Contacts of the helix formed by residues 73 - 102 (chain B) in PDB entry 3E8G
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 73 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 4.0 20.6 - - + +
46B GLU* 2.7 24.6 + - - +
72B GLN* 1.3 82.1 - - + +
74B ASP* 1.3 64.2 + - - +
75B PHE* 3.4 9.8 + - - +
76B GLY* 2.8 21.0 + - - -
77B LYS* 3.1 18.0 + - - +
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Residues in contact with ASP 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B GLN 4.5 3.1 - - - +
73B THR* 1.3 73.8 - - - +
75B PHE* 1.3 58.7 + - - +
77B LYS* 3.8 23.4 + - - +
78B ILE* 3.1 34.7 + - + +
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Residues in contact with PHE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 3.6 18.8 - + - -
45B VAL* 3.6 28.3 - - + -
73B THR* 3.7 9.2 - - - +
74B ASP* 1.3 79.1 - - - +
76B GLY* 1.3 61.5 + - - +
78B ILE* 2.7 35.2 - - + +
79B PHE* 3.3 11.3 - + + +
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Residues in contact with GLY 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 3.5 21.4 - - - -
42B TYR* 5.1 0.2 - - - -
46B GLU* 3.5 19.5 - - - -
71B PRO* 3.8 7.2 - - - -
73B THR* 2.8 11.3 + - - -
75B PHE* 1.3 77.4 - - - +
77B LYS* 1.3 53.3 + - - +
79B PHE* 3.8 1.0 - - - +
80B THR* 2.5 39.0 + - - -
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Residues in contact with LYS 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PRO* 3.2 34.3 - - + +
72B GLN* 4.0 16.5 + - - +
73B THR 3.1 11.8 + - - +
74B ASP* 3.8 21.8 + - - +
75B PHE 3.2 0.2 - - - -
76B GLY* 1.3 74.0 - - - +
78B ILE* 1.3 66.5 + - + +
79B PHE 3.1 1.3 - - - -
80B THR* 3.3 4.7 + - - -
81B ILE* 3.1 32.0 + - + +
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Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ASP* 3.1 13.7 - - + +
75B PHE* 2.7 57.7 - - + +
77B LYS* 1.3 77.2 - - + +
79B PHE* 1.3 69.1 + - + +
81B ILE* 3.5 13.4 + - + +
82B LEU* 3.1 35.4 + - + +
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Residues in contact with PHE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B SER* 4.6 5.6 - - - -
38B GLY* 4.4 4.3 - - - -
41B PHE* 3.4 60.3 - + + -
42B TYR* 3.6 22.7 - + - -
75B PHE* 3.3 19.3 - + + +
76B GLY 3.8 0.9 - - - +
77B LYS 3.1 0.2 - - - -
78B ILE* 1.3 82.8 - - + +
80B THR* 1.3 58.0 + - - +
82B LEU* 3.0 9.1 + - - +
83B TYR* 2.6 63.9 + + - +
502B MPD 3.2 31.2 - - + -
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Residues in contact with THR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TYR* 2.9 26.3 + - - +
56B PHE* 4.6 6.5 - - + -
60B THR* 4.2 10.5 - - + -
71B PRO* 3.3 23.2 - - + +
76B GLY 2.5 24.7 + - - -
77B LYS* 3.3 5.6 + - - -
79B PHE* 1.3 75.1 - - - +
81B ILE* 1.3 58.3 - - + +
83B TYR* 3.5 2.3 - - + +
84B ILE* 2.8 55.4 + - + +
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Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LYS* 3.1 19.3 + - + +
78B ILE* 3.6 15.5 - - + +
80B THR* 1.3 78.3 - - + +
82B LEU* 1.3 68.1 + - + +
84B ILE* 3.5 9.3 + - + +
85B PHE* 3.3 41.3 + - + -
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ILE* 3.1 23.1 + - + +
79B PHE* 3.0 9.5 + - - +
81B ILE* 1.3 80.3 - - + +
83B TYR* 1.3 60.5 + - - +
85B PHE* 3.4 5.4 + - + +
86B ILE* 2.9 41.4 + - + +
502B MPD 3.8 20.9 - - + -
