Contacts of the helix formed by residues 79 - 111 (chain B) in PDB entry 5C5B
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 79 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LYS* 3.0 30.4 + - - +
68B TYR* 4.9 0.2 + - - -
77B LYS 3.5 3.0 + - - -
78B GLY* 1.3 73.6 - - - -
80B GLU* 1.3 83.7 + - - +
81B GLU* 2.7 47.2 + - - +
82B VAL* 3.3 4.5 - - + +
83B ILE* 3.2 24.8 + - - +
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Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LYS* 4.2 14.0 - - - +
78B GLY 3.3 15.3 - - - +
79B ASP* 1.3 86.1 + - - +
81B GLU* 1.3 56.9 + - - -
82B VAL 3.5 0.2 - - - -
83B ILE* 3.7 20.1 - - + +
84B SER* 2.8 29.8 + - - -
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Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LYS* 5.2 0.9 + - - +
79B ASP* 2.7 28.4 + - - +
80B GLU* 1.3 77.5 - - - +
82B VAL* 1.3 58.3 + - + +
84B SER* 2.7 16.3 + - - -
85B THR* 2.7 27.6 + - - -
232B MET* 4.2 25.4 - - - +
236B ILE* 4.5 12.6 - - - +
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Residues in contact with VAL 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LYS* 3.3 47.3 - - + +
196A LEU* 4.9 4.7 - - + -
197A LEU* 4.0 30.5 - - + -
68B TYR* 3.7 24.2 - - + +
79B ASP 3.3 11.4 - - - +
81B GLU* 1.3 84.0 - - + +
83B ILE* 1.3 63.5 + - - +
85B THR* 3.8 7.4 - - - -
86B LEU* 2.9 39.7 + - + +
236B ILE* 5.7 0.9 - - + -
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Residues in contact with ILE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TYR* 3.8 16.6 - - + -
69B GLU* 3.3 46.4 - - + +
78B GLY* 3.5 21.1 - - - +
79B ASP 3.2 21.3 + - - +
80B GLU* 3.7 17.9 - - + +
81B GLU 3.3 0.2 - - - -
82B VAL* 1.3 82.8 - - - +
84B SER* 1.3 60.4 + - - +
87B HIS* 2.9 28.1 + - + +
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Residues in contact with SER 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLU 2.8 17.4 + - - -
81B GLU* 2.7 22.5 + - - -
83B ILE* 1.3 79.8 - - - +
85B THR* 1.3 62.2 + - - +
87B HIS* 3.2 7.4 + - - +
88B TYR* 2.9 24.5 + - - +
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Residues in contact with THR 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 3.7 21.3 - - + -
81B GLU 2.7 21.2 + - - -
82B VAL* 3.9 4.0 - - - -
84B SER* 1.3 80.5 + - - +
86B LEU* 1.3 57.4 + - - +
88B TYR* 3.3 7.0 + - - +
89B PHE* 2.9 57.5 + - + -
225B PHE* 4.9 7.5 - - + -
229B VAL* 4.3 17.9 - - + +
232B MET* 3.8 14.9 - - - +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A TYR* 3.7 9.4 - - - +
196A LEU* 3.5 33.9 - - + -
197A LEU* 4.0 22.4 - - + -
200A LEU* 4.1 23.3 - - + -
65B LEU* 3.8 19.4 - - + +
68B TYR* 3.5 33.4 - - + -
69B GLU* 4.1 4.0 - - - +
82B VAL* 2.9 25.2 + - - +
83B ILE 3.9 2.7 - - - +
85B THR* 1.3 71.5 - - + +
87B HIS* 1.3 59.9 + - - +
89B PHE* 3.7 6.1 - - - +
90B SER* 2.9 29.3 + - - -
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Residues in contact with HIS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 3.6 24.1 - - + +
69B GLU* 4.0 10.0 + - - +
83B ILE* 2.9 21.8 + - + +
84B SER* 3.2 8.0 + - - +
