Contacts of the helix formed by residues 97 - 132 (chain B) in PDB entry 4MBS
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 GLY 97 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TRP* 2.8 27.3 + - - +
95B ASP 3.6 2.0 - - - -
96B PHE* 1.3 80.3 - - - +
98B ASN* 1.3 59.4 + - - -
99B THR 3.6 2.0 - - - -
100B MET 3.6 0.2 + - - -
101B CYS* 3.2 12.5 + - - +
169B SER* 3.9 7.2 - - - -
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Residues in contact with ASN 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLY* 1.3 69.0 - - - -
99B THR* 1.4 69.5 + - - +
101B CYS* 3.3 2.4 + - - +
102B GLN* 3.2 40.2 + - - +
168B ARG* 3.4 16.7 - - - +
169B SER* 3.1 39.2 + - - +
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Residues in contact with THR 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLY 3.6 0.4 - - - -
98B ASN* 1.4 80.5 + - - +
100B MET* 1.3 59.8 + - - +
102B GLN* 3.2 9.2 + - - +
103B LEU* 2.9 39.9 + - + +
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Residues in contact with MET 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE* 4.1 25.1 - - + -
94B TRP* 4.1 2.2 - - - -
96B PHE* 3.2 44.4 + - + +
97B GLY 3.6 1.5 - - - +
99B THR* 1.3 80.4 - - - +
101B CYS* 1.3 55.7 + - - +
103B LEU* 3.3 28.0 + - + -
104B LEU* 2.9 48.5 + - + +
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Residues in contact with CYS 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TRP* 3.6 20.4 - - - +
97B GLY 3.2 5.0 + - - +
98B ASN* 3.3 13.0 + - - +
100B MET* 1.3 77.9 - - - +
102B GLN* 1.3 55.9 + - - +
104B LEU* 4.2 0.9 - - - +
105B THR* 2.7 36.0 + - - -
167B THR* 3.6 16.6 - - - -
168B ARG* 3.6 13.7 - - - -
169B SER* 4.3 3.4 - - - +
178B CYS* 2.1 55.1 - - - -
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Residues in contact with GLN 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ASN* 3.2 33.5 + - - +
99B THR* 3.8 8.3 - - - +
101B CYS* 1.3 74.4 - - - +
103B LEU* 1.3 60.7 + - - +
105B THR* 3.9 3.9 - - - -
106B GLY* 2.9 25.8 + - - -
164B ILE* 2.8 48.4 + - + +
165B ILE* 3.9 10.1 + - - +
167B THR* 3.3 25.2 + - - +
168B ARG* 4.9 0.2 - - - -
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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
----------------------------------------------------------
99B THR* 2.9 26.6 + - + +
100B MET* 3.6 31.6 - - + +
102B GLN* 1.3 78.0 - - - +
104B LEU* 1.3 61.5 + - + +
106B GLY* 3.3 2.8 + - - -
107B LEU* 2.9 53.0 + - + +
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Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 4.4 2.2 - - + +
82B THR* 3.4 30.3 - - + +
85B PHE* 3.6 52.5 - - + -
86B TRP* 4.1 15.7 - - + -
94B TRP* 3.6 21.3 - - + -
100B MET* 2.9 31.4 + - + +
101B CYS 4.4 0.9 - - - +
103B LEU* 1.3 79.7 - - + +
105B THR* 1.3 60.7 + - - +
107B LEU* 3.3 13.3 + - + -
108B TYR* 3.0 25.8 + - - +
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Residues in contact with THR 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B TRP* 3.9 17.0 - - - -
101B CYS 2.7 23.7 + - - -
102B GLN 4.0 3.4 - - - -
104B LEU* 1.3 73.7 - - - +
106B GLY* 1.3 61.2 + - - +
108B TYR* 3.3 6.7 + - - +
109B PHE* 3.1 53.4 + - + -
163B ASN 4.5 5.6 - - - +
164B ILE* 4.8 1.8 - - - -
167B THR* 3.5 36.5 - - + +
178B CYS* 4.1 2.6 - - - -
1101B MRV 4.5 9.3 - - + +
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Residues in contact with GLY 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B GLN 2.9 17.0 + - - -
103B LEU* 3.4 5.4 - - - -
104B LEU 3.2 0.2 - - - -
105B THR* 1.3 74.9 - - - +
107B LEU* 1.3 56.1 + - - +
108B TYR 3.3 0.2 + - - -
109B PHE* 3.3 3.2 + - - +
