Contacts of the helix formed by residues 180 - 216 (chain E) in PDB entry 2OZB
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 SER 180 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178E GLN 4.0 0.4 + - - -
179E LEU* 1.3 76.5 - - - +
181E GLU* 1.3 65.9 + - - +
182E GLU* 3.6 11.0 + - - +
183E GLU* 3.0 35.2 + - - +
184E LEU* 3.0 22.6 + - - +
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Residues in contact with GLU 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E ASN* 5.4 1.6 + - - -
179E LEU 5.5 0.5 - - - +
180E SER* 1.3 74.7 - - - +
182E GLU* 1.3 57.8 + - + +
184E LEU* 3.6 20.7 + - - +
185E GLU* 3.1 34.0 + - - +
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Residues in contact with GLU 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B ARG* 5.0 2.4 + - - -
214B PHE* 3.3 41.1 - - + -
180E SER* 3.1 9.6 - - - +
181E GLU* 1.3 78.1 - - + +
183E GLU* 1.3 67.1 + - + +
184E LEU 3.3 0.2 - - - -
185E GLU* 4.1 15.6 - - + +
186E ARG* 3.4 23.6 + - - +
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Residues in contact with GLU 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E LYS 6.2 0.2 - - - +
120E LYS* 2.9 45.0 + - - +
179E LEU* 3.5 19.0 - - + -
180E SER* 3.0 36.8 + - - +
182E GLU* 1.3 80.8 - - + +
184E LEU* 1.3 59.1 + - - +
186E ARG* 3.6 26.4 + - - +
187E LEU* 3.3 26.9 + - + +
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Residues in contact with LEU 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E TYR* 6.0 0.4 - - + -
143E GLY* 4.1 10.8 - - - -
144E ASN* 3.5 55.9 - - + +
179E LEU* 4.1 12.3 - - + -
180E SER 3.0 11.3 + - - +
181E GLU* 3.7 27.6 - - - +
183E GLU* 1.3 73.8 - - - +
185E GLU* 1.3 56.6 + - - +
186E ARG 3.1 1.3 - - - -
187E LEU* 2.9 8.5 + - + +
188E GLU* 2.7 43.0 + - - +
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Residues in contact with GLU 185 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211B ARG* 4.4 6.3 + - - +
181E GLU* 3.1 21.2 + - - +
182E GLU* 4.2 16.8 - - - +
184E LEU* 1.3 75.7 - - - +
186E ARG* 1.3 57.1 + - - +
188E GLU* 3.6 10.2 + - - +
189E GLU* 2.9 52.2 + - + +
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Residues in contact with ARG 186 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B GLU* 3.6 24.8 + - - +
207B TYR* 5.1 0.7 + - - -
211B ARG* 3.5 28.7 + - - +
214B PHE* 4.7 15.5 - - - -
113E PHE* 3.4 26.3 - - + -
117E LYS* 3.3 36.9 - - - +
182E GLU 3.4 19.1 + - - +
183E GLU* 3.6 27.5 + - - +
184E LEU 3.1 0.6 - - - -
185E GLU* 1.3 80.7 - - - +
187E LEU* 1.3 60.6 + - - +
189E GLU* 3.7 2.1 + - - +
190E ALA* 3.3 20.4 + - - +
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Residues in contact with LEU 187 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E PHE* 5.2 3.6 - - + -
114E ILE* 3.7 45.8 - - + +
117E LYS* 3.8 28.7 - - + +
118E TYR* 3.5 29.4 - - + +
139E VAL* 4.9 7.2 - - + -
179E LEU* 3.6 21.5 - - + -
183E GLU* 3.3 9.5 + - + +
184E LEU* 2.9 11.9 + - + +
186E ARG* 1.3 76.8 - - + +
188E GLU* 1.3 65.5 + - - +
190E ALA* 3.1 4.7 + - - +
191E CYS* 2.9 29.0 + - - -
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Residues in contact with GLU 188 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E LYS* 5.0 14.6 - - + +
184E LEU* 2.7 27.5 + - - +
185E GLU* 3.6 10.0 + - - +
187E LEU* 1.3 74.2 - - - +
189E GLU* 1.3 64.4 + - + +
191E CYS* 3.2 6.8 + - - +
192E ASP* 3.0 37.1 + - - +
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Residues in contact with GLU 189 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B TYR* 3.5 20.3 - - + -
210B SER* 2.5 35.5 + - - -
211B ARG* 2.8 36.0 + - - +
185E GLU* 2.9 35.8 + - + +
186E ARG 4.2 1.1 - - - +
188E GLU* 1.3 75.5 - - + +
190E ALA* 1.3 56.7 + - - +
192E ASP* 3.5 6.8 + - - +
193E MET* 3.1 27.9 + - - +
