Contacts of the helix formed by residues 183 - 211 (chain B) in PDB entry 2XWU
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 PRO 183 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B ARG 4.7 0.2 - - - +
182B LEU* 1.3 88.6 - - + +
184B GLN* 1.3 59.9 + - - +
185B TYR* 4.2 4.3 - - + +
186B ARG* 2.7 34.6 + - + +
187B LYS* 2.5 34.8 + - - +
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Residues in contact with GLN 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B LEU 3.9 2.0 + - - -
183B PRO* 1.3 71.1 - - - +
185B TYR* 1.3 61.6 + - - +
187B LYS* 4.1 5.0 - - - +
188B GLY* 3.1 18.7 + - - -
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Residues in contact with TYR 185 (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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183B PRO* 2.9 5.4 + - + +
184B GLN* 1.3 80.8 - - - +
186B ARG* 1.3 65.6 + - - +
188B GLY* 4.1 0.7 - - - -
189B LEU* 3.5 17.3 + - - +
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Residues in contact with ARG 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU 3.1 15.6 + - - -
133B SER* 3.0 33.5 + - - +
135B MET 3.4 12.6 + - - -
136B PRO* 4.7 3.2 - - - +
182B LEU* 3.8 19.1 - - + +
183B PRO* 2.7 40.5 + - + +
185B TYR* 1.3 74.8 - - - +
187B LYS* 1.3 63.8 + - - +
189B LEU* 3.1 17.8 + - - +
190B VAL* 2.6 43.6 + - - +
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Residues in contact with LYS 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B PHE* 4.1 12.7 - - + -
182B LEU* 4.0 22.2 - - + +
183B PRO 2.5 21.9 + - - +
184B GLN* 4.1 4.0 - - - +
186B ARG* 1.3 74.6 - - - +
188B GLY* 1.3 56.8 + - - +
190B VAL* 3.4 7.0 + - - +
191B ARG* 2.8 31.2 + - - +
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Residues in contact with GLY 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B GLN 3.1 16.7 + - - -
185B TYR 3.5 1.7 + - - -
186B ARG 3.2 0.6 - - - -
187B LYS* 1.3 77.7 - - - +
189B LEU* 1.3 54.3 + - - +
191B ARG* 3.3 5.9 + - - +
192B THR* 2.4 41.1 + - - -
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Residues in contact with LEU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PRO* 4.2 26.7 - - + +
185B TYR 3.5 10.8 + - - +
186B ARG* 3.1 14.0 + - - +
188B GLY* 1.3 77.9 - - - +
190B VAL* 1.3 57.3 + - - +
192B THR* 3.3 6.9 + - - -
193B SER* 3.0 29.1 + - - -
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Residues in contact with VAL 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 3.9 29.6 - - + +
135B MET* 3.8 15.5 - - + +
177B PHE* 3.3 32.3 - - + -
182B LEU* 4.2 10.5 - - + -
186B ARG* 2.6 49.8 + - - +
187B LYS* 3.7 7.9 - - - +
189B LEU* 1.3 74.5 - - - +
191B ARG* 1.3 59.7 + - - +
193B SER 3.3 1.2 + - - -
194B LEU* 2.8 28.7 + - + +
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Residues in contact with ARG 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B PHE* 3.3 33.0 - - + -
187B LYS 2.8 19.8 + - - +
188B GLY* 3.7 6.3 - - - +
190B VAL* 1.3 75.3 - - - +
192B THR* 1.3 58.7 + - - +
194B LEU* 3.2 9.3 + - - +
195B ALA* 2.9 50.2 + - - +
232B LEU* 2.6 51.7 + - - +
233B GLU* 4.2 11.7 + - - +
234B VAL* 4.5 5.3 - - - +
235B PRO* 6.0 0.4 - - - +
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Residues in contact with THR 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B GLY 2.4 27.2 + - - -
189B LEU* 3.4 8.0 - - - -
191B ARG* 1.3 74.4 - - - +
193B SER* 1.3 67.6 + - - +
195B ALA* 3.2 16.7 + - - +
196B VAL* 3.3 18.2 + - + +
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Residues in contact with SER 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B MET* 3.6 23.6 - - - -
136B PRO* 3.9 24.0 - - - -