110B ILE* 3.0 41.4 + - - +
164B ILE* 3.6 25.5 - - - +
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B PHE* 3.9 48.4 - - + +
81B LEU* 4.9 12.3 - - + -
82B THR* 3.8 16.6 - - + -
103B LEU* 2.9 44.5 + - + +
104B LEU* 3.3 14.3 + - + -
106B GLY* 1.3 71.5 - - - +
108B TYR* 1.3 56.2 + - - +
110B ILE* 4.7 7.4 - - + -
111B GLY* 2.9 27.4 + - - -
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Residues in contact with TYR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 3.3 45.5 - + - +
82B THR* 3.7 11.0 - - + +
86B TRP* 3.6 22.7 - + + -
104B LEU 3.0 13.1 + - - +
105B THR* 3.4 12.8 - - - +
106B GLY 3.2 0.4 - - - -
107B LEU* 1.3 74.5 - - - +
109B PHE* 1.4 63.3 + + + +
112B PHE* 3.1 28.2 + - - +
248B TRP* 4.1 2.8 - - - -
283B GLU* 2.9 34.5 + - - +
287B MET* 4.0 5.7 - - + +
1101B MRV 3.4 70.8 - + + +
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Residues in contact with PHE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B THR* 3.1 48.6 + - + +
106B GLY* 4.0 1.8 - - - +
108B TYR* 1.4 76.3 - + - +
110B ILE* 1.4 60.6 + - - +
112B PHE* 3.2 5.6 + - - +
113B PHE* 2.9 49.1 + + - -
160B SER* 3.3 20.0 - - - +
163B ASN* 3.4 44.2 - - + -
164B ILE* 5.6 0.4 - - + -
167B THR* 5.5 0.2 - - - -
198B ILE* 4.5 9.4 - - + -
1101B MRV 3.4 61.0 - + + -
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B PHE* 4.6 9.4 - - + -
106B GLY* 3.0 28.5 + - - +
107B LEU* 4.4 7.6 - - + +
109B PHE* 1.4 70.2 - - - +
111B GLY* 1.3 58.1 + - - +
114B SER* 2.5 36.7 + - - -
153B TRP* 3.9 27.8 - - + -
156B ALA* 4.2 8.9 - - + +
157B VAL* 4.1 35.2 - - + -
160B SER* 3.6 19.1 - - - +
164B ILE* 4.4 13.5 - - + -
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Residues in contact with GLY 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B SER* 3.5 28.1 + - - +
78B PHE* 4.4 7.8 - - - +
79B PHE* 4.1 8.9 - - - -
107B LEU 2.9 20.7 + - - -
108B TYR 4.0 0.7 - - - -
110B ILE* 1.3 76.0 - - - +
112B PHE* 1.3 58.4 + - - +
114B SER* 3.5 4.6 + - - -
115B GLY* 3.3 17.8 + - - -
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Residues in contact with PHE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B PHE* 3.8 11.1 - + + -
108B TYR 3.1 19.7 + - - +
109B PHE 3.2 3.3 + - - +
111B GLY* 1.3 73.1 - - - +
113B PHE* 1.3 95.8 + + - +
115B GLY* 3.3 3.5 + - - -
116B ILE* 3.3 21.5 + - + +
198B ILE* 4.4 15.0 - - + -
202B GLY* 4.2 16.2 - - - -
244B TYR* 3.5 27.6 - + - -
248B TRP* 3.8 38.4 - + - -
251B TYR* 6.3 0.4 - + - -
252B ASN* 5.2 3.8 - - - -
1101B MRV 3.7 34.5 - + + -
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Residues in contact with PHE 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B PHE* 2.9 43.2 + + - +
112B PHE* 1.3 93.5 - + - +
114B SER* 1.3 63.4 + - - +
115B GLY 3.3 0.2 + - - -
116B ILE* 3.4 6.9 - - + +
117B PHE* 3.0 42.8 + + + -
156B ALA* 4.2 8.7 - - + -
159B ALA* 3.8 25.4 - - + -
160B SER* 3.3 15.0 - - - -
197B LYS* 4.2 17.5 - - + -
198B ILE* 4.3 18.4 - - + -
201B LEU* 3.5 42.8 - - + -
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Residues in contact with SER 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B SER* 3.3 16.0 - - - -
110B ILE 2.5 24.7 + - - -
113B PHE* 1.3 76.7 - - - +
115B GLY* 1.3 57.6 + - - +
117B PHE* 3.1 12.3 + - - +
118B PHE* 2.8 50.4 + - - -
152B THR* 5.1 1.3 - - - -
153B TRP* 3.3 28.3 - - - -
156B ALA* 3.9 8.9 - - - +
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Residues in contact with GLY 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 3.4 19.0 - - - +
75B SER* 3.3 19.2 + - - -
76B ASP* 6.1 0.4 - - - -
111B GLY 3.3 9.0 + - - -
112B PHE 3.3 4.9 + - - -
113B PHE 3.2 0.6 - - - -