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Residues in contact with ALA 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207B TYR* 3.6 21.2 - - - +
110E ILE* 3.8 9.2 - - + +
113E PHE* 4.2 14.4 - - + -
114E ILE* 3.9 23.6 - - + -
186E ARG 3.3 12.5 + - - +
187E LEU* 3.1 8.1 + - - +
189E GLU* 1.3 76.1 - - - +
191E CYS* 1.3 54.1 + - - +
193E MET* 3.2 2.8 + - - +
194E ALA* 2.8 35.7 + - - +
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Residues in contact with CYS 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E ILE* 3.8 15.5 - - - -
136E ILE* 3.8 24.9 - - + -
139E VAL* 3.5 32.8 - - - -
140E LYS* 4.2 22.4 - - + -
187E LEU 2.9 17.9 + - - +
188E GLU* 3.5 8.7 - - - +
190E ALA* 1.3 72.0 - - - +
192E ASP* 1.3 66.9 + - - +
194E ALA* 3.1 3.6 + - - +
195E LEU* 2.9 29.4 + - + +
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Residues in contact with ASP 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140E LYS* 3.0 37.9 + - - +
188E GLU* 3.0 29.3 + - - +
189E GLU* 3.9 6.9 - - - +
191E CYS* 1.3 74.3 - - - +
193E MET* 1.3 63.7 + - - +
195E LEU* 3.2 7.4 + - - +
196E GLU* 3.0 29.1 + - - +
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Residues in contact with MET 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ALA* 5.5 2.0 - - + -
203B ARG* 4.1 11.7 - - + +
204B ILE* 3.9 34.1 - - + -
207B TYR* 3.6 51.6 - - + -
110E ILE* 4.3 5.2 - - + -
189E GLU 3.1 18.3 + - - +
190E ALA 3.2 4.4 + - - +
192E ASP* 1.3 75.6 - - - +
194E ALA* 1.3 57.7 + - - +
196E GLU* 3.3 21.4 + - + -
197E LEU* 2.9 47.7 + - + +
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Residues in contact with ALA 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E LEU* 3.6 17.9 - - + +
110E ILE* 3.8 23.1 - - + +
133E LEU* 5.9 0.2 - - - -
136E ILE* 4.0 26.0 - - + -
190E ALA 2.8 13.6 + - - +
191E CYS 3.4 8.3 - - - +
193E MET* 1.3 76.5 - - - +
195E LEU* 1.3 57.8 + - + +
197E LEU* 3.3 3.3 + - - +
198E ASN* 2.9 29.2 + - - +
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Residues in contact with LEU 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E LEU* 4.4 18.4 - - + -
136E ILE* 3.6 22.9 - - + -
137E ARG* 4.5 20.2 - - + +
140E LYS* 4.0 31.2 - - + -
191E CYS 2.9 20.3 + - - +
192E ASP* 3.7 8.3 - - - +
194E ALA* 1.3 74.6 - - + +
196E GLU* 1.3 61.5 + - - +
198E ASN* 3.3 7.1 + - - +
199E ALA* 3.0 27.5 + - - +
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Residues in contact with GLU 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B ARG* 4.2 39.7 + - + +
192E ASP* 3.0 20.1 + - - +
193E MET* 3.6 21.3 - - + +
195E LEU* 1.3 77.8 - - - +
197E LEU* 1.3 57.2 + - - +
199E ALA* 3.3 10.9 + - - +
200E SER* 3.0 28.7 + - - -
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Residues in contact with LEU 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ALA* 5.9 1.1 - - + -
99B LEU* 3.9 20.9 - - + -
204B ILE* 3.9 24.9 - - + -
103E ILE* 3.4 14.7 - - + +
106E GLU* 3.6 32.5 - - + -
107E LEU* 3.4 20.6 - - + -
110E ILE* 3.8 14.4 - - + -
193E MET* 2.9 30.6 + - + +
194E ALA* 3.7 1.8 - - - +
196E GLU* 1.3 75.0 - - - +
198E ASN* 1.3 65.0 + - - +
200E SER* 4.0 8.5 - - - +
201E LYS* 3.0 25.5 + - - +
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Residues in contact with ASN 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E LEU* 3.9 10.6 - - + +
133E LEU* 3.4 40.5 - - + +
137E ARG* 5.1 4.6 - - - +
194E ALA 2.9 17.6 + - - +
195E LEU* 3.6 9.0 + - - +
196E GLU 3.3 0.2 - - - -
197E LEU* 1.3 79.2 - - - +
199E ALA* 1.3 63.1 + - - +
201E LYS* 3.1 27.8 + - - +
202E HIS* 3.2 44.1 + - - -
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Residues in contact with ALA 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E LEU 3.0 14.0 + - - +
