Contacts of the helix formed by residues 194 - 228 (chain D) in PDB entry 5UHF
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 ARG 194 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D LEU* 3.2 34.4 - - + +
184D LEU* 3.1 28.9 + - + +
185D GLU* 3.3 47.3 + - - +
188D GLY* 4.0 2.4 - - - -
189D ALA* 2.8 31.2 + - + +
190D LYS 3.7 8.9 + - - +
191D ALA* 3.5 21.4 + - - +
192D ASP 3.1 0.6 - - - -
193D ALA* 1.3 78.4 - - - +
195D ARG* 1.3 58.8 + - - +
196D LYS 3.3 1.3 - - - -
197D VAL* 3.8 4.5 - - - -
198D ARG* 3.1 23.4 + - - +
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Residues in contact with ARG 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D ALA 3.7 5.0 + - - +
192D ASP* 3.0 26.6 + - - +
194D ARG* 1.3 79.2 - - - +
196D LYS* 1.3 62.2 + - - +
197D VAL 3.3 0.2 - - - -
198D ARG* 3.6 28.4 - - - +
199D ASP* 2.9 51.0 + - - +
202D GLU* 5.3 1.8 + - - -
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Residues in contact with LYS 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192D ASP 3.6 5.2 + - - +
193D ALA* 4.0 12.6 - - - +
195D ARG* 1.3 81.4 - - - +
197D VAL* 1.3 61.1 + - + +
199D ASP* 4.1 3.8 - - - +
200D GLY* 3.1 22.5 + - - -
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Residues in contact with VAL 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D ARG* 5.0 5.2 + - - +
177D LEU* 3.5 10.7 - - + +
180D ASP* 4.9 12.6 - - + -
181D LEU* 3.8 20.6 - - + -
184D LEU* 3.6 30.1 - - + -
193D ALA 3.6 17.9 - - - +
194D ARG* 3.6 1.9 + - - +
195D ARG 3.3 0.2 - - - -
196D LYS* 1.3 80.0 - - + +
198D ARG* 1.3 64.1 + - - +
200D GLY* 3.8 2.6 - - - +
201D GLY 3.1 15.4 + - - -
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Residues in contact with ARG 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D LEU* 3.6 30.0 - - - +
178D GLU* 4.1 23.8 + - - -
181D LEU* 3.6 23.2 - - + +
194D ARG 3.1 17.5 + - - +
195D ARG* 3.6 35.1 - - - +
196D LYS 3.3 0.4 - - - -
197D VAL* 1.3 75.8 - - - +
199D ASP* 1.3 64.6 + - - +
201D GLY* 3.0 4.0 + - - -
202D GLU* 3.0 48.2 + - - +
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Residues in contact with ASP 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195D ARG* 2.9 42.2 + - - +
196D LYS* 4.2 4.6 - - - +
198D ARG* 1.3 79.6 - - - +
200D GLY* 1.3 58.0 + - - +
202D GLU* 3.9 14.2 - - - +
203D ARG* 3.0 28.8 + - - +
206D ARG* 4.3 3.9 + - - +
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Residues in contact with GLY 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D ARG* 4.9 1.6 - - - -
196D LYS 3.1 17.8 + - - -
197D VAL* 3.7 3.1 + - - -
198D ARG 3.1 0.6 - - - -
199D ASP* 1.3 78.0 - - - +
201D GLY* 1.3 60.5 + - - +
203D ARG* 3.5 5.6 + - - +
204D GLU* 3.1 31.0 + - - +
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Residues in contact with GLY 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D ARG* 3.7 24.9 - - - +
177D LEU* 3.7 20.0 - - - -
197D VAL 3.1 7.1 + - - -
198D ARG 3.0 7.2 + - - -
200D GLY* 1.3 77.7 - - - +
202D GLU* 1.3 55.5 + - - +
204D GLU* 3.4 2.6 + - - +
205D MET* 3.1 33.6 + - - +
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Residues in contact with GLU 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D LEU* 4.9 5.4 - - + -
195D ARG* 5.3 1.7 + - - -
198D ARG* 3.0 43.6 + - - +
199D ASP* 4.0 13.7 - - - +
201D GLY* 1.3 73.8 - - - +
203D ARG* 1.3 63.6 + - - +
