - - - -
92A LEU* 1.3 75.4 - - - +
94A GLY* 1.3 68.8 + - - +
433B VAL* 4.4 17.9 - - + +
436B TYR* 3.8 26.7 - - + +
437B LYS* 3.7 55.4 - - + -
440B PHE* 4.1 14.6 - - + -
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Residues in contact with GLY 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A SER 2.9 15.6 + - - +
91A SER* 4.0 7.9 - - - -
92A LEU 3.4 2.0 - - - -
93A ILE* 1.3 88.7 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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