86B LEU* 1.3 75.4 - - - +
88B TYR* 1.3 63.6 + - - +
90B SER* 2.6 23.9 + - - -
91B LYS* 3.0 11.1 + - + +
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Residues in contact with TYR 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B SER 2.9 12.0 + - - +
85B THR* 3.3 8.7 + - - +
87B HIS* 1.3 77.6 - - - +
89B PHE* 1.3 66.1 + + - +
91B LYS* 3.0 12.3 + - + +
92B VAL* 3.0 41.1 + - + +
222B MET* 3.6 24.5 - - + +
225B PHE* 3.4 54.5 - + + +
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Residues in contact with PHE 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 4.7 7.2 - - + -
200A LEU* 3.7 34.5 - - + -
201A LEU* 4.5 7.2 - - - -
204A MET* 3.7 37.2 - - + -
65B LEU* 3.7 17.5 - - + -
85B THR* 2.9 41.2 + - + +
86B LEU* 3.7 3.1 - - + +
88B TYR* 1.3 82.2 - + - +
90B SER* 1.3 57.1 + - - +
92B VAL* 3.3 4.8 + - + +
93B VAL* 2.9 34.3 + - - +
222B MET* 5.9 1.8 - - - -
225B PHE* 4.1 15.3 - + - -
226B LEU* 3.9 21.8 - - + -
229B VAL* 4.6 10.1 - - + -
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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
----------------------------------------------------------
62B SER* 3.2 20.0 + - - +
65B LEU* 3.6 22.8 - - - +
66B LEU* 3.3 26.5 - - - +
86B LEU 2.9 16.2 + - - -
87B HIS* 2.6 17.7 + - - -
89B PHE* 1.3 75.8 - - - +
91B LYS* 1.3 57.1 + - - +
93B VAL* 3.5 3.1 + - - +
94B ASP* 2.9 34.0 + - - +
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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 HIS* 3.0 10.4 + - + +
88B TYR* 3.0 16.1 + - + +
90B SER* 1.3 82.4 + - - +
92B VAL* 1.3 63.4 + - + +
94B ASP* 3.0 12.5 + - - +
95B GLU* 3.0 30.5 + - - +
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A MET* 3.7 27.4 - - + -
88B TYR* 3.0 33.3 + - + +
89B PHE* 3.6 9.0 - - + +
91B LYS* 1.3 76.0 - - + +
93B VAL* 1.3 58.7 + - - +
95B GLU* 3.1 16.3 + - - +
96B LEU* 2.9 26.4 + - + +
217B MET* 4.2 7.2 - - + +
218B PHE* 3.9 21.5 - - + -
222B MET* 4.1 28.0 - - + -
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LEU* 5.3 0.4 - - + -
203A TYR* 4.2 6.5 - - + +
204A MET* 3.7 17.0 - - + -
58B THR* 3.2 36.7 - - + +
61B LEU* 3.8 28.0 - - + -
62B SER* 3.7 14.8 - - - +
65B LEU* 4.4 5.6 - - + -
89B PHE 2.9 22.2 + - - +
90B SER* 3.7 5.4 - - - +
92B VAL* 1.3 75.6 - - - +
94B ASP* 1.3 57.4 + - - +
96B LEU* 3.7 8.5 - - - +
97B ASN* 2.9 27.2 + - - +
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Residues in contact with ASP 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B GLN* 5.5 1.7 - - - -
62B SER* 2.7 32.4 + - - -
66B LEU* 5.2 5.2 - - - +
90B SER* 2.9 17.9 + - - +
91B LYS* 3.3 12.4 - - - +
93B VAL* 1.3 77.6 - - - +
95B GLU* 1.3 56.6 + - + +
97B ASN* 3.2 11.9 - - - +
98B LEU* 2.9 33.2 + - + +
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LYS* 3.0 21.5 + - - +
92B VAL* 3.1 17.6 + - - +
94B ASP* 1.3 76.0 - - + +
96B LEU* 1.3 57.5 + - - +
98B LEU* 2.9 32.6 + - + +
99B LEU* 3.0 17.3 + - + +
217B MET* 3.5 29.5 - - + +
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TYR* 3.8 19.5 - - + +
