Contacts of the helix formed by residues 64 - 95 (chain B) in PDB entry 4DAJ
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 ILE 64 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B THR* 1.3 79.0 - - - +
65B TRP* 1.3 56.9 + - - +
67B VAL* 3.6 8.3 - - - +
68B VAL* 2.9 30.1 + - - +
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Residues in contact with TRP 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B THR 3.1 5.1 - - - +
64B ILE* 1.3 77.9 - - - +
66B GLN* 1.3 94.5 + - + +
68B VAL* 3.1 8.5 + - - +
69B PHE* 2.9 28.3 + - + +
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Residues in contact with GLN 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B THR* 3.0 33.2 - - - +
65B TRP* 1.3 98.1 - - + +
67B VAL* 1.3 62.5 + - + +
69B PHE* 2.8 27.9 + - + +
70B ILE* 2.9 9.9 + - - +
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B THR* 3.0 30.9 + - - +
64B ILE* 3.6 9.0 - - - +
66B GLN* 1.3 81.2 - - + +
68B VAL* 1.3 65.1 + - - +
69B PHE 3.1 0.3 + - - -
70B ILE* 3.2 6.8 + - - +
71B ALA* 2.9 21.3 + - - +
128B ILE* 5.5 9.0 - - + +
129B ILE* 4.9 25.4 - - + +
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Residues in contact with VAL 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE 2.9 17.8 + - - +
65B TRP* 3.6 5.6 - - - +
67B VAL* 1.3 77.3 - - - +
69B PHE* 1.3 61.7 + - - +
71B ALA* 3.3 19.5 - - + +
72B PHE* 4.1 7.6 + - - +
129B ILE* 5.9 5.2 - - + -
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Residues in contact with PHE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B TRP* 2.9 21.1 + - + +
66B GLN* 2.8 25.1 + - + +
68B VAL* 1.3 79.7 - - - +
70B ILE* 1.3 60.5 + - - +
71B ALA 3.2 0.9 + - - -
72B PHE* 3.6 8.3 + - - +
73B LEU* 3.8 6.1 + - - +
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Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLN 2.9 13.4 + - - +
67B VAL* 3.2 6.7 + - - +
69B PHE* 1.3 71.3 - - - +
71B ALA* 1.3 56.6 + - - +
72B PHE 3.3 0.2 - - - -
73B LEU* 2.7 47.9 + - + +
74B THR* 3.0 12.8 + - + +
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL 2.9 13.3 + - - +
68B VAL* 3.3 20.0 - - - +
69B PHE 3.1 0.2 - - - -
70B ILE* 1.3 76.2 - - - +
72B PHE* 1.3 65.7 + - + +
74B THR* 2.4 35.9 + - - -
75B GLY* 3.3 0.7 + - - -
125B THR* 3.6 8.1 - - - +
129B ILE* 3.7 30.5 - - + -
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Residues in contact with PHE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B VAL 4.1 4.6 + - - +
69B PHE 3.6 5.9 + - - +
70B ILE 3.3 0.2 - - - -
71B ALA* 1.3 85.5 - - + +
73B LEU* 1.3 60.1 + - - +
74B THR 3.2 0.2 - - - -
75B GLY* 3.3 14.6 - - - +
76B PHE* 2.9 23.7 + - - +
79B LEU* 6.2 3.1 - - + -
129B ILE* 6.1 3.6 - - + -
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PHE 3.8 4.6 + - - +
70B ILE* 2.7 34.8 + - + +
72B PHE* 1.3 76.0 - - - +
74B THR* 1.3 59.8 + - + +
76B PHE* 3.0 29.0 - - + +
77B LEU* 3.0 35.7 + - + +
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Residues in contact with THR 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 3.1 16.8 - - + +
71B ALA* 2.4 25.8 + - - +
73B LEU* 1.3 77.8 - - + +
75B GLY* 1.3 59.6 + - - +
77B LEU* 3.2 9.8 + - + +
78B ALA* 2.8 32.4 + - - +
121B MET 4.7 0.2 + - - -
125B THR* 3.1 22.0 + - + +
128B ILE* 6.0 2.0 - - + -
530B TRP* 3.5 39.3 - - + +
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Residues in contact with GLY 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ALA 3.3 0.4 + - - -
72B PHE* 3.3 25.4 + - - -
73B LEU 3.1 0.6 - - - -
74B THR* 1.3 83.7 + - - +
76B PHE* 1.3 51.7 + - - +
78B ALA* 3.2 5.9 + - - +