114B SER* 1.3 82.4 + - - +
116B ILE* 1.3 61.3 + - - +
118B PHE 3.4 0.2 + - - -
119B ILE* 3.2 22.4 + - - +
244B TYR* 5.6 0.9 - - - -
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Residues in contact with ILE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PHE* 3.3 14.8 + - + +
113B PHE* 3.4 19.1 - - + +
115B GLY* 1.3 75.2 - - - +
117B PHE* 1.4 62.8 + - + +
119B ILE* 3.2 17.4 + - + +
120B ILE* 3.0 30.7 + - + +
201B LEU 3.8 18.4 - - - +
202B GLY* 4.5 3.4 - - - +
206B PRO* 3.7 33.7 - - + -
241B MET* 5.0 1.8 - - + -
244B TYR* 3.6 55.9 - - + +
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Residues in contact with PHE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B PHE* 3.0 37.8 + + + -
114B SER* 3.4 9.0 - - - +
116B ILE* 1.4 85.1 - - + +
118B PHE* 1.3 57.7 + - - +
120B ILE* 3.5 16.2 + - + +
121B LEU* 3.1 32.8 + - + +
152B THR* 3.5 31.9 - - + -
155B VAL* 3.9 19.1 - - + -
156B ALA* 3.9 26.2 - - + -
159B ALA* 5.1 1.1 - - + -
201B LEU* 4.2 39.0 - - + -
205B LEU* 4.6 9.2 - - + -
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Residues in contact with PHE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B TYR* 4.0 23.2 - + - +
71B ASN* 3.5 42.6 - - + -
72B LEU* 4.2 10.8 - - + -
114B SER* 2.8 34.2 + - - +
115B GLY 4.0 4.0 - - - +
117B PHE* 1.3 74.6 - - - +
119B ILE* 1.4 61.2 + - - +
121B LEU* 3.9 16.4 - - + +
122B LEU* 3.1 34.7 + - - +
149B SER* 3.7 20.2 - - - -
152B THR* 3.6 26.2 - - + -
153B TRP* 3.5 36.1 - + - -
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Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 3.9 17.3 - - + -
115B GLY 3.2 18.0 + - - +
116B ILE* 3.2 12.5 + - + +
118B PHE* 1.4 73.9 - - - +
120B ILE* 1.4 61.7 + - - +
122B LEU* 3.4 9.0 + - + +
123B THR* 3.1 28.3 + - - +
237B ILE* 5.0 1.5 - - + +
240B ILE* 3.7 28.5 - - + -
241B MET* 3.8 39.9 - - + -
244B TYR* 3.9 34.3 - - + -
289B HIS* 4.7 8.1 - - + -
293B ASN* 4.8 1.1 - - - +
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Residues in contact with ILE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ILE* 3.0 24.4 + - + +
117B PHE* 3.6 13.2 - - + +
119B ILE* 1.4 75.1 - - - +
121B LEU* 1.4 60.2 + - + +
123B THR* 3.1 5.8 + - - -
124B ILE* 2.9 46.7 + - + +
201B LEU 5.0 0.2 - - - +
205B LEU* 3.8 34.8 - - + -
206B PRO* 4.0 21.1 - - + -
209B VAL* 4.0 15.7 - - + +
241B MET* 4.0 21.1 - - + -
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Residues in contact with LEU 121 (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 39.0 - - + +
117B PHE 3.1 20.8 + - - +
118B PHE* 3.9 23.1 - - + +
119B ILE 3.5 0.2 - - - -
120B ILE* 1.4 77.3 - - + +
122B LEU* 1.3 53.1 + - - +
124B ILE* 3.8 14.2 - - + +
125B ASP* 2.8 35.3 + - - +
148B THR* 4.8 11.2 - - + +
152B THR* 3.4 28.3 - - + +
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Residues in contact with LEU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B THR* 3.7 33.9 - - + +
68B TYR* 3.6 28.3 - - + -
69B LEU* 3.9 24.7 - - + -
72B LEU* 4.0 19.7 - - + -
118B PHE 3.1 23.6 + - - +
119B ILE* 3.7 8.1 - - + +
120B ILE 3.3 0.2 - - - -
121B LEU* 1.3 73.7 - - - +
123B THR* 1.3 57.9 + - - +
125B ASP* 3.5 9.2 + - - +
126B ARG* 3.1 22.5 + - - +
237B ILE* 3.6 25.8 - - + +
240B ILE* 4.5 9.2 - - + -
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Residues in contact with THR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ILE 3.1 13.7 + - - -
120B ILE 3.1 9.5 + - - -
122B LEU* 1.3 73.9 - - - +
124B ILE* 1.4 58.8 + - - +
126B ARG* 3.3 5.0 + - - +
127B TYR* 3.0 25.1 + - - +
209B VAL* 4.0 13.5 - - + +
213B CYS* 3.7 21.3 - - + -
214B TYR* 3.6 35.8 + - + -
217B ILE* 4.4 2.1 - - + +