196E GLU* 3.5 15.7 - - - +
197E LEU 3.3 0.2 - - - -
198E ASN* 1.3 79.3 - - - +
200E SER* 1.3 58.8 + - - +
202E HIS* 3.2 8.7 + - - +
203E ARG* 3.0 25.3 + - - +
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Residues in contact with SER 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B GLU* 6.1 2.9 - - - -
200B SER* 3.7 27.2 + - - -
203B ARG* 5.7 4.3 - - - -
103E ILE* 4.7 8.0 - - - +
196E GLU 3.0 18.3 + - - -
197E LEU* 3.8 12.3 + - - +
198E ASN 3.3 0.2 - - - -
199E ALA* 1.3 74.5 - - - +
201E LYS* 1.3 61.1 + - - +
203E ARG* 3.8 8.5 - - - +
204E ILE* 2.9 41.6 + - - +
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Residues in contact with LYS 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E THR* 4.1 14.5 - - - +
103E ILE* 3.7 28.8 - - + +
104E GLU* 3.5 42.0 - - + +
107E LEU* 5.0 9.4 - - + +
133E LEU* 5.0 4.4 - - - +
197E LEU 3.0 18.4 + - - +
198E ASN* 3.1 28.4 + - - +
200E SER* 1.3 77.7 + - - +
202E HIS* 1.3 73.6 + - + +
204E ILE* 3.4 3.5 + - - +
205E TYR* 2.9 30.7 + - + +
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Residues in contact with HIS 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E LEU* 5.9 1.1 - - + -
198E ASN* 3.2 47.1 + - - +
199E ALA* 3.7 8.2 - - - +
201E LYS* 1.3 89.7 + - - +
203E ARG* 1.3 60.2 + - - +
205E TYR* 3.3 10.8 + + + +
206E GLU* 2.9 40.6 + - - +
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Residues in contact with ARG 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B GLU* 5.2 2.0 + - - -
192B ASP* 4.2 31.7 + - - +
193B MET* 4.2 12.9 - - + +
196B GLU* 3.7 35.1 + - + +
199E ALA 3.0 16.5 + - - +
200E SER* 3.4 8.7 + - - +
202E HIS* 1.3 77.2 - - - +
204E ILE* 1.3 62.5 + - + +
206E GLU* 3.5 23.0 + - - +
207E TYR* 3.4 34.1 + - - +
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Residues in contact with ILE 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ILE* 6.3 0.9 - - + -
193B MET* 3.7 29.4 - - + -
197B LEU* 4.1 18.2 - - + -
200B SER* 6.1 0.4 - - - +
96E ALA* 3.4 38.8 - - + +
99E LEU* 4.2 8.7 - - + -
100E THR* 3.5 8.7 - - + -
103E ILE* 3.5 29.6 - - + -
200E SER* 2.9 28.3 + - - +
201E LYS 3.8 3.4 - - - +
203E ARG* 1.3 74.2 - - - +
205E TYR* 1.3 58.7 + - - +
207E TYR* 2.9 19.6 + - - +
208E VAL* 3.0 11.9 + - + +
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Residues in contact with TYR 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E ASN* 3.6 28.7 - - - -
100E THR* 4.2 10.3 - - + +
201E LYS* 2.9 20.9 + - + +
202E HIS* 3.9 11.4 - + + +
204E ILE* 1.3 76.4 - - - +
206E GLU* 1.3 59.7 + - - +
208E VAL* 3.8 14.8 - - + -
209E GLU* 3.1 53.4 + - + +
224E GLY* 4.4 1.9 - - - -
225E ALA* 3.6 8.5 + - - +
226E SER* 3.0 36.2 + - - -
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Residues in contact with GLU 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E HIS* 2.9 28.9 + - - +
203E ARG* 3.7 27.8 + - - +
204E ILE 3.1 0.8 - - - -
205E TYR* 1.3 75.9 - - - +
207E TYR* 1.3 62.3 + - - +
209E GLU* 3.5 12.1 + - - +
210E SER* 3.1 26.0 + - - -
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Residues in contact with TYR 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B GLU* 5.0 0.9 - - - -
110B ILE* 5.0 1.6 - - + +
113B PHE* 5.4 1.4 - - - -
186B ARG 5.2 0.6 + - - -
189B GLU* 3.7 41.5 - - + -
190B ALA* 3.8 19.6 - - - +
193B MET* 3.7 31.6 - - + -
89E GLU* 4.6 4.9 + - - +
92E VAL* 3.7 18.1 - - + +
93E ILE* 3.6 28.2 - - + +
96E ALA* 4.3 19.7 - - + -
203E ARG* 3.4 22.3 + - - +
204E ILE 2.9 8.6 + - - +
206E GLU* 1.3 79.4 - - - +
208E VAL* 1.3 62.3 + - - +
210E SER* 3.8 3.8 - - - -
211E ARG* 3.0 46.4 + - + +
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Residues in contact with VAL 208 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E ILE* 3.9 22.2 - - + +