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B THR* 2.8 45.1 + - + -
35B LEU* 3.6 1.7 - - - -
38B GLY* 3.4 20.5 - - - -
42B TYR* 3.9 18.2 - + - -
57B SER* 3.5 28.2 - - - -
60B THR* 4.9 5.8 - - + -
61B LEU* 3.4 40.9 - - + +
79B PHE* 2.6 42.6 + + + +
80B THR* 3.5 5.4 - - - +
82B LEU* 1.3 74.1 - - - +
84B ILE* 1.3 53.6 + - - +
86B ILE* 4.7 2.2 - - - -
87B GLY* 2.7 33.4 + - - -
502B MPD 4.3 20.1 - - + +
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Residues in contact with ILE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B THR* 3.5 29.6 - - + +
61B LEU* 4.0 6.7 - - - -
80B THR* 2.8 37.2 + - + +
81B ILE* 3.7 9.4 - - + +
82B LEU 3.3 0.2 - - - -
83B TYR* 1.3 76.0 - - - +
85B PHE* 1.3 68.8 + - + +
88B ILE* 2.9 59.0 + - + +
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Residues in contact with PHE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ILE* 3.3 37.8 + - + +
82B LEU* 4.0 6.5 - - + +
84B ILE* 1.3 88.0 - - + +
86B ILE* 1.3 66.9 + - + +
88B ILE* 4.5 3.8 + - - +
89B GLY* 4.7 4.9 + - - -
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 2.9 29.3 + - + +
83B TYR* 4.2 2.0 - - + +
85B PHE* 1.3 82.7 - - + +
87B GLY* 1.3 59.9 + - - +
89B GLY* 4.7 1.9 + - - -
90B LEU* 4.6 10.9 + - - +
502B MPD 3.9 39.5 - - + -
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Residues in contact with GLY 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B THR* 4.7 9.4 - - - -
61B LEU* 4.2 17.5 - - - -
83B TYR 2.7 22.8 + - - -
86B ILE* 1.3 74.9 - - - +
88B ILE* 1.3 64.1 + - - +
89B GLY 3.3 2.0 - - - -
90B LEU* 3.2 7.2 + - - +
91B VAL* 3.0 27.8 + - - +
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Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B THR 4.8 1.6 - - - +
61B LEU* 3.7 26.3 - - - +
63B THR* 3.7 22.0 - - + -
84B ILE* 2.9 46.9 + - + +
85B PHE* 5.2 1.8 - - - +
86B ILE 3.8 0.2 - - - -
87B GLY* 1.3 70.3 - - - +
89B GLY* 1.3 64.9 + - - +
91B VAL* 4.6 0.2 - - - -
92B PHE* 3.0 45.0 + - + +
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Residues in contact with GLY 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE 4.7 5.6 + - - -
86B ILE 4.7 1.8 + - - -
87B GLY 3.3 1.0 - - - -
88B ILE* 1.3 79.7 - - - +
90B LEU* 1.3 57.1 + - - +
92B PHE* 3.6 2.5 + - - +
93B GLY* 3.0 25.8 + - - -
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 3.9 21.8 - - + -
30B LEU* 3.6 41.3 - - + +
31B THR* 3.9 13.2 - - - +
34B THR* 3.2 32.1 - - + +
86B ILE 4.6 8.7 + - - +
87B GLY* 3.2 9.7 + - - +
89B GLY* 1.3 73.9 - - - +
91B VAL* 1.3 62.1 + - + +
93B GLY* 3.1 3.1 + - - -
94B PHE* 2.8 26.7 + - - +
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Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B THR* 4.3 21.3 - - + -
34B THR* 5.4 2.9 - - + -
35B LEU* 5.3 4.0 - - + -
61B LEU* 3.7 38.1 - - + +
62B THR* 3.9 29.2 - - + -
87B GLY* 3.0 19.3 + - - +
88B ILE 4.0 2.2 - - - +
90B LEU* 1.3 77.9 - - + +
92B PHE* 1.3 59.5 + - + +
94B PHE* 3.3 8.3 + - + +
95B ILE* 2.9 35.8 + - + +
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Residues in contact with PHE 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LEU 3.5 21.3 - - - -
62B THR* 3.1 31.6 - - - -
63B THR* 3.9 15.0 - - + -
88B ILE* 3.0 35.6 + - + +
89B GLY* 4.3 2.5 - - - +
91B VAL* 1.3 77.3 - - + +
93B GLY* 1.3 61.4 + - - +
