Contacts of the helix formed by residues 97 - 132 (chain B) in PDB entry 5VBL
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 PHE 97 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PRO 5.4 0.2 - - - -
84B LEU* 3.3 52.5 - - + -
87B THR* 3.7 29.8 - - + -
88B TYR 5.0 0.4 - - - -
95B TRP* 3.4 38.0 - + + +
96B PRO* 1.4 96.7 - - + +
98B GLY* 1.3 62.2 + - - +
101B PHE* 3.4 32.6 - - + +
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Residues in contact with GLY 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B TRP* 2.8 26.6 + - - +
96B PRO* 3.5 3.6 + - - +
97B PHE* 1.3 78.6 - - - +
99B THR* 1.3 63.3 + - - -
100B PHE 3.5 2.5 - - - -
102B CYS* 3.3 5.7 + - - +
170B THR* 3.7 9.6 - - - -
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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
----------------------------------------------------------
98B GLY* 1.3 70.7 - - - -
100B PHE* 1.4 64.2 + - + +
102B CYS* 3.4 2.5 + - - +
103B LYS* 3.0 41.0 + - + +
169B THR* 4.0 14.6 - - - +
170B THR* 3.4 34.2 + - - +
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Residues in contact with PHE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B GLY* 3.5 1.0 - - - -
99B THR* 1.4 82.6 - - + +
101B PHE* 1.3 85.7 + + + +
103B LYS* 3.4 11.9 + - + +
104B LEU* 3.0 49.3 + - + +
165B MET* 5.3 14.3 - - + +
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Residues in contact with PHE 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 4.9 18.4 - - + -
95B TRP* 3.6 5.4 - - + -
97B PHE* 3.4 37.2 - - + +
98B GLY 3.9 1.4 + - - -
99B THR 3.4 0.2 - - - -
100B PHE* 1.3 98.7 - + + +
102B CYS* 1.4 55.8 + - - +
104B LEU* 4.5 17.5 - - + +
105B SER* 2.8 37.6 + - - -
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Residues in contact with CYS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B TRP* 3.5 16.0 - - - +
98B GLY 3.3 18.8 + - - +
99B THR 3.5 4.3 - - - +
100B PHE 3.3 0.4 - - - -
101B PHE* 1.4 74.1 - - - +
103B LYS* 1.4 61.2 + - - +
105B SER* 4.2 0.2 - - - -
106B SER* 2.9 32.6 + - - -
168B ARG* 4.3 3.8 - - - +
169B THR* 4.1 26.7 - - - -
170B THR* 3.7 5.6 - - + -
181B CYS* 2.0 54.0 - - - -
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Residues in contact with LYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B THR* 3.0 28.9 + - + +
100B PHE* 3.5 11.7 - - + +
101B PHE 3.3 0.2 - - - -
102B CYS* 1.4 75.8 - - - +
104B LEU* 1.4 57.4 + - - +
106B SER* 4.2 1.0 - - - -
107B TYR* 3.2 27.9 + - - +
164B VAL 4.8 0.3 - - - +
165B MET* 3.4 46.4 - - + +
166B VAL* 3.6 11.2 + - - +
168B ARG* 2.8 39.8 + - - +
169B THR* 3.6 17.4 - - - +
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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 THR* 6.0 2.0 - - + -
100B PHE* 3.0 40.6 + - + +
101B PHE* 4.1 18.4 - - + +
103B LYS* 1.4 75.0 - - - +
105B SER* 1.4 63.4 + - - +
107B TYR* 3.5 12.2 + - + +
108B LEU* 3.2 48.0 + - + +
165B MET* 4.3 14.3 - - + -
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Residues in contact with SER 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B THR* 3.4 29.4 + - - -