96E ALA* 4.0 15.0 - - + -
97E ASN* 3.8 50.0 - - + +
100E THR* 5.2 0.2 - - + -
204E ILE* 3.0 18.4 + - + +
205E TYR* 3.9 20.0 - - + +
206E GLU 3.3 0.2 - - - -
207E TYR* 1.3 77.1 - - + +
209E GLU* 1.3 57.8 + - - +
211E ARG* 3.8 0.3 - - - -
212E MET* 2.8 33.6 + - + +
225E ALA* 4.1 12.3 - - + +
229E ALA* 4.7 0.7 - - + -
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Residues in contact with GLU 209 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205E TYR* 3.1 52.9 + - + +
206E GLU* 3.9 12.3 - - - +
208E VAL* 1.3 75.3 - - - +
210E SER* 1.3 62.7 + - - +
212E MET* 3.4 1.2 + - - +
213E SER* 3.0 27.1 + - - -
220E SER* 5.8 0.3 - - - -
225E ALA* 3.7 21.1 + - + +
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Residues in contact with SER 210 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B GLU* 2.7 38.7 + - - -
206E GLU 3.1 16.7 + - - -
207E TYR 3.8 1.6 - - - -
209E GLU* 1.3 77.4 - - - +
211E ARG* 1.3 63.8 + - - +
213E SER* 3.0 22.2 + - - -
214E PHE* 3.5 7.6 + - - +
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Residues in contact with ARG 211 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B GLU 5.0 2.2 + - - -
185B GLU* 4.3 7.9 + - - +
186B ARG* 3.0 42.3 - - - +
189B GLU* 3.2 37.3 + - - -
89E GLU* 2.6 29.5 + - - +
93E ILE* 3.6 23.6 - - + -
207E TYR* 3.0 39.3 + - + +
208E VAL 4.1 0.9 - - - +
210E SER* 1.3 76.5 + - - +
212E MET* 1.3 59.0 + - - +
214E PHE* 2.9 36.2 + - - +
215E ILE* 2.8 32.2 + - + +
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Residues in contact with MET 212 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E TYR* 5.9 1.3 - - - -
93E ILE* 3.9 25.1 - - + -
208E VAL* 2.8 26.2 + - + +
209E GLU 4.0 0.4 - - - +
211E ARG* 1.3 72.5 - - - +
213E SER* 1.3 56.3 + - - +
214E PHE 3.0 0.2 - - - -
215E ILE* 4.3 13.0 - - + +
216E ALA* 2.7 44.3 + - + +
220E SER* 3.4 17.0 - - - +
225E ALA* 3.8 27.1 - - + +
228E ALA* 3.8 25.6 - - + -
229E ALA* 4.1 12.3 - - - +
232E MET* 3.9 28.7 - - + +
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Residues in contact with SER 213 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209E GLU 3.0 15.3 + - - -
210E SER* 3.0 16.9 + - - -
212E MET* 1.3 76.8 - - - +
214E PHE* 1.3 56.4 + - - +
217E PRO* 3.5 30.6 - - - +
220E SER* 4.4 6.4 + - - -
312E THR 4.9 2.6 - - - +
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Residues in contact with PHE 214 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B GLU* 3.8 44.0 - - + -
186B ARG* 4.7 13.2 - - + -
89E GLU* 4.3 9.0 - - - -
210E SER 3.5 7.1 + - - +
211E ARG* 2.9 41.0 + - - +
213E SER* 1.3 82.0 + - - +
215E ILE* 1.3 71.1 + - + +
216E ALA 3.4 0.6 + - - -
217E PRO* 3.6 9.2 - - - +
309E HIS* 5.5 4.9 - - - -
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Residues in contact with ILE 215 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89E GLU* 3.6 44.0 - - + +
90E TYR* 4.0 17.3 - - + +
93E ILE* 3.9 17.7 - - + -
211E ARG 2.8 17.4 + - - +
212E MET* 4.2 9.9 - - + +
214E PHE* 1.3 86.0 - - + +
216E ALA* 1.3 57.7 + - + +
217E PRO* 4.0 1.9 - - - +
232E MET* 4.0 27.8 - - - -
238E LEU* 3.3 22.4 - - + +
306E ASP* 4.6 2.4 - - - +
309E HIS* 5.1 6.1 + - - -
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Residues in contact with ALA 216 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212E MET* 2.7 20.8 + - + +
215E ILE* 1.3 76.0 - - - +
217E PRO* 1.3 66.8 - - - +
218E ASN 3.3 0.2 + - - -
219E LEU* 4.1 8.7 - - + -
220E SER* 3.1 22.0 + - - -
232E MET* 4.0 27.1 - - + -
238E LEU* 4.4 2.9 - - + -
306E ASP* 3.2 23.2 - - + +
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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
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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