205D MET* 4.1 9.5 - - - +
206D ARG* 3.1 37.2 + - - +
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Residues in contact with ARG 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D ASP 3.0 19.5 + - - +
200D GLY* 3.7 8.3 - - - +
202D GLU* 1.3 75.5 - - - +
204D GLU* 1.3 64.9 + - + +
206D ARG* 3.3 45.9 + - - +
207D GLN* 3.1 59.9 + - - +
210D ASP* 5.7 2.2 + - - -
207F ASP 4.8 11.1 - - - +
208F GLU* 3.9 22.2 + - - +
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Residues in contact with GLU 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D ARG* 2.8 37.7 + - + +
200D GLY 3.1 20.6 + - - +
201D GLY 3.7 4.5 - - - +
203D ARG* 1.3 76.0 - - + +
205D MET* 1.3 65.0 + - - +
207D GLN* 3.0 15.0 + - - +
208D ILE* 2.9 30.4 + - + +
211D ARG* 5.1 0.2 + - - -
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Residues in contact with MET 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D LEU* 3.3 44.3 - - + +
173D ARG* 3.6 26.0 - - + -
174D ALA* 4.3 15.9 - - + -
177D LEU* 4.2 19.7 - - - -
201D GLY 3.1 21.7 + - - +
202D GLU* 4.1 9.4 - - - +
204D GLU* 1.3 75.9 - - - +
206D ARG* 1.3 60.0 + - - +
208D ILE* 3.3 3.1 + - - -
209D ARG* 3.0 27.9 + - - +
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Residues in contact with ARG 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D ASP* 4.3 3.8 + - - +
202D GLU* 3.1 25.0 + - - +
203D ARG* 3.3 63.9 - - - +
204D GLU 3.1 0.2 - - - -
205D MET* 1.3 74.0 - - - +
207D GLN* 1.3 65.1 - - - +
209D ARG* 3.3 10.4 + - - +
210D ASP* 3.0 35.4 + - - +
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Residues in contact with GLN 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D ARG* 3.1 54.7 + - - +
204D GLU* 3.0 12.5 + - - +
206D ARG* 1.3 76.7 - - - +
208D ILE* 1.3 58.6 + - - +
210D ASP* 3.8 6.8 - - - +
211D ARG* 2.9 65.2 + - + +
214D ARG* 5.5 0.8 + - - +
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Residues in contact with ILE 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D ARG* 4.7 7.2 - - + +
169D GLU* 3.6 58.3 - - + +
170D LEU* 3.7 22.9 - - + -
173D ARG* 4.5 12.3 - - + -
204D GLU* 2.9 24.6 + - + +
205D MET* 3.4 10.5 - - - +
206D ARG 3.2 0.2 - - - -
207D GLN* 1.3 76.8 - - - +
209D ARG* 1.3 62.2 + - - +
211D ARG* 3.6 18.3 - - - +
212D ALA* 3.1 22.7 + - + +
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Residues in contact with ARG 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D ARG* 4.4 25.4 - - - +
167D ASP* 5.4 3.4 + - - -
170D LEU* 3.4 27.3 - - + +
205D MET* 3.0 18.7 + - - +
206D ARG* 3.3 11.3 + - - +
208D ILE* 1.3 76.6 - - - +
210D ASP* 1.3 67.7 + - - +
212D ALA* 3.5 3.3 + - - +
213D GLN* 2.9 35.6 + - + +
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Residues in contact with ASP 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203D ARG* 5.7 1.9 + - - -
206D ARG* 3.0 27.5 + - - +
207D GLN* 3.8 6.0 + - - +
209D ARG* 1.3 86.1 - - - +
211D ARG* 1.3 66.7 + - - +
213D GLN* 3.2 8.6 + - - +
214D ARG* 3.0 45.5 + - - +
210F GLU* 4.4 16.8 - - - +
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Residues in contact with ARG 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D GLU* 5.3 3.8 + - - -
207D GLN* 2.9 59.9 + - + +
208D ILE* 3.6 19.8 - - - +
210D ASP* 1.3 77.0 - - - +
212D ALA* 1.3 61.9 + - - +
214D ARG* 3.3 27.1 + - - +
215D GLU* 3.3 19.2 + - - +