79B LEU* 2.8 47.2 + - - +
122B ASN* 5.4 5.2 - - - -
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Residues in contact with PHE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE 2.9 12.3 + - - +
73B LEU* 3.0 28.7 - - + +
75B GLY* 1.3 76.4 - - - +
77B LEU* 1.3 97.0 + - + -
79B LEU* 3.8 8.3 - - - +
80B VAL* 2.9 49.0 + - + +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 3.0 28.5 + - + +
74B THR* 3.2 12.8 + - - +
76B PHE* 1.3 102.1 - - + +
78B ALA* 1.3 57.7 + - - +
80B VAL* 3.4 6.4 + - + +
81B THR* 2.9 30.7 + - - -
121B MET* 4.3 10.5 - - + -
530B TRP* 4.8 10.3 - - + -
534B ILE* 4.4 22.7 - - + -
537B THR* 3.5 14.9 - - + +
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Residues in contact with ALA 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B THR 2.8 20.2 + - - +
75B GLY* 3.7 7.0 - - - +
77B LEU* 1.3 71.5 - - - +
79B LEU* 1.3 60.3 + - + +
81B THR* 3.2 9.0 + - - -
82B ILE* 2.9 34.6 + - + +
117B GLY 4.5 6.5 - - - +
121B MET* 3.9 32.6 - - + +
122B ASN* 4.5 12.6 - - - +
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE* 6.2 3.8 - - + -
75B GLY* 2.8 33.4 + - - +
76B PHE* 3.8 6.5 - - - +
78B ALA* 1.3 70.4 - - + +
80B VAL* 1.3 66.1 + - + +
82B ILE* 2.9 40.7 - - + +
83B ILE* 2.9 21.4 + - + +
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B PHE* 2.9 49.6 + - + +
77B LEU* 3.5 6.7 - - + +
79B LEU* 1.3 77.1 - - + +
81B THR* 1.3 56.3 + - - +
83B ILE* 3.4 15.4 - - + +
84B GLY* 2.9 26.7 + - - -
537B THR* 3.7 22.5 - - + +
540B PRO* 5.7 0.2 - - - +
541B VAL* 5.6 8.1 - - + -
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Residues in contact with THR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU 2.9 10.2 + - - -
78B ALA 3.3 8.7 - - - -
79B LEU 3.2 0.2 - - - -
80B VAL* 1.3 76.6 - - - +
82B ILE* 1.3 58.5 + - - +
84B GLY* 3.2 1.4 + - - -
85B ASN* 2.9 55.1 + - - +
113B ASP 3.5 14.8 - - - +
117B GLY* 4.2 3.6 - - - -
121B MET* 3.5 20.2 - - - -
536B SER* 3.8 16.4 - - - +
537B THR* 2.5 33.9 + - - +
540B PRO* 4.6 1.0 - - - +
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Residues in contact with ILE 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ALA* 2.9 16.5 + - + +
79B LEU* 2.9 53.4 - - + +
81B THR* 1.3 74.9 - - - +
83B ILE* 1.3 63.2 + - + +
85B ASN* 4.1 4.0 - - - +
86B ILE* 2.9 32.4 + - - +
114B LEU* 4.5 10.8 - - + +
117B GLY* 4.0 7.0 - - - +
118B VAL* 3.9 33.4 - - + +
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Residues in contact with ILE 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU* 2.9 27.3 + - + +
80B VAL* 3.4 19.7 - - + +
82B ILE* 1.3 81.0 - - + +
84B GLY* 1.3 71.1 + - - +
86B ILE* 3.1 12.3 - - + +
87B LEU* 2.9 34.4 + - + +
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Residues in contact with GLY 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL 2.9 19.6 + - - -
81B THR 3.7 0.4 - - - -
83B ILE* 1.3 80.6 - - - +
85B ASN* 1.3 57.5 + - - +
87B LEU* 3.1 11.4 - - - +
88B VAL* 2.9 27.4 + - - +
540B PRO* 3.7 20.7 - - - +
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Residues in contact with ASN 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B THR* 2.9 31.0 + - - +
82B ILE 4.2 1.3 - - - +
84B GLY* 1.3 72.1 - - - +
86B ILE* 1.3 61.3 + - - +
88B VAL* 2.9 9.8 + - - +
89B ILE* 2.9 31.9 + - - +
110B ALA* 3.3 30.7 - - - +
113B ASP* 3.0 22.7 - - - +
114B LEU* 3.0 31.0 - - + +
536B SER 3.9 1.4 + - - -
540B PRO* 2.8 24.6 - - - +
543B TYR* 5.1 0.3 - - - -
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ILE 2.9 20.2 + - - +
83B ILE* 3.1 23.3 - - + +
85B ASN* 1.3 75.5 - - - +