94B PHE 3.2 0.2 - - - -
95B ILE* 3.8 23.7 - - + +
96B HIS* 2.9 28.6 + - - +
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Residues in contact with GLY 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU* 4.2 8.1 - - - -
89B GLY 3.0 16.4 + - - -
90B LEU* 3.1 4.9 + - - -
92B PHE* 1.3 78.1 - - - +
94B PHE* 1.3 61.1 + - - +
96B HIS* 3.5 4.2 + - - +
97B LYS* 2.9 36.9 + - - +
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Residues in contact with PHE 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 3.4 33.9 - + - -
27B LEU* 4.0 15.8 - - + +
28B PHE* 3.7 51.1 - + - -
31B THR* 3.3 33.2 - - + +
90B LEU 2.8 8.5 + - - +
91B VAL* 3.5 9.2 - - + +
93B GLY* 1.3 74.7 - - - +
95B ILE* 1.3 67.9 + - + +
97B LYS* 3.3 1.0 + - - +
98B LEU* 2.8 49.8 + - + +
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Residues in contact with ILE 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B THR* 4.4 13.0 - - + -
91B VAL* 2.9 39.0 + - + +
92B PHE* 3.8 31.2 - - + +
93B GLY 3.4 0.2 - - - -
94B PHE* 1.3 83.1 - - + +
96B HIS* 1.3 58.4 + - - +
98B LEU* 3.6 12.9 - - + +
99B ALA* 2.9 31.0 + - + +
103B GLN* 5.0 0.2 - - - +
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Residues in contact with HIS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PHE 2.9 18.5 + - - +
93B GLY* 3.6 6.7 - - - +
95B ILE* 1.3 78.4 - - - +
97B LYS* 1.3 88.5 + - + +
99B ALA* 3.1 7.2 + - - +
100B VAL* 2.9 54.4 + - + +
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Residues in contact with LYS 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLU* 3.7 34.8 + - + +
24B PHE* 4.3 14.7 - - + -
27B LEU* 3.4 25.4 - - + -
93B GLY* 2.9 28.1 + - - +
94B PHE* 3.3 3.1 + - - +
96B HIS* 1.3 98.5 + - + +
98B LEU* 1.3 60.1 + - - +
100B VAL* 5.0 0.6 - - - +
101B ASN* 2.8 51.1 + - - +
102B VAL 3.7 0.3 + - - -
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 3.7 33.5 - - + -
94B PHE* 2.8 37.7 + - + +
95B ILE* 3.6 12.3 - - + +
97B LYS* 1.3 74.7 - - - +
99B ALA* 1.3 58.1 - - - +
102B VAL* 3.1 25.2 + - + +
103B GLN* 2.9 47.2 + - + +
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 2.9 20.9 + - + +
96B HIS* 3.4 6.7 - - - +
98B LEU* 1.3 78.1 - - - +
100B VAL* 1.3 61.3 + - + +
103B GLN* 3.3 19.9 - - + +
104B LEU* 2.8 32.4 + - - +
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Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LYS* 5.7 3.4 - - - +
96B HIS* 2.9 43.9 + - + +
97B LYS* 5.0 0.4 - - - +
99B ALA* 1.3 80.5 - - + +
101B ASN* 1.3 73.4 + - - +
104B LEU* 3.6 22.6 - - + +
105B PRO* 3.4 16.5 - - - +
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Residues in contact with ASN 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LYS* 3.3 46.6 + - + +
23B GLU* 3.7 21.6 + - - -
24B PHE* 5.3 2.4 - - + +
97B LYS* 2.8 44.7 + - + +
100B VAL* 1.3 87.8 - - - +
102B VAL* 1.3 65.0 + - + +
105B PRO* 3.7 14.0 - - - +
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Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B PHE* 3.8 45.5 - - + -
98B LEU* 3.1 22.7 + - + +
100B VAL 3.6 0.4 - - - -
101B ASN* 1.3 85.1 - - + +
103B GLN* 1.3 69.1 + - + +
104B LEU 3.5 0.4 - - - -
105B PRO* 3.5 4.0 - - - +
106B SER* 3.2 25.4 + - - -
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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