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Residues in contact with ALA 212 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D VAL* 4.2 10.8 - - + +
166D ARG* 3.8 35.0 - - + +
208D ILE* 3.1 14.9 + - + +
209D ARG 3.7 4.3 - - - +
211D ARG* 1.3 80.1 - - - +
213D GLN* 1.3 61.8 + - - +
215D GLU* 3.4 8.1 + - - +
216D LEU* 3.1 29.1 + - + +
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Residues in contact with GLN 213 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D ARG* 3.8 21.0 + - - -
209D ARG* 2.9 22.9 + - + +
210D ASP* 3.5 12.8 - - - +
211D ARG 3.2 0.4 - - - -
212D ALA* 1.3 78.4 - - - +
214D ARG* 1.3 52.8 + - + +
216D LEU* 3.3 12.8 + - - +
217D ASP* 2.7 58.9 + - - +
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Residues in contact with ARG 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207D GLN* 5.5 0.6 + - - +
210D ASP* 3.0 30.3 + - + +
211D ARG* 3.6 35.6 - - - +
212D ALA 3.3 0.2 - - - -
213D GLN* 1.3 74.7 - - + +
215D GLU* 1.3 60.0 + - - +
217D ASP* 3.3 10.3 + - - +
218D ARG* 2.8 30.8 + - - +
208F GLU* 5.4 8.3 + - - -
210F GLU* 6.2 1.8 - - - +
213F ARG* 3.9 44.2 - - - +
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Residues in contact with GLU 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D GLU* 4.4 6.4 - - - +
162D VAL* 4.1 25.7 - - + +
211D ARG 3.3 9.3 + - - +
212D ALA* 3.6 11.9 - - - +
213D GLN 3.3 0.2 - - - -
214D ARG* 1.3 78.4 - - - +
216D LEU* 1.3 58.0 + - - +
218D ARG* 3.1 37.5 + - - +
219D LEU* 2.8 44.5 + - + +
247D ARG* 5.7 0.3 + - - -
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Residues in contact with LEU 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D ARG* 3.0 68.8 + - + +
162D VAL* 3.7 17.3 - - + -
163D GLU* 3.7 23.8 - - + +
166D ARG* 4.1 19.5 - - - +
212D ALA* 3.1 20.5 + - + +
213D GLN* 3.6 15.5 - - - +
215D GLU* 1.3 76.5 - - - +
217D ASP* 1.3 59.6 + - - +
219D LEU* 4.3 3.8 - - + -
220D GLU* 2.9 25.7 + - - +
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Residues in contact with ASP 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213D GLN* 2.7 46.5 + - - +
214D ARG* 3.4 10.8 - - - +
215D GLU 3.1 0.2 - - - -
216D LEU* 1.3 76.6 - - - +
218D ARG* 1.3 60.3 + - - +
220D GLU* 3.3 15.6 + - - +
221D ASP* 2.8 41.6 + - - +
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Residues in contact with ARG 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D ARG 2.8 14.8 + - - +
215D GLU* 3.3 37.8 + - - +
217D ASP* 1.3 76.5 - - - +
219D LEU* 1.3 54.5 + - + +
221D ASP* 2.9 7.9 + - + +
222D ILE* 2.6 53.7 + - + +
243D GLU* 2.7 37.0 + - - +
247D ARG* 5.2 2.8 - - - +
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Residues in contact with LEU 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D MET* 4.1 14.8 - - + +
158D GLU* 3.4 47.8 - - + +
159D ARG* 4.0 26.2 - - + +
162D VAL* 4.0 20.4 - - + -
215D GLU* 2.8 32.0 + - + +
216D LEU* 3.9 7.4 - - + +
218D ARG* 1.3 74.0 - - + +
220D GLU* 1.3 57.2 + - - +
222D ILE* 3.7 9.8 - - + +
223D TRP* 3.1 29.1 + - - +
247D ARG* 3.5 21.3 - - - +
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Residues in contact with GLU 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D ARG* 3.9 11.4 - - - +
216D LEU 2.9 17.8 + - - +
217D ASP* 3.3 20.7 - - - +
218D ARG 3.0 0.2 - - - -
219D LEU* 1.3 76.7 - - - +
221D ASP* 1.3 64.5 + - - +