87B LEU* 1.3 65.0 + - + +
89B ILE* 3.9 4.4 - - + +
90B VAL* 2.9 49.4 + - + +
114B LEU* 4.5 16.3 - - + +
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ILE* 2.9 27.7 + - + +
84B GLY* 3.1 13.9 - - - +
86B ILE* 1.3 79.4 - - + +
88B VAL* 1.3 65.6 + - + +
90B VAL* 4.7 5.8 - - + -
91B ALA* 2.9 31.0 + - + +
554B PHE* 4.6 32.3 - - + +
556B THR 6.0 0.2 - - - +
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Residues in contact with VAL 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLY 2.9 17.8 + - - +
85B ASN* 2.9 14.2 + - - +
87B LEU* 1.3 75.6 - - + +
89B ILE* 1.3 57.1 + - - +
91B ALA* 3.9 3.5 - - - +
92B PHE* 2.9 35.1 + - + +
106B LEU* 4.4 5.2 - - + +
107B LEU* 4.8 5.8 - - - -
110B ALA* 3.3 25.6 - - + -
540B PRO* 4.0 8.1 - - + +
543B TYR* 3.5 37.2 - - + -
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Residues in contact with ILE 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ASN 2.9 15.6 + - - +
86B ILE* 3.9 7.4 - - + +
88B VAL* 1.3 73.1 - - - +
90B VAL* 1.3 70.5 + - + +
92B PHE* 3.2 6.5 + - - +
93B LYS* 2.9 27.8 + - + +
107B LEU* 4.9 14.6 - - + -
110B ALA* 4.6 10.3 - - + -
111B CYS* 4.0 28.5 - - - -
114B LEU* 3.5 30.1 - - + -
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Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ILE* 2.9 37.3 + - + +
87B LEU* 4.0 7.0 - - + +
89B ILE* 1.3 81.3 - - + +
91B ALA* 1.3 66.4 + - - +
93B LYS* 3.2 4.9 + - - +
94B VAL* 2.9 33.9 + - + +
----------------------------------------------------------
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Residues in contact with ALA 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 2.9 20.8 + - + +
88B VAL* 3.9 3.1 - - - +
90B VAL* 1.3 80.2 - - - +
92B PHE* 1.3 62.2 + - - +
94B VAL* 3.1 13.5 - - - +
95B ASN* 2.9 26.7 + - - +
98B LEU* 3.5 7.9 - - + -
550B PHE* 6.0 1.1 - - - +
553B THR* 3.8 26.7 - - + +
554B PHE* 5.0 6.3 - - + +
----------------------------------------------------------
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Residues in contact with PHE 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B VAL* 2.9 23.2 + - + +
89B ILE* 3.5 5.6 - - - +
91B ALA* 1.3 76.6 - - - +
93B LYS* 1.3 67.0 + - + +
95B ASN 2.9 26.0 - - - +
98B LEU* 2.8 40.3 - - + +
99B LYS* 3.7 19.8 - - + +
100B THR 4.5 0.2 - - - -
103B ASN* 3.3 33.0 - - + -
104B TYR* 4.0 23.6 - + - -
107B LEU* 3.3 34.5 - - + -
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Residues in contact with LYS 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ILE* 2.9 21.6 + - + +
90B VAL* 3.8 4.5 - - - +
92B PHE* 1.3 84.5 - - + +
94B VAL* 1.3 58.8 + - - +
95B ASN 3.7 1.6 + - - +
----------------------------------------------------------
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Residues in contact with VAL 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B VAL* 2.9 23.7 + - + +
91B ALA* 3.1 24.2 - - - +
92B PHE 3.1 0.4 - - - -
93B LYS* 1.3 77.4 - - - +
95B ASN* 1.3 60.6 + - + +
96B LYS 4.3 0.5 + - - -
553B THR* 4.5 7.9 - - + -
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Residues in contact with ASN 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ALA 2.9 15.4 + - - +
92B PHE 2.9 18.0 + - - +
93B LYS 3.3 1.7 - - - -
94B VAL* 1.3 80.3 - - + +
96B LYS* 1.3 66.3 + - - +
97B GLN* 2.6 39.0 + - - +
98B LEU* 3.4 24.6 + - + +
99B LYS* 3.6 5.5 + - - +
549B THR* 4.4 3.8 - - - +
553B THR* 3.0 32.1 + - + +
----------------------------------------------------------
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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