Contacts of the helix formed by residues 185 - 211 (chain B) in PDB entry 4Y5U
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 GLU 185 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ARG* 3.5 31.9 + - - +
182B LEU* 3.3 24.6 + - + +
183B LEU 2.9 0.8 + - - -
184B GLN* 1.3 74.7 - - - +
186B THR* 1.3 58.9 + - - +
187B THR* 3.2 2.7 - - - -
188B GLY* 3.1 8.3 + - - +
189B GLU* 3.0 37.5 + - - +
260B ARG* 5.9 1.1 - - - +
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Residues in contact with THR 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 3.8 17.1 - - + +
140B ARG* 3.7 36.7 + - + -
141B VAL* 4.8 0.9 - - + +
144B ILE* 5.2 2.2 - - + -
183B LEU* 1.6 45.1 + - + +
184B GLN* 4.0 4.5 - - - -
185B GLU* 1.3 72.0 - - - +
187B THR* 1.3 62.7 + - - +
189B GLU* 3.5 10.4 + - - +
190B LEU* 3.0 21.5 + - - +
238B LEU* 4.3 22.0 - - + +
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Residues in contact with THR 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B GLN* 3.6 29.8 + - + +
186B THR* 1.3 78.4 - - - +
188B GLY* 1.3 58.7 + - - -
190B LEU* 3.3 8.4 - - - +
191B GLU* 2.9 32.4 + - - +
238B LEU* 3.8 14.4 - - + -
257B LEU* 4.2 7.2 - - + -
260B ARG* 2.6 35.2 + - - +
261B LEU* 3.6 28.7 - - + -
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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
----------------------------------------------------------
185B GLU* 3.1 11.2 + - - +
187B THR* 1.3 77.6 + - - +
189B GLU* 1.3 60.4 + - - +
190B LEU 3.1 1.8 - - - -
191B GLU* 3.5 16.0 - - - +
192B ALA* 2.9 29.5 + - - +
260B ARG* 4.5 3.5 - - - +
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Residues in contact with GLU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ARG* 3.9 32.2 + - + +
137B LEU* 4.0 17.1 - - + +
140B ARG* 2.2 47.4 + - - -
185B GLU* 3.0 24.3 + - - +
186B THR* 3.5 12.0 - - - +
188B GLY* 1.3 74.9 - - - +
190B LEU* 1.3 59.0 + - - +
192B ALA* 4.1 6.4 - - - +
193B ALA* 3.7 17.7 + - - +
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B LEU* 3.7 15.4 - - + +
186B THR 3.0 13.3 + - - +
187B THR* 3.3 12.3 - - - +
188B GLY 3.1 0.2 - - - -
189B GLU* 1.3 76.1 - - - +
191B GLU* 1.3 58.3 + - - +
192B ALA 3.2 0.4 - - - -
193B ALA* 3.3 3.4 + - - +
194B LYS* 2.9 26.1 + - + +
231B LEU* 3.8 28.5 - - + +
234B ILE* 3.7 25.6 - - + -
235B TYR* 4.5 14.8 - - + -
238B LEU* 4.9 3.4 - - + -
261B LEU* 4.4 20.0 - - + -
264B VAL* 3.9 26.5 - - + -
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B THR* 2.9 25.3 + - - +
188B GLY* 3.1 12.2 + - - +
190B LEU* 1.3 75.7 - - - +
192B ALA* 1.3 60.6 + - - +
194B LYS* 3.4 12.9 + - - +
195B ALA* 3.1 23.2 + - - +
260B ARG* 3.3 49.5 + - - +
261B LEU* 6.1 0.7 - - + -
264B VAL* 3.7 23.8 - - + +
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Residues in contact with ALA 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B GLY 2.9 16.3 + - - +
189B GLU* 4.1 7.9 - - - +
191B GLU* 1.3 76.0 - - - +
193B ALA* 1.3 60.5 + - - +
195B ALA* 3.6 7.2 + - - +
196B LEU* 3.2 22.8 + - - +
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Residues in contact with ALA 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLY 6.6 0.2 - - - -
134B LEU* 6.4 2.5 - - + -
137B LEU* 4.6 3.8 - - + -
189B GLU 3.7 13.7 + - - +
190B LEU* 3.3 11.1 + - - +
192B ALA* 1.3 77.3 - - - +
194B LYS* 1.3 62.5 + - - +
196B LEU* 3.2 27.1 - - + +
197B VAL* 3.3 8.7 + - - +
231B LEU* 3.7 30.8 - - + +
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Residues in contact with LYS 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B LEU* 2.9 16.8 + - + +
191B GLU* 3.6 10.6 + - - +
192B ALA 3.3 0.2 - - - -
193B ALA* 1.3 73.2 - - - +
