Contacts of the helix formed by residues 73 - 103 (chain B) in PDB entry 1KWV
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 ALA 73 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 1.3 61.5 + - + +
75B GLU* 3.4 8.2 + - - -
76B VAL* 2.9 21.0 + - - +
77B LYS* 2.7 50.8 + - - +
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Residues in contact with ILE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 3.8 27.4 - - + -
73B ALA* 1.3 79.0 - - + +
75B GLU* 1.3 71.9 + - - +
77B LYS* 3.2 6.9 + - + +
78B LEU* 2.9 23.4 + - + +
74C ILE* 4.1 14.8 - - + -
75C GLU* 3.8 34.5 - - + +
78C LEU* 3.9 24.5 - - + +
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Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 4.2 22.0 - - + +
73B ALA 4.4 6.2 + - - -
74B ILE* 1.3 85.4 + - - +
76B VAL* 1.3 60.1 + - + +
78B LEU* 3.6 3.2 - - - +
79B ALA* 3.0 28.4 + - - +
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Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ALA* 2.9 23.2 + - - +
75B GLU* 1.3 78.1 - - + +
77B LYS* 1.3 66.6 + - + +
79B ALA* 3.2 5.8 + - + +
80B ASN* 2.9 41.6 + - - +
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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
----------------------------------------------------------
73B ALA* 2.7 33.3 + - - +
74B ILE* 3.6 8.3 - - + +
76B VAL* 1.3 73.8 - - + +
78B LEU* 1.3 58.3 + - - +
80B ASN* 3.4 6.9 + - - +
81B MET* 3.0 38.8 + - - +
78C LEU* 4.1 22.2 - - + -
82C GLU* 5.6 6.3 + - - +
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 3.2 36.1 - - + +
77A LYS* 3.5 35.9 - - + -
78A LEU* 3.7 15.7 - - + +
81A MET* 3.4 26.9 - - + +
74B ILE 2.9 16.4 + - - +
75B GLU* 3.6 4.9 - - - +
77B LYS* 1.3 73.6 - - - +
79B ALA* 1.3 65.0 + - - +
81B MET* 3.2 1.5 + - - -
82B GLU* 2.9 30.2 + - - +
78C LEU* 3.3 28.9 - - + +
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLU 3.0 16.6 + - - +
76B VAL* 3.2 6.7 + - - +
78B LEU* 1.3 76.2 - - - +
80B ASN* 1.3 68.6 + - - +
82B GLU* 3.1 19.3 + - - +
83B ALA* 3.1 21.1 + - - +
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Residues in contact with ASN 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL* 2.9 36.1 + - - +
77B LYS* 3.8 7.7 - - - +
79B ALA* 1.3 81.6 - - - +
81B MET* 1.3 57.3 + - + +
83B ALA* 3.3 8.8 + - - +
84B GLU* 3.1 30.7 + - + +
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Residues in contact with MET 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A MET* 3.5 20.6 - - + -
77B LYS* 3.0 24.4 + - - +
78B LEU 3.2 4.5 + - - +
80B ASN* 1.3 74.6 - - + +
82B GLU* 1.3 60.5 + - - +
84B GLU* 3.2 9.6 + - + +
85B ILE* 2.9 33.4 + - - +
78C LEU* 3.7 29.2 - - + +
81C MET* 3.3 36.8 - - + -
82C GLU* 3.4 28.0 - - + +
85C ILE* 3.7 12.7 - - + +
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Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LYS* 4.2 35.4 + - - +
80A ASN* 5.1 8.4 + - - +
81A MET* 3.4 17.5 - - + -
78B LEU* 2.9 19.7 + - - +
79B ALA* 3.1 20.3 + - - +
81B MET* 1.3 76.0 - - - +
83B ALA* 1.3 57.6 + - - +
85B ILE* 3.4 8.0 + - + +
86B ASN* 3.1 36.6 + - - +
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Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ALA 3.1 12.3 + - - +
80B ASN* 3.5 12.8 - - - +
81B MET 3.1 0.2 - - - -
82B GLU* 1.3 75.9 - - - +
84B GLU* 1.3 64.6 + - + +
86B ASN* 3.2 10.8 + - - +
87B THR* 3.0 27.6 + - - +
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Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASN 3.1 19.9 + - - +
81B MET* 3.2 13.2 + - + +
83B ALA* 1.3 75.6 - - + +
85B ILE* 1.3 58.8 + - - +
87B THR* 3.4 12.4 + - - +
88B LEU* 3.0 27.9 + - - +