84B LEU* 4.0 5.5 - - - +
85B TRP* 2.8 29.7 + - - -
95B TRP* 3.7 20.6 - - - -
101B PHE 2.8 24.0 + - - -
102B CYS 4.2 0.4 - - - -
104B LEU* 1.4 73.7 - - - +
106B SER* 1.3 61.1 + - - +
108B LEU* 3.6 4.9 + - - +
109B ILE* 3.3 23.2 + - - +
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Residues in contact with SER 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B TRP* 3.4 9.4 - - - -
102B CYS 2.9 19.4 + - - -
103B LYS 4.3 1.1 - - - -
105B SER* 1.3 74.9 - - - +
107B TYR* 1.4 64.5 + - - +
109B ILE* 3.4 17.3 + - - +
110B PHE* 3.3 25.2 - - - -
164B VAL* 3.8 9.0 - - - -
168B ARG* 3.3 47.1 + - - -
181B CYS* 3.4 1.6 - - - -
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Residues in contact with TYR 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LYS 3.2 19.5 + - - +
104B LEU* 3.6 14.6 - - + +
106B SER* 1.4 76.6 - - - +
108B LEU* 1.4 66.3 + - + +
109B ILE 3.3 0.3 + - - -
110B PHE* 3.4 3.3 + - - -
111B VAL* 2.9 46.4 + - + +
158B ALA* 3.2 33.6 + - - +
161B ALA* 3.2 41.3 - - + +
162B MET* 3.9 19.4 - - + +
164B VAL* 4.1 8.4 - - - +
165B MET* 3.7 28.9 - - + -
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Residues in contact with LEU 108 (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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74B ALA 5.3 0.2 - - - +
77B THR* 4.1 34.0 + - + +
78B PHE* 3.8 10.6 - - - +
81B THR* 3.8 25.4 - - + +
104B LEU* 3.2 36.3 + - + +
105B SER 3.6 6.3 + - - +
106B SER 3.4 0.4 - - - -
107B TYR* 1.4 82.5 - - + +
109B ILE* 1.4 62.7 + - - +
111B VAL* 3.9 17.4 - - + +
112B ASN* 3.3 22.7 + - - +
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Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A 200 4.5 10.3 - - + +
78B PHE* 3.7 24.0 - - + -
85B TRP* 3.5 41.1 - - + +
105B SER 3.3 11.4 - - - +
106B SER* 3.5 12.6 - - - +
107B TYR 3.2 1.0 - - - -
108B LEU* 1.4 75.9 - - - +
110B PHE* 1.3 76.6 + - + +
112B ASN* 3.4 7.4 + - - +
113B MET* 2.9 28.8 + - + +
168B ARG* 5.7 2.7 - - - +
264B TYR* 5.9 1.6 - - + +
299B TYR* 3.6 33.9 - - + +
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Residues in contact with PHE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A 200 3.8 18.4 - - - -
106B SER 3.3 17.0 - - - -
107B TYR 3.4 2.8 + - - +
109B ILE* 1.3 85.6 - - + +
111B VAL* 1.4 58.2 + - - +
113B MET* 3.4 24.6 - - + +
114B TYR* 2.9 47.9 + - + -
161B ALA* 3.9 16.8 - - + -
164B VAL* 3.7 27.4 - - + -
168B ARG* 4.8 9.2 - - - -
205B SER* 3.5 25.1 - - - -
264B TYR* 4.3 6.1 - - - -
268B LYS* 5.1 0.7 - - - -
1102B OLC 3.4 33.4 - - - -
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Residues in contact with VAL 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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74B ALA* 6.0 0.7 - - + -
77B THR* 5.6 4.0 - - - +
107B TYR* 2.9 56.1 + - + +
108B LEU* 4.1 18.6 - - + +
110B PHE* 1.4 74.2 - - - +
112B ASN* 1.4 54.7 + - - +
114B TYR 3.4 0.2 + - - -
115B ALA* 2.8 37.4 + - - +
154B TRP* 4.1 26.0 - - + -
157B ALA* 3.9 14.7 - - + +
158B ALA* 4.5 4.0 - - + +
161B ALA* 3.7 11.7 - - + -