204A MET* 6.1 0.2 - - - -
207A GLN* 3.4 34.8 - - + +
211A PHE* 3.6 31.9 - - + -
58B THR* 5.1 2.9 - - + -
92B VAL* 2.9 14.8 + - + +
93B VAL* 3.7 8.1 - - - +
95B GLU* 1.3 74.9 - - - +
97B ASN* 1.3 57.4 + - - +
99B LEU* 3.2 15.8 + - + +
100B HIS* 2.9 53.2 + - + +
210B PHE* 4.9 0.2 - - + -
217B MET* 3.7 9.1 - - - -
218B PHE* 4.1 13.5 - - + -
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Residues in contact with ASN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B CYS* 3.0 32.3 + - - +
58B THR* 3.1 16.5 + - - +
59B GLN* 3.6 17.6 - - - +
62B SER* 6.3 0.2 - - - -
93B VAL 2.9 15.6 + - - +
94B ASP* 3.2 16.9 - - - +
96B LEU* 1.3 76.7 - - - +
98B LEU* 1.3 60.7 + - - +
100B HIS* 3.3 4.6 + - - +
101B THR* 2.8 46.2 + - - -
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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
----------------------------------------------------------
94B ASP* 2.9 17.9 + - + +
95B GLU* 2.9 20.0 + - + +
97B ASN* 1.3 81.1 - - - +
99B LEU* 1.3 69.0 + - + +
101B THR* 3.2 8.9 + - - +
102B GLU* 2.9 23.6 + - - +
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A PHE* 4.7 1.8 - - + -
95B GLU* 3.0 18.0 + - + +
96B LEU* 3.4 16.8 - - + +
98B LEU* 1.3 79.9 - - + +
100B HIS* 1.3 63.0 + - - +
102B GLU* 3.1 8.7 + - - +
103B LEU* 2.9 22.5 + - - +
210B PHE* 3.9 22.7 - - + +
213B LYS* 3.7 24.9 - - + +
214B GLY* 3.5 37.7 - - - +
217B MET* 3.5 24.5 - - + -
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Residues in contact with HIS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A GLN* 5.5 3.3 + - - -
54A LEU* 5.0 5.2 - - + -
100A HIS* 5.9 2.2 - + - -
203A TYR* 5.7 0.2 + - - -
207A GLN* 5.1 3.6 + - - -
210A PHE* 6.0 1.8 - + - -
51B GLN* 3.0 24.7 + - - +
54B MET* 3.5 32.7 - - + +
55B CYS* 3.4 25.0 - - - +
58B THR* 4.3 10.0 - - + +
96B LEU* 2.9 55.4 + - + +
97B ASN* 3.7 5.4 - - - +
99B LEU* 1.3 73.0 - - - +
101B THR* 1.3 56.9 + - - +
103B LEU* 3.3 4.6 + - - +
104B ALA* 2.9 24.8 + - - +
210B PHE* 3.6 25.5 - + - -
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Residues in contact with THR 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B CYS* 3.4 18.2 - - + +
97B ASN* 2.8 33.0 + - - -
98B LEU* 3.2 9.6 + - - +
100B HIS* 1.3 78.1 - - - +
102B GLU* 1.3 58.4 + - - +
104B ALA* 3.2 4.7 + - + +
105B LYS* 2.9 30.6 + - + +
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Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU 2.9 12.7 + - - +
99B LEU* 3.1 11.0 + - - +
101B THR* 1.3 76.2 - - - +
103B LEU* 1.3 57.1 + - - +
105B LYS* 3.4 8.5 + - - +
106B GLN* 2.9 48.4 + - + +
209B ASN* 4.9 12.8 + - - +
213B LYS* 6.4 1.1 - - + +
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A HIS* 6.2 1.8 - - + +
51B GLN* 3.4 35.2 - - + +
99B LEU 2.9 13.8 + - - +
100B HIS 3.6 7.4 - - - +
102B GLU* 1.3 77.2 - - - +
104B ALA* 1.3 56.6 + - - +
106B GLN* 3.2 5.1 + - - +
107B LEU* 2.9 42.7 + - + +
206B GLY* 3.6 32.1 - - - +
207B GLN* 3.6 26.5 - - - +
209B ASN* 5.3 1.5 + - - -
210B PHE* 3.6 35.2 - - + -
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TYR* 3.4 25.0 - - + -