195B ALA* 1.3 67.9 + - - +
196B LEU 3.0 1.5 + - - -
197B VAL* 3.2 2.8 + - - +
198B LEU* 3.2 34.8 + - + +
231B LEU* 4.0 9.8 - - + +
263B GLU* 5.1 2.0 + - - +
264B VAL* 3.9 42.8 - - + +
267B THR* 3.6 36.2 + - + +
268B LEU* 4.3 16.4 - - + +
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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 GLU 3.1 13.2 + - - +
192B ALA* 3.8 8.3 - - - +
193B ALA 3.5 0.2 - - - -
194B LYS* 1.3 85.6 - - - +
196B LEU* 1.3 61.8 + - - +
198B LEU* 3.5 9.8 + - - +
199B LYS* 3.3 26.9 + - + +
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Residues in contact with LEU 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B PHE* 5.7 7.2 - - + +
192B ALA 3.2 11.5 + - - +
193B ALA* 3.2 23.1 - - + +
195B ALA* 1.3 82.3 - - - +
197B VAL* 1.3 62.0 + - + +
199B LYS* 3.3 23.9 - - + +
200B ARG* 3.4 9.0 + - - +
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Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ALA 3.3 10.7 + - - +
194B LYS 3.2 7.9 + - - +
196B LEU* 1.3 76.6 - - + +
198B LEU* 1.3 61.4 + - - +
199B LYS 3.1 2.0 - - - -
200B ARG* 3.1 8.1 + - + +
201B ILE* 2.9 38.2 + - + +
224B LEU* 4.6 9.9 - - + +
227B ARG* 4.5 26.5 - - + -
228B CYS* 4.0 26.7 - - - -
231B LEU* 4.5 13.9 - - + -
268B LEU* 4.3 11.7 - - + -
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Residues in contact with LEU 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 LYS* 3.2 38.9 + - + +
195B ALA* 3.7 9.0 - - - +
196B LEU 3.3 0.2 - - - -
197B VAL* 1.3 79.1 - - + +
199B LYS* 1.3 57.3 + - - +
201B ILE* 3.4 9.9 + - + +
202B GLN* 3.1 31.6 + - - +
267B THR* 3.8 24.9 - - + +
268B LEU* 4.0 17.9 - - + -
271B SER* 3.2 33.3 + - - +
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Residues in contact with LYS 199 (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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195B ALA* 3.3 16.1 + - + +
196B LEU* 3.3 19.3 - - + +
198B LEU* 1.3 77.1 - - - +
200B ARG* 1.3 62.8 + - - +
202B GLN* 3.5 9.0 + - + +
203B ILE* 3.1 35.2 + - + +
435B MET* 5.2 2.8 - - + +
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Residues in contact with ARG 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU 3.4 9.0 + - - +
197B VAL* 3.1 12.5 + - + +
199B LYS* 1.3 79.0 - - - +
201B ILE* 1.3 62.6 + - - +
203B ILE* 3.3 34.6 + - + +
204B TRP* 3.1 26.0 + - - +
207B GLN* 3.7 4.8 + - - +
219B GLU* 2.5 43.5 + - - -
220B SER 5.0 2.0 + - - -
223B PRO* 5.5 6.7 - - - +
224B LEU* 3.7 36.7 - - + +
227B ARG* 4.5 18.1 - - - +
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Residues in contact with ILE 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B VAL* 2.9 30.2 + - + +
198B LEU* 3.5 11.4 - - + +
199B LYS 3.2 0.2 - - - -
200B ARG* 1.3 77.3 - - - +
202B GLN* 1.3 58.7 + - - +
204B TRP* 3.6 3.0 + - - +
205B LYS* 3.0 36.9 + - - +
224B LEU* 3.9 24.2 - - + -
228B CYS* 4.9 3.8 - - - -
268B LEU* 5.5 0.7 - - + -
271B SER* 3.4 38.4 - - - +
272B CYS* 5.0 0.9 - - - -
274B LEU* 3.8 30.3 - - + -
296B LEU* 4.7 14.1 - - + -
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Residues in contact with GLN 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU 3.1 16.5 + - - +
199B LYS* 3.5 11.0 - - + +
200B ARG 3.3 0.2 - - - -
201B ILE* 1.3 74.0 - - - +
203B ILE* 1.3 64.9 + - - +
205B LYS* 3.4 30.1 + - - +
206B ARG* 3.2 21.8 + - - +
271B SER* 5.8 0.5 + - - -
435B MET* 3.6 36.8 + - + +
436B ASP* 3.4 24.2 + - - +
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Residues in contact with ILE 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LYS* 3.1 29.2 + - + +
200B ARG* 3.3 32.5 + - + +
202B GLN* 1.3 75.5 - - - +
204B TRP* 1.3 56.4 + - - +