189B LEU 3.0 16.2 + - - -
190B VAL 3.9 0.4 - - - -
192B THR* 1.3 76.1 - - - +
194B LEU* 1.3 57.0 + - - +
196B VAL* 3.1 12.0 + - - +
197B GLU* 3.0 31.6 + - - +
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Residues in contact with LEU 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 3.7 26.5 - - + -
135B MET* 3.5 19.2 - - + +
173B LEU* 4.4 11.9 - - + -
174B PRO* 5.2 4.7 - - + -
177B PHE* 3.7 32.1 - - + -
190B VAL 2.8 15.7 + - - +
191B ARG* 3.3 13.7 - - - +
193B SER* 1.3 74.9 - - - +
195B ALA* 1.3 63.2 + - - +
197B GLU* 3.3 11.0 + - + +
198B CYS 3.2 16.5 + - - -
229B TRP* 3.6 34.1 - - + -
232B LEU* 4.5 10.8 - - + -
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Residues in contact with ALA 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ARG* 2.9 31.5 + - - +
192B THR* 3.2 11.2 + - - +
194B LEU* 1.3 76.5 - - - +
196B VAL* 1.3 62.9 + - + +
198B CYS* 3.4 19.1 + - - +
199B GLY 4.1 2.3 + - - -
234B VAL* 5.6 5.6 - - + +
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Residues in contact with VAL 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B THR* 3.6 17.5 - - + +
193B SER* 3.1 12.5 + - - +
195B ALA* 1.3 75.3 - - + +
197B GLU* 1.3 68.7 + - - +
198B CYS 3.1 2.0 - - - -
199B GLY* 3.1 15.6 + - - -
200B ALA 4.3 0.9 + - - -
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Residues in contact with GLU 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B MET* 4.2 15.2 - - + +
139B TRP 4.3 2.3 - - - +
140B PRO 3.3 16.2 - - - +
141B CYS* 4.1 5.7 - - - +
142B ALA* 2.9 34.2 + - + +
143B VAL* 3.4 46.0 + - + +
144B ALA 4.6 0.9 + - - -
173B LEU* 6.0 0.4 - - + -
193B SER* 3.0 22.0 + - - +
194B LEU* 3.3 16.8 + - + +
196B VAL* 1.3 80.2 - - - +
198B CYS* 1.3 56.8 + - - +
199B GLY 3.0 0.7 - - - -
200B ALA* 3.0 19.4 + - - +
201B VAL* 3.4 3.6 + - - +
229B TRP* 4.6 2.5 - - + -
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Residues in contact with CYS 198 (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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194B LEU 3.2 6.6 + - - +
195B ALA* 3.4 15.5 - - - +
196B VAL 3.1 1.2 - - - -
197B GLU* 1.3 75.0 - - - +
199B GLY* 1.3 62.4 + - - +
200B ALA 3.2 0.4 - - - -
201B VAL* 3.8 4.5 - - - -
202B PHE* 3.3 55.6 + - - +
229B TRP* 3.7 31.8 - - + -
234B VAL* 4.0 23.3 - - + -
238B ASP* 6.2 0.2 - - - -
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Residues in contact with GLY 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ALA 4.1 1.8 + - - -
196B VAL 3.1 11.7 + - - -
197B GLU 3.0 2.0 - - - -
198B CYS* 1.3 80.0 - - - +
200B ALA* 1.3 58.3 + - - +
202B PHE* 5.7 0.2 - - - -
203B PRO* 2.8 26.6 - - - +
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Residues in contact with ALA 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B VAL* 3.3 28.0 - - + +
144B ALA* 4.5 11.9 - - + +
147B VAL* 5.2 3.6 - - + +
196B VAL 4.3 1.0 + - - -
197B GLU* 3.0 8.2 + - - +
199B GLY* 1.3 79.4 - - - +
201B VAL* 1.3 65.6 + - - +
203B PRO* 3.5 9.6 - - - +
204B LEU* 3.7 12.3 + - - +
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B VAL* 3.7 12.6 - - + -
170B LEU* 3.6 28.0 - - + -
197B GLU 3.4 6.8 + - - +
198B CYS* 3.5 7.8 + - - +
199B GLY 3.5 0.2 - - - -
200B ALA* 1.3 74.6 - - - +
202B PHE* 1.3 73.1 + - + +
204B LEU* 3.0 17.8 + - - +
205B LEU* 3.2 26.5 + - + +
225B CYS* 4.6 4.9 - - - -
229B TRP* 3.4 53.8 - - + +
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Residues in contact with PHE 202 (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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198B CYS* 3.3 33.6 + - - +
201B VAL* 1.3 81.7 - - + +
203B PRO* 1.4 72.9 - - + +
205B LEU* 2.8 12.0 + - + +