51B GLN* 3.9 23.3 - - + +
52B ASN* 4.4 9.0 - - + +
55B CYS* 4.2 11.0 - - - -
100B HIS 2.9 14.6 + - - +
101B THR* 3.2 9.2 + - + +
103B LEU* 1.3 75.2 - - - +
105B LYS* 1.3 57.4 + - - +
107B LEU* 3.2 4.3 + - - +
108B ALA 2.9 23.7 + - - -
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Residues in contact with LYS 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TYR* 5.3 0.7 - - - -
101B THR* 2.9 18.5 + - + +
102B GLU* 3.8 10.8 - - - +
104B ALA* 1.3 76.5 - - - +
106B GLN* 1.3 59.9 + - - +
108B ALA* 3.8 5.1 - - - +
109B ASP* 2.9 40.6 + - - +
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Residues in contact with GLN 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLU* 2.9 34.7 + - + +
103B LEU* 3.4 11.2 - - + +
105B LYS* 1.3 76.6 - - - +
107B LEU* 1.3 59.3 + - + +
109B ASP* 4.8 4.2 - - - +
110B THR* 2.4 63.7 + - - +
202B GLY* 4.5 2.9 + - - +
205B HIS* 4.8 5.7 - - - +
206B GLY* 4.2 24.3 - - - +
209B ASN* 4.2 19.7 - - - +
----------------------------------------------------------
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B VAL* 3.8 23.8 - - + -
48B TYR* 4.1 12.1 - - + -
51B GLN* 3.9 33.4 - - + +
103B LEU* 2.9 33.5 + - + +
104B ALA* 3.6 5.6 - - - +
106B GLN* 1.3 75.8 - - + +
108B ALA* 1.3 58.2 + - - +
111B MET* 3.0 27.9 + - + +
112B VAL* 2.9 29.0 + - - +
203B PHE* 3.8 36.8 - - + +
206B GLY* 5.9 0.7 - - - -
207B GLN* 4.6 1.3 - - - +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B TYR* 3.6 25.5 - - + +
104B ALA 2.9 15.5 + - - +
105B LYS* 3.8 7.2 - - - +
106B GLN 3.3 0.2 - - - -
107B LEU* 1.3 78.2 - - - +
109B ASP* 1.3 67.0 + - - +
112B VAL* 4.1 8.0 - - - +
113B LEU* 3.3 30.3 + - - +
----------------------------------------------------------
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Residues in contact with ASP 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LYS* 2.9 26.1 + - - +
106B GLN* 4.8 4.9 - - - +
108B ALA* 1.3 82.9 - - - +
110B THR* 1.3 69.3 + - + +
113B LEU* 4.3 10.3 - - - +
114B PRO* 3.1 21.8 - - - +
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Residues in contact with THR 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B GLN* 2.4 49.7 + - - +
109B ASP* 1.3 81.8 - - + +
111B MET* 1.3 58.4 + - - +
114B PRO* 3.7 11.5 - - - +
198B GLU* 3.8 4.0 - - - +
199B PRO* 3.5 16.6 - - - +
202B GLY* 3.4 33.5 + - - -
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Residues in contact with MET 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PHE* 5.7 2.5 - - - -
44B MET* 3.6 44.6 - - - +
47B VAL* 4.0 20.0 - - + -
48B TYR 5.0 0.2 - - - +
107B LEU* 3.0 43.7 + - + +
109B ASP 3.4 1.4 - - - -
110B THR* 1.3 81.7 + - - +
112B VAL* 1.3 71.2 + - + +
114B PRO* 3.3 7.2 - - - +
115B ILE* 3.1 23.2 - - - +
199B PRO* 3.6 20.8 - - + +
203B PHE* 3.6 34.8 - - + +
----------------------------------------------------------
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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).
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