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Residues in contact with ASN 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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74B ALA* 3.0 36.3 - - - +
75B ASP* 3.0 24.6 + - - +
78B PHE* 3.7 27.6 - - + -
108B LEU 3.3 19.1 + - - +
109B ILE 3.5 5.2 + - - +
111B VAL* 1.4 77.1 - - - +
113B MET* 1.4 56.5 + - - +
116B SER* 2.7 45.0 + - - -
261B LYS* 4.9 10.7 - - - +
299B TYR* 6.2 0.6 - - - -
302B SER* 4.0 5.7 + - - -
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Residues in contact with MET 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 2.9 18.5 + - + +
110B PHE* 3.4 30.3 - - + +
112B ASN* 1.4 80.2 - - - +
114B TYR* 1.3 75.2 + - + +
116B SER* 3.5 7.0 + - - -
117B ALA* 3.4 19.2 - - - +
205B SER* 3.4 40.8 - - - +
209B GLY* 4.1 9.9 - - - +
257B PHE* 5.2 1.9 - - - -
261B LYS* 5.2 15.0 - - + +
264B TYR* 4.3 13.2 - - + -
265B HIS* 3.9 28.3 - - + +
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Residues in contact with TYR 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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110B PHE* 2.9 37.2 + + + +
113B MET* 1.3 91.8 - - + +
115B ALA* 1.4 54.9 + - - +
117B ALA* 3.2 4.2 + - - +
118B PHE* 2.9 59.7 + + + -
157B ALA* 3.8 17.5 - - + -
160B LEU* 3.7 36.6 - - + -
161B ALA* 3.9 1.3 - - - -
205B SER* 3.0 33.5 + - - -
208B VAL* 3.7 19.5 - - + -
209B GLY* 3.7 14.8 - - - -
1102B OLC 3.2 21.7 - - + +
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Residues in contact with ALA 115 (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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74B ALA* 4.0 20.2 - - + -
111B VAL 2.8 23.2 + - - +
114B TYR* 1.4 71.3 - - - +
116B SER* 1.4 55.9 + - - +
118B PHE* 3.4 2.6 + - - +
119B CYS* 2.9 37.0 + - - -
153B LEU* 4.1 12.2 - - + +
154B TRP* 4.1 23.6 - - + -
157B ALA* 3.8 11.7 - - + +
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Residues in contact with SER 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 3.6 23.4 - - - +
74B ALA* 4.5 4.1 - - - +
75B ASP* 4.4 13.7 - - - -
112B ASN* 2.7 28.8 + - - -
113B MET* 3.5 7.6 + - - -
115B ALA* 1.4 72.7 - - - +
117B ALA* 1.3 65.4 + - - +
119B CYS 3.5 0.3 + - - -
120B LEU* 3.2 31.4 + - - +
257B PHE* 4.3 14.2 - - - -
261B LYS* 4.7 5.6 + - - -
301B ASN* 5.5 5.8 - - - -
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Residues in contact with ALA 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 MET 3.4 15.9 - - - +
114B TYR* 3.2 5.5 + - - +
116B SER* 1.3 80.6 + - - +
118B PHE* 1.4 60.0 + - + +
120B LEU* 3.6 2.3 + - - -
121B THR* 3.2 30.1 + - - +
209B GLY* 3.5 20.6 - - - +
213B PRO* 4.0 14.1 - - + -
217B MET* 3.6 5.5 - - - +
257B PHE* 3.8 21.5 - - + -
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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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114B TYR* 2.9 42.2 + + + +
115B ALA 3.9 2.7 - - - +
117B ALA* 1.4 79.0 - - + +
119B CYS* 1.4 58.7 + - - +
121B THR* 2.8 23.1 + - + +
122B GLY* 3.1 13.3 + - - -
153B LEU* 3.6 45.9 - - + +