85C ILE* 4.3 17.9 - - + -
89C LYS* 2.8 35.7 + - - +
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Residues in contact with ILE 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A MET* 3.4 38.4 - - + +
84A GLU* 4.1 20.9 - - + +
85A ILE* 3.8 17.0 - - + -
88A LEU* 4.5 9.9 - - + -
81B MET 2.9 19.9 + - - +
82B GLU* 3.6 7.6 - - + +
84B GLU* 1.3 74.1 - - - +
86B ASN* 1.3 67.3 + - - +
88B LEU* 3.2 9.3 + - + +
89B LYS* 2.9 47.3 + - + +
85C ILE* 3.6 21.3 - - + -
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Residues in contact with ASN 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU* 6.0 1.6 - - - -
82B GLU* 3.1 21.3 + - - +
83B ALA* 3.5 10.5 - - - +
85B ILE* 1.3 79.4 - - - +
87B THR* 1.3 62.7 + - - +
89B LYS* 3.3 22.9 + - - +
90B SER* 3.1 26.6 + - - -
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Residues in contact with THR 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ALA 3.0 14.0 + - - -
84B GLU* 3.5 17.0 - - - +
86B ASN* 1.3 77.3 - - - +
88B LEU* 1.3 57.5 + - - +
90B SER* 3.4 7.3 + - - -
91B LYS* 3.0 30.1 + - + +
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 3.7 25.1 - - + -
84B GLU 3.0 15.5 + - - +
85B ILE* 3.2 7.8 + - + +
87B THR* 1.3 75.5 - - - +
89B LYS* 1.3 59.9 + - - +
91B LYS* 3.2 10.2 + - + +
92B LEU* 2.9 30.0 + - + +
85C ILE* 4.3 14.1 - - + +
88C LEU* 3.9 25.8 - - + +
89C LYS* 3.9 36.3 - - + -
92C LEU* 3.7 26.0 - - + -
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Residues in contact with LYS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU* 2.8 35.0 + - + +
88A LEU* 3.6 30.3 - - + -
91A LYS* 6.2 2.2 - - - +
85B ILE* 2.9 30.9 + - + +
86B ASN* 3.3 19.8 + - - +
88B LEU* 1.3 76.4 - - - +
90B SER* 1.3 61.5 + - - +
92B LEU* 3.4 3.0 + - - +
93B GLU* 3.1 22.7 + - - +
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Residues in contact with SER 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ASN 3.1 13.4 + - - -
87B THR* 3.7 8.9 - - - -
88B LEU 3.3 0.2 - - - -
89B LYS* 1.3 74.0 - - - +
91B LYS* 1.3 60.4 + - - +
93B GLU* 3.1 17.8 + - - +
94B LEU* 2.9 28.4 + - - +
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Residues in contact with LYS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B THR* 3.0 20.2 + - + +
88B LEU* 3.2 13.2 + - + +
90B SER* 1.3 78.4 - - - +
92B LEU* 1.3 61.8 + - - +
94B LEU* 3.2 15.9 + - + +
95B THR* 2.9 24.3 + - - -
89C LYS 5.4 0.8 + - - -
92C LEU* 3.5 22.4 - - + +
93C GLU* 4.4 20.6 + - - +
96C ASN* 3.6 22.8 + - - +
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 4.0 20.9 - - + +
91A LYS* 3.8 31.6 - - + -
92A LEU* 3.9 31.6 - - + +
95A THR* 3.7 23.1 - - + +
88B LEU* 2.9 17.9 + - + +
89B LYS* 3.8 5.8 - - - +
91B LYS* 1.3 75.3 - - - +
93B GLU* 1.3 63.6 + - - +
95B THR* 3.0 8.6 + - - -
96B ASN* 3.0 29.6 + - - +
92C LEU* 3.9 16.5 - - + +
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Residues in contact with GLU 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LYS 3.1 14.4 + - - +
90B SER* 3.4 18.1 + - - +
92B LEU* 1.3 76.6 - - - +
94B LEU* 1.3 63.0 + - - +
96B ASN* 3.2 12.6 + - + +
97B LYS* 3.0 52.4 + - + +
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B SER 2.9 13.0 + - - +
91B LYS* 3.3 18.8 - - + +
93B GLU* 1.3 79.3 - - - +
95B THR* 1.3 63.4 + - - +
97B LYS* 3.1 8.5 + - - +
98B LEU* 2.9 30.0 + - + +
130C GLU 4.2 6.7 - - - +
131C LEU* 3.5 36.1 - - + +
132C ARG* 3.4 33.0 - - + -
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Residues in contact with THR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A THR* 4.0 23.1 - - + -
91B LYS* 2.9 15.0 + - - +
92B LEU* 3.0 12.8 + - + -
94B LEU* 1.3 77.3 - - - +