237B ILE* 3.9 10.5 - - - +
241B MET* 3.4 20.8 - - + +
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Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ILE* 2.9 39.2 + - + +
121B LEU* 4.1 14.8 - - + +
123B THR* 1.4 72.9 - - - +
125B ASP* 1.4 64.4 + - - +
127B TYR* 3.1 15.1 + - + +
128B LEU* 3.0 39.0 + - + +
209B VAL* 4.4 9.9 - - + -
213B CYS* 4.2 14.8 - - - -
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Residues in contact with ASP 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B MET* 3.5 34.9 - - + +
65B THR* 2.9 32.2 + - - +
68B TYR* 4.1 4.0 - - + -
121B LEU 2.8 23.2 + - - +
122B LEU* 3.5 11.4 - - - +
123B THR 3.3 0.2 - - - -
124B ILE* 1.4 71.9 - - - +
126B ARG* 1.4 69.7 + - - +
128B LEU* 3.5 2.4 + - - +
129B ALA* 3.3 16.8 + - - +
140B ARG* 2.8 39.2 + - - -
237B ILE* 5.1 0.3 - - - +
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Residues in contact with ARG 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B THR* 3.6 7.6 + - - +
122B LEU 3.1 15.8 + - - +
123B THR* 3.7 5.4 - - - +
124B ILE 3.3 0.2 - - - -
125B ASP* 1.4 92.6 + - - +
127B TYR* 1.4 63.5 + - - +
129B ALA* 3.3 15.0 + - - +
130B VAL* 3.0 30.1 + - + +
140B ARG* 3.6 19.8 - - - +
214B TYR* 5.6 0.7 - - - +
217B ILE* 4.3 9.6 - - + -
230B ARG* 3.0 34.8 + - - +
233B ASP* 3.6 34.1 + - - +
234B VAL* 3.6 26.9 - - + +
237B ILE* 3.5 32.9 - - + +
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Residues in contact with TYR 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B THR 3.0 13.6 + - - +
124B ILE* 3.4 15.5 - - + +
126B ARG* 1.4 74.5 - - - +
128B LEU* 1.3 63.6 + - + +
131B VAL* 2.8 60.4 + - + +
132B HIS* 3.5 32.6 + + - -
212B ILE* 4.2 9.8 + - + +
213B CYS* 3.3 52.9 - - + -
216B GLY* 4.0 10.6 - - - -
217B ILE* 3.9 9.4 - - + +
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Residues in contact with LEU 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B MET* 4.7 11.0 - - + -
124B ILE* 3.0 31.9 + - + +
125B ASP* 3.7 5.4 - - - +
127B TYR* 1.3 77.4 - - + +
129B ALA* 1.3 61.1 + - - +
132B HIS* 2.9 50.1 + - + +
135B PHE* 3.7 34.8 - - + -
136B ALA* 3.7 12.3 - - + -
139B ALA* 5.2 8.1 - - + -
140B ARG* 4.3 14.1 - - + -
144B PHE* 6.0 4.7 - - + -
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ASP 3.3 11.0 + - - +
126B ARG* 3.7 28.7 - - - +
128B LEU* 1.3 77.3 - - - +
130B VAL* 1.3 57.1 + - - +
133B ALA* 3.4 17.3 - - - -
136B ALA* 3.8 11.6 - - - +
140B ARG* 3.8 19.5 - - - +
230B ARG* 3.3 27.5 + - + -
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Residues in contact with VAL 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ARG* 3.0 18.6 + - + +
127B TYR 4.3 0.7 - - - +
129B ALA* 1.3 79.1 - - + +
131B VAL* 1.4 61.4 + - - +
132B HIS 3.7 0.2 - - - -
133B ALA* 4.5 4.0 + - - +
217B ILE* 4.1 17.7 - - + +
220B THR* 3.3 34.8 - - + +
221B LEU* 3.7 25.4 - - + -
230B ARG* 3.8 36.9 + - - +
231B HIS* 4.1 10.3 - - + -
234B VAL* 3.8 17.0 - - + -
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B TYR* 2.8 46.1 + - + +
130B VAL* 1.4 72.5 - - - +
132B HIS* 1.3 83.5 + - + +
133B ALA 3.6 1.4 + - - -
216B GLY* 3.5 35.7 - - - +
217B ILE* 3.7 8.7 - - + +
220B THR* 3.7 14.9 + - - +
223B ARG* 5.7 5.1 + - - +
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Residues in contact with HIS 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B TYR* 3.5 40.6 + + - -
128B LEU* 2.9 23.6 + - + +
131B VAL* 1.3 92.1 + - + +
133B ALA* 1.4 52.6 + - - +
134B VAL* 3.5 3.4 - - - -
135B PHE* 3.1 27.2 + + + -
136B ALA* 2.8 30.1 + - - +
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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