156B LEU* 4.0 27.4 - - + -
157B ALA 4.1 2.9 - - - -
160B LEU* 4.0 17.3 - - + -
208B VAL* 3.3 32.3 - - + -
213B PRO* 4.2 10.5 - - + -
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Residues in contact with CYS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PHE* 3.5 32.6 - - - +
70B SER* 3.7 17.3 - - - -
71B LEU* 3.7 28.3 - - + -
115B ALA* 2.9 24.2 + - - +
116B SER 3.8 5.4 - - - +
117B ALA 3.4 0.2 - - - -
118B PHE* 1.4 74.8 - - - +
120B LEU* 1.3 57.9 + - - +
122B GLY* 3.4 1.0 + - - -
123B LEU* 2.9 35.4 + - + +
153B LEU* 4.0 17.7 - - - -
154B TRP* 5.7 0.2 - - - -
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 3.9 25.4 - - + -
116B SER* 3.2 23.5 + - - +
117B ALA 3.7 5.8 - - - +
118B PHE 3.3 0.2 - - - -
119B CYS* 1.3 74.5 - - - +
121B THR* 1.4 58.1 + - - +
123B LEU* 3.4 13.1 + - + +
124B SER* 2.9 33.1 + - - -
217B MET* 3.8 10.3 - - + -
250B ILE* 4.9 1.1 - - + +
253B LEU* 3.8 14.6 - - + +
254B VAL* 3.8 28.0 - - + -
257B PHE* 3.6 46.0 - - + -
305B ASN* 5.8 1.6 - - - +
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Residues in contact with THR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ALA 3.2 13.0 + - - +
118B PHE* 2.8 32.9 + - + +
120B LEU* 1.4 72.4 - - - +
122B GLY* 1.3 54.3 + - - +
124B SER* 3.6 2.1 - - - -
125B PHE* 2.8 37.4 + - - +
213B PRO* 3.3 39.5 - - + +
216B ILE* 4.3 21.6 - - + +
217B MET* 3.8 9.9 - - + -
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Residues in contact with GLY 122 (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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67B PHE* 3.7 32.7 - - - -
118B PHE 3.1 13.1 + - - -
119B CYS 3.4 5.4 + - - -
121B THR* 1.3 76.7 + - - +
123B LEU* 1.4 55.1 + - - +
125B PHE* 3.9 4.8 - - - +
126B ASP* 3.0 29.5 + - - +
149B ALA* 5.8 2.5 - - - -
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Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ALA* 3.6 41.3 - - + +
67B PHE* 3.7 13.0 - - + -
68B ILE* 3.9 15.5 - - + -
71B LEU* 4.8 8.1 - - + -
119B CYS 2.9 26.5 + - - +
120B LEU* 3.6 17.3 - - + +
121B THR 3.4 0.2 - - - -
122B GLY* 1.4 73.9 - - - +
124B SER* 1.4 62.0 + - - +
126B ASP* 3.4 8.2 + - - +
127B ARG* 3.3 26.7 + - - +
250B ILE* 3.7 26.6 - - + +
253B LEU* 4.4 21.5 - - + -
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Residues in contact with SER 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU 2.9 21.4 + - - -
121B THR* 3.6 5.4 - - - -
123B LEU* 1.4 74.6 - - - +
125B PHE* 1.4 57.6 + - - +
127B ARG* 3.3 8.1 + - - +
128B TYR* 3.1 24.1 + - - +
217B MET* 3.7 32.9 + - - +
220B CYS* 3.9 14.8 - - - +
224B ILE* 3.9 2.6 - - - +
250B ILE* 3.9 17.5 - - - +
254B VAL* 4.1 5.4 - - - +
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Residues in contact with PHE 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B THR 2.8 21.7 + - - +
122B GLY* 4.1 4.7 - - - +
124B SER* 1.4 69.6 - - - +
126B ASP* 1.4 57.9 + - - +
128B TYR* 3.3 26.3 + + - +
129B LEU* 3.0 59.0 + - + +
145B SER* 4.8 7.4 - - - -
216B ILE* 5.3 7.2 - - + -
220B CYS* 3.8 22.4 - - - -