223D TRP* 3.4 3.6 + - - +
224D SER* 2.8 34.7 + - - -
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Residues in contact with ASP 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D ASP* 2.8 28.7 + - - +
218D ARG* 3.6 6.2 + - + +
220D GLU* 1.3 80.8 - - - +
222D ILE* 1.3 60.7 + - + +
224D SER* 4.0 6.6 - - - -
225D THR* 2.3 35.1 + - - +
240D LEU* 4.5 7.2 - - + +
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Residues in contact with ILE 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D MET* 4.4 7.0 - - + -
218D ARG* 2.6 45.2 + - + +
219D LEU* 3.7 15.0 - - + +
221D ASP* 1.3 72.6 - - - +
223D TRP* 1.3 64.7 + - - +
225D THR* 3.1 13.2 + - - -
226D PHE* 3.1 13.5 + - - +
240D LEU* 4.2 20.9 - - + -
243D GLU* 4.3 19.7 - - + +
244D LEU* 4.6 8.9 - - + +
247D ARG* 3.9 44.6 - - - +
248D TYR* 4.3 11.0 - - + -
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Residues in contact with TRP 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D LEU* 3.8 23.3 - - + -
151D LEU* 3.7 22.4 - - + -
152D GLU* 3.4 45.1 - - + +
155D MET* 3.7 24.0 - - + -
159D ARG* 6.4 0.2 - - - -
219D LEU 3.1 16.2 + - - +
220D GLU* 4.0 2.7 - - - +
222D ILE* 1.3 78.7 - - - +
224D SER* 1.3 62.9 + - - +
226D PHE* 4.0 18.8 - + - +
227D THR* 2.5 51.3 + - + +
248D TYR* 3.4 28.9 - + - -
----------------------------------------------------------
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Residues in contact with SER 224 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220D GLU* 2.8 22.4 + - - -
221D ASP* 4.0 9.4 - - - -
223D TRP* 1.3 80.0 - - - +
225D THR* 1.3 62.9 + - - +
227D THR* 3.7 3.6 + - - -
228D LYS* 3.2 51.1 + - - +
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Residues in contact with THR 225 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221D ASP* 2.3 27.4 + - - +
222D ILE 3.1 5.6 + - - -
224D SER* 1.3 76.7 - - - +
226D PHE* 1.3 64.4 + - - +
228D LYS* 3.1 24.0 - - - +
229D LEU* 3.3 21.4 + - + +
233D GLN* 5.0 4.3 - - - +
235D ILE* 4.9 7.0 - - + -
240D LEU* 4.1 21.9 - - + +
244D LEU* 4.3 13.9 - - + -
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Residues in contact with PHE 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D ARG* 3.4 41.9 + - + -
148D LEU* 4.9 5.2 - - + -
151D LEU* 3.8 30.7 - - + -
222D ILE 3.1 12.2 + - - +
223D TRP* 4.0 30.3 - + - +
225D THR* 1.3 76.1 - - - +
227D THR* 1.3 70.3 + - - +
228D LYS 3.3 0.3 + - - -
229D LEU* 3.5 14.0 + - + +
244D LEU* 4.1 10.9 - - + +
248D TYR* 3.5 44.9 - + + -
251D TYR* 4.1 19.5 - + + -
252D PHE* 5.3 6.1 - + - -
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Residues in contact with THR 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D ARG* 3.0 21.5 + - - +
148D LEU* 4.9 17.7 - - + -
223D TRP* 2.5 49.0 + - + +
224D SER* 3.9 5.4 - - - -
226D PHE* 1.3 83.0 - - - +
228D LYS* 1.3 66.1 + - + +
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Residues in contact with LYS 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144D ARG* 4.4 0.2 - - - +
224D SER* 3.2 38.5 + - - +
225D THR* 3.1 9.6 - - - +
226D PHE 3.2 0.4 - - - -
227D THR* 1.3 84.6 - - + +
229D LEU* 1.3 58.2 + - - +
233D GLN* 3.0 22.1 + - - +
----------------------------------------------------------
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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