Contacts of the helix formed by residues 187 - 218 (chain B) in PDB entry 1UPX
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 187 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B VAL* 5.5 0.2 - - - -
185B SER 3.5 3.5 + - - -
186B LEU* 1.3 76.4 - - - +
188B VAL* 1.3 64.9 + - - +
189B ALA* 3.5 10.0 + - - +
190B ASP* 3.0 33.6 + - - -
191B LEU* 3.0 22.8 + - - +
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Residues in contact with VAL 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ASP* 4.8 2.0 - - - +
138B ASP* 3.9 28.0 - - + +
139B VAL* 4.3 18.1 - - + +
142B LEU* 3.8 20.6 - - + +
187B SER* 1.3 73.4 - - - +
189B ALA* 1.3 57.9 + - - +
191B LEU* 3.1 5.8 + - - +
192B VAL* 2.9 35.3 + - + +
519B VAL* 5.6 1.8 - - + -
522B VAL* 5.9 5.6 - - + -
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B SER* 3.2 9.4 + - - +
188B VAL* 1.3 79.4 - - - +
190B ASP* 1.3 62.5 + - - +
192B VAL* 3.4 8.1 + - - +
193B ALA* 3.0 23.4 + - - +
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Residues in contact with ASP 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B SER 4.4 1.6 - - - +
186B LEU* 3.5 31.0 - - + +
187B SER* 3.0 40.2 + - - +
189B ALA* 1.3 76.5 - - - +
191B LEU* 1.3 57.8 + - - +
193B ALA* 3.3 8.3 + - - +
194B LEU* 2.9 27.3 + - - +
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Residues in contact with LEU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B VAL* 3.9 43.5 - - + +
142B LEU* 3.8 19.5 - - + -
143B ARG* 4.7 13.5 - - + +
146B ILE* 3.6 20.7 - - + +
180B LYS 4.8 5.4 - - - +
181B THR* 5.3 2.0 - - - -
186B LEU* 4.1 31.6 - - + +
187B SER 3.0 17.1 + - - +
188B VAL* 3.1 7.8 + - - +
190B ASP* 1.3 76.0 - - - +
192B VAL* 1.3 59.4 + - - +
194B LEU* 3.3 8.0 + - + -
195B THR* 2.9 31.9 + - - -
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU* 4.1 19.7 - - + -
188B VAL* 2.9 28.4 + - + +
189B ALA* 3.4 8.0 + - - +
191B LEU* 1.3 75.3 - - - +
193B ALA* 1.3 62.5 + - - +
195B THR* 3.1 17.8 + - - -
196B LEU* 3.2 21.6 + - + +
519B VAL* 6.0 1.3 - - + -
522B VAL* 4.3 22.7 - - + -
523B LEU* 6.2 2.5 - - + -
526B GLN* 4.2 25.8 - - - +
527B PHE* 6.3 1.1 - - + -
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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
----------------------------------------------------------
189B ALA 3.0 13.6 + - - +
190B ASP* 3.5 11.4 - - - +
191B LEU 3.3 0.2 - - - -
192B VAL* 1.3 77.4 - - - +
194B LEU* 1.3 57.6 + - - +
196B LEU* 3.2 10.3 + - - +
197B GLU* 2.9 27.3 + - - +
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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
----------------------------------------------------------
146B ILE* 3.9 22.0 - - + -
173B PHE* 3.9 18.8 - - + -
176B GLU* 6.5 0.4 - - + -
177B ALA* 4.1 15.0 - - + +
180B LYS* 3.7 44.2 - - + +
181B THR* 5.1 0.7 - - + -
186B LEU* 4.8 2.5 - - + -
190B ASP 2.9 16.9 + - - +
191B LEU* 3.7 15.0 - - + +
192B VAL 3.2 0.2 - - - -
193B ALA* 1.3 76.1 - - - +
195B THR* 1.3 52.9 + - - +
197B GLU* 3.7 21.8 - - - +
198B THR* 2.8 40.6 + - - +
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Residues in contact with THR 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU* 3.7 13.6 - - + +
145B LEU* 3.7 26.9 - - + +
146B ILE* 3.4 21.7 - - + +
191B LEU 2.9 17.4 + - - -
192B VAL* 3.1 12.3 + - - -
194B LEU* 1.3 76.3 - - - +
196B LEU* 1.3 60.6 + - + +
198B THR* 3.3 6.0 + - - -
199B GLY* 3.1 21.7 + - - -
495B LEU* 3.7 24.9 - - + +
498B LEU* 6.3 0.4 - - + -
523B LEU* 5.5 7.9 - - + -
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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
----------------------------------------------------------
192B VAL* 3.2 19.0 + - + +
193B ALA* 3.2 9.2 + - - +
195B THR* 1.3 80.6 - - + +
197B GLU* 1.3 63.9 