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Residues in contact with ASP 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B SER* 2.7 42.7 + - - +
64B ALA* 4.1 4.6 + - + +
67B PHE* 4.6 9.3 - - + -
122B GLY 3.0 19.1 + - - +
123B LEU* 3.5 9.6 - - - +
124B SER 3.3 0.2 - - - -
125B PHE* 1.4 76.5 - - - +
127B ARG* 1.4 78.7 + - - +
129B LEU* 4.8 2.2 - - - -
130B ALA* 3.3 22.2 + - - +
142B LEU* 3.4 35.6 - - - +
146B GLY* 5.4 0.9 - - - -
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Residues in contact with ARG 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B SER* 3.5 11.9 + - - -
64B ALA* 5.2 0.6 - - - +
123B LEU 3.3 15.6 + - - +
124B SER* 3.5 9.9 - - - +
125B PHE 3.3 0.2 - - - -
126B ASP* 1.4 98.1 + - - +
128B TYR* 1.4 54.2 - - - +
130B ALA* 3.6 19.8 - - - +
131B ILE* 2.8 54.6 + - + +
142B LEU* 5.3 0.2 - - - +
224B ILE* 3.6 15.5 - - + -
246B LEU* 3.5 35.6 - - - +
247B LEU* 3.8 37.0 - - + +
250B ILE* 3.7 19.4 - - + +
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Residues in contact with TYR 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B SER 3.1 13.9 + - - +
125B PHE* 3.3 41.5 + + - +
127B ARG* 1.4 75.7 - - - +
129B LEU* 1.4 61.6 - - + +
132B VAL* 3.1 58.2 + - + +
133B ARG 3.5 1.0 + - - -
134B PRO* 3.6 37.6 - - + +
220B CYS* 4.0 18.2 - - - -
223B PHE* 3.7 38.2 - + + -
224B ILE* 3.5 11.1 - - + +
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B PHE* 3.0 52.7 + - + +
126B ASP* 4.8 1.3 - - - -
127B ARG 3.5 0.2 - - - -
128B TYR* 1.4 81.9 - - + +
130B ALA* 1.3 56.3 + - - +
133B ARG* 3.3 22.7 - - - +
134B PRO* 4.6 15.0 - - + -
135B VAL* 6.4 1.3 - - + -
140B LEU* 3.5 36.5 - - + +
142B LEU* 3.7 25.4 - - + -
145B SER* 3.9 21.1 - - - +
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Residues in contact with ALA 130 (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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126B ASP 3.3 17.9 + - - +
127B ARG* 3.6 22.7 - - - +
128B TYR 3.2 0.8 - - - -
129B LEU* 1.3 76.4 - - - +
131B ILE* 1.3 60.7 + - + +
133B ARG* 2.9 29.7 + - - -
140B LEU* 5.5 0.4 - - - -
142B LEU* 4.4 16.1 - - + +
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Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ARG* 2.8 43.7 + - + +
130B ALA* 1.3 72.3 - - - +
132B VAL* 1.3 61.7 + - - +
133B ARG* 3.4 19.7 + - - +
224B ILE* 3.8 26.5 - - + +
227B THR* 3.4 24.2 + - - +
228B ILE* 4.0 16.2 - - + -
244B ARG* 3.5 35.2 - - + +
247B LEU* 4.2 22.7 - - + -
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Residues in contact with VAL 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B TYR* 3.1 43.7 + - + +
131B ILE* 1.3 76.4 - - - +
133B ARG* 1.4 72.3 + - - +
134B PRO* 4.7 8.3 - - + -
223B PHE* 3.4 38.1 - - + +
224B ILE* 3.7 11.9 - - + +
227B THR* 3.9 24.1 - - + +
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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
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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) + - + + + + + -
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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