206B GLU* 2.8 35.8 + - - +
226B PHE* 3.6 32.8 - + - -
229B TRP* 3.9 19.1 - + + -
230B VAL* 5.2 0.4 - - + -
234B VAL* 4.0 17.3 - - + -
238B ASP* 3.4 29.4 - - + -
239B CYS* 3.7 21.8 - - - -
242B LEU* 3.9 14.4 - - + -
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Residues in contact with PRO 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B GLY* 2.8 30.5 - - - +
200B ALA* 3.5 6.5 - - - +
201B VAL 3.4 3.1 - - - -
202B PHE* 1.4 93.0 - - + +
204B LEU* 1.3 62.1 + - - +
206B GLU* 3.3 16.3 + - - +
207B GLN* 3.0 29.5 + - - +
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Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B VAL* 3.5 34.3 - - + -
151B GLN* 5.2 5.6 - - - +
163B CYS* 6.1 0.7 - - - -
166B LEU* 3.6 20.0 - - + -
167B LEU* 5.3 2.0 - - + -
170B LEU* 3.8 20.4 - - + -
200B ALA 3.7 8.2 + - - +
201B VAL 3.0 9.7 + - - +
203B PRO* 1.3 77.9 - - - +
205B LEU* 1.3 66.9 + - + +
207B GLN* 3.2 19.1 + - + +
208B LEU* 3.2 45.2 + - + +
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Residues in contact with LEU 205 (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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167B LEU* 3.7 29.4 - - + -
170B LEU* 5.3 1.6 - - + -
201B VAL* 3.5 28.9 - - + +
202B PHE* 2.8 10.4 + - + +
204B LEU* 1.3 78.8 - - + +
206B GLU* 1.3 64.6 + - - +
208B LEU* 3.4 4.2 + - - +
209B LEU* 3.2 28.9 + - - +
222B VAL* 3.9 20.6 - - + +
225B CYS* 4.0 14.1 - - + +
226B PHE* 4.0 26.5 - - - +
242B LEU* 3.8 26.2 - - + -
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Residues in contact with GLU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B PHE* 2.8 37.3 + - - +
203B PRO* 3.5 14.6 - - - +
205B LEU* 1.3 75.8 - - - +
207B GLN* 1.3 65.1 + - - +
209B LEU* 3.2 5.8 + - - +
210B GLN* 3.0 24.9 + - - +
238B ASP 5.1 2.4 - - - +
241B ALA* 3.4 29.8 - - + +
242B LEU* 3.9 24.6 - - + +
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Residues in contact with GLN 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B GLN* 5.7 2.6 + - - -
203B PRO* 3.0 18.9 + - - +
204B LEU* 3.3 23.2 - - + +
206B GLU* 1.3 75.6 - - - +
208B LEU* 1.3 66.2 + - + +
210B GLN* 3.1 16.4 + - - +
211B GLN* 3.1 15.8 + - - +
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Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B CYS* 3.9 31.4 - - - -
167B LEU* 4.0 13.0 - - + -
204B LEU* 3.2 34.9 + - + +
205B LEU* 3.8 6.1 - - - +
206B GLU 3.4 0.2 - - - -
207B GLN* 1.3 80.4 - - + +
209B LEU* 1.3 61.3 + - - +
211B GLN* 3.6 4.6 - - + +
214B SER* 2.4 39.8 + - - +
218B VAL* 4.5 6.1 - - + -
222B VAL* 3.7 28.7 - - + -
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LEU 3.2 5.2 - - - +
206B GLU* 3.2 7.3 + - - +
207B GLN 3.2 0.6 - - - -
208B LEU* 1.3 74.3 - - - +
210B GLN* 1.3 59.6 + - - +
211B GLN 3.1 5.2 - - - -
219B ARG* 2.4 46.0 + - + +
222B VAL* 3.0 42.8 - - + -
223B LEU* 5.0 13.0 - - + -
242B LEU* 3.8 19.3 - - + +
245B ALA* 3.6 37.7 - - + +
246B ALA 5.0 1.1 - - - +
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Residues in contact with GLN 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLU 3.0 15.5 + - - +
207B GLN* 3.7 5.2 - - - +
209B LEU* 1.3 75.9 - - - +
211B GLN* 1.3 58.4 + - - +
212B PRO* 3.0 14.2 - - - +
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Residues in contact with GLN 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLN 3.1 14.8 + - - +
208B LEU* 4.3 1.6 - - + -
209B LEU 3.1 2.4 - - - -
210B GLN* 1.3 77.5 - - - +
212B PRO* 1.3 63.4 - - - +
213B SER* 2.9 22.0 + - - +
214B SER* 3.0 28.5 + - - +
219B ARG* 3.6 6.4 + - - -
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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