96B ASN* 1.3 62.2 + - - +
98B LEU* 3.5 5.9 + - - +
99B HIS* 3.0 23.2 + - - +
92C LEU* 3.4 12.3 - - + +
95C THR* 4.2 5.4 - - + -
96C ASN* 2.8 34.1 + - - +
99C HIS* 4.1 17.1 + - + +
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Residues in contact with ASN 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LYS* 6.2 0.3 - - - +
95A THR* 2.8 42.7 + - - +
98A LEU* 6.0 4.0 - - - +
92B LEU* 3.0 23.0 + - - +
93B GLU* 3.5 12.7 - - - +
95B THR* 1.3 76.0 - - - +
97B LYS* 1.3 58.1 + - + +
99B HIS* 3.5 7.2 + - - +
100B ALA* 3.1 28.8 + - - +
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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
----------------------------------------------------------
93B GLU* 3.0 47.7 + - + +
94B LEU* 3.5 10.8 - - - +
96B ASN* 1.3 75.6 - - + +
98B LEU* 1.3 66.1 + - - +
100B ALA* 3.3 6.0 + - - +
101B PHE* 2.9 24.1 + - - +
130C GLU* 3.7 35.5 + - + +
131C LEU* 3.7 17.6 - - + +
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LEU* 2.9 22.8 + - + +
95B THR* 4.0 5.8 - - - +
97B LYS* 1.3 76.9 - - - +
99B HIS* 1.3 58.9 + - - +
101B PHE* 3.3 9.0 + - + +
102B SER* 2.9 28.8 + - - -
96C ASN* 6.2 1.6 - - - +
103C MET* 4.2 30.7 - - + -
111C PHE* 4.8 3.8 - - + -
113C VAL* 4.9 1.8 - - + -
131C LEU* 3.7 22.6 - - + +
219C PHE* 3.5 44.0 - - + -
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Residues in contact with HIS 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A THR* 6.1 1.3 - - + -
98A LEU* 4.0 26.1 - - + +
99A HIS* 3.8 27.9 + + + -
102A SER* 2.8 36.8 + - - -
103A MET* 4.9 2.7 - - + -
95B THR* 3.0 19.7 + - + +
96B ASN* 3.6 7.6 + - - +
98B LEU* 1.3 77.1 - - - +
100B ALA* 1.3 66.0 + - - +
102B SER* 2.7 25.7 + - - -
103B MET* 3.0 26.3 + - + +
111B PHE* 4.2 11.7 - + - -
99C HIS* 4.4 17.3 - + + +
103C MET* 5.9 1.3 - - - -
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Residues in contact with ALA 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ASN 3.1 17.8 + - - +
97B LYS* 3.8 6.5 - - - +
99B HIS* 1.3 76.6 + - - +
101B PHE* 1.3 61.7 + - - +
103B MET* 3.1 9.5 + - - +
104B GLY 3.3 0.3 + - - -
105B LYS* 2.9 52.2 + - + +
111B PHE* 4.0 26.8 - - + -
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Residues in contact with PHE 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LYS 2.9 17.9 + - - +
98B LEU* 3.5 8.1 - - + +
100B ALA* 1.3 76.9 - - - +
102B SER* 1.3 60.3 + - - +
104B GLY 2.9 18.0 + - - -
105B LYS* 4.3 6.9 - - - +
113C VAL* 3.5 32.1 - - + -
114C THR* 3.7 10.1 - - - -
115C ASN* 3.1 63.0 - - + +
127C LEU* 3.4 29.8 - - + -
131C LEU* 3.7 21.5 - - + -
215C ALA 4.1 7.0 - - - -
217C CYS* 3.9 24.0 - - + -
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Residues in contact with SER 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A MET* 5.2 1.7 - - - +
98B LEU 2.9 18.5 + - - -
99B HIS* 2.7 25.3 + - - -
101B PHE* 1.3 73.4 - - - +
103B MET* 1.3 67.7 + - - +
104B GLY 3.2 2.1 + - - -
103C MET* 3.6 34.5 - - - +
113C VAL* 3.7 20.1 - - - +
114C THR 4.1 7.5 - - - +
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Residues in contact with MET 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A SER* 3.6 27.8 - - - +
103A MET* 3.3 28.3 - - - +
99B HIS* 3.0 40.6 + - + +
100B ALA 3.1 2.2 + - - +
101B PHE 3.1 0.8 - - - -
102B SER* 1.3 82.8 - - - +
104B GLY* 1.3 58.3 + - - +
105B LYS 3.6 0.4 + - - -
111B PHE* 3.6 24.4 - - + -
112B PHE 4.9 4.0 - - - +
113B VAL* 4.5 9.4 - - + -
114B THR 5.8 0.4 - - - +
----------------------------------------------------------
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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