206B ARG* 3.3 7.5 + - - +
207B GLN* 3.1 39.8 + - - +
435B MET* 4.6 12.1 - - + -
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Residues in contact with TRP 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B ARG* 3.1 20.9 + - - +
201B ILE* 3.8 4.9 - - + +
202B GLN 3.3 0.2 - - - -
203B ILE* 1.3 74.3 - - - +
205B LYS* 1.3 75.0 + - + +
207B GLN* 3.4 9.1 + - - +
208B GLN* 2.9 60.1 + - - +
217B PHE* 3.5 26.4 - + - -
219B GLU* 3.3 44.4 + - + +
220B SER 4.1 1.6 + - - -
221B LEU* 3.2 50.1 - - + +
224B LEU* 4.1 7.9 - - + -
274B LEU* 4.8 11.4 - - + -
275B VAL 4.1 11.2 - - - -
276B GLU* 4.6 7.9 - - + -
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Residues in contact with LYS 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ILE* 3.0 24.5 + - - +
202B GLN* 3.4 33.3 + - - +
204B TRP* 1.3 89.4 - - + +
206B ARG* 1.3 59.6 + - - +
208B GLN* 3.7 10.5 - - - +
209B GLN* 2.9 27.4 + - - +
274B LEU* 3.6 24.8 - - + +
408B LEU* 5.5 2.1 - - - +
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Residues in contact with ARG 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLN 3.2 13.8 + - - +
203B ILE* 3.7 8.1 - - - +
204B TRP 3.3 0.4 - - - -
205B LYS* 1.3 74.4 - - - +
207B GLN* 1.3 63.7 + - - +
209B GLN* 3.2 27.4 + - - +
210B LEU* 3.1 45.5 + - + +
430B ASN 3.2 18.8 + - - -
431B ALA 2.9 23.4 + - - -
432B PHE* 4.7 0.8 - - - +
433B SER* 3.6 26.0 + - - -
435B MET* 3.9 30.9 - - + +
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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
----------------------------------------------------------
200B ARG* 3.7 6.7 + - - +
203B ILE* 3.1 29.8 + - - +
204B TRP* 3.5 9.5 - - - +
206B ARG* 1.3 77.7 - - - +
208B GLN* 1.3 56.7 + - - +
210B LEU* 3.5 8.9 + - + +
211B ALA* 3.2 24.3 + - - +
215B ALA* 5.3 1.7 - - - +
216B PRO 5.6 5.0 - - - +
217B PHE* 3.7 18.1 - - + +
219B GLU* 2.9 34.0 + - + +
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Residues in contact with GLN 208 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B TRP* 2.9 38.7 + - + +
205B LYS* 3.7 11.5 - - - +
207B GLN* 1.3 74.3 - - - +
209B GLN* 1.3 64.6 + - - +
211B ALA* 3.5 9.9 + - - +
212B GLY* 3.5 8.3 + - - -
217B PHE* 3.5 30.0 - - + -
275B VAL 3.3 22.4 + - - +
276B GLU 3.8 11.9 + - - -
278B GLN* 3.6 34.9 + - + +
408B LEU* 4.4 7.6 - - - +
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Residues in contact with GLN 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LYS 2.9 17.7 + - - +
206B ARG* 3.2 34.0 + - - +
208B GLN* 1.3 77.6 - - - +
210B LEU* 1.3 60.4 + - - +
212B GLY* 3.1 10.4 + - - -
408B LEU* 3.8 32.6 - - + +
429B ASP* 3.8 8.6 + - - -
430B ASN* 3.5 38.0 + - - +
433B SER* 3.7 25.2 + - - -
434B GLU 5.4 1.6 - - - +
435B MET* 5.9 0.7 - - - -
437B ARG* 4.0 14.6 - - - +
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Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B ARG* 3.1 53.8 + - + +
207B GLN* 4.0 7.9 - - + +
209B GLN* 1.3 72.0 - - - +
211B ALA* 1.3 61.1 + - - +
212B GLY 3.0 4.9 - - - -
213B ASN* 3.1 20.9 + - + +
215B ALA* 3.3 27.1 + - + +
430B ASN 3.6 17.9 - - - +
431B ALA* 4.0 11.0 - - + +
453B GLU* 5.7 4.5 - - - +
454B THR* 5.5 3.1 - - - +
457B LEU* 6.5 1.6 - - + -
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Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B GLN 3.2 17.3 + - - +
208B GLN* 3.6 8.5 - - + +
209B GLN 3.2 0.2 - - - -
210B LEU* 1.3 71.1 - - - +
212B GLY* 1.3 58.8 + - - +
213B ASN 3.0 5.7 + - - -
214B GLY* 3.3 10.4 + - - -
215B ALA* 3.7 17.1 - - - +
217B PHE* 3.6 32.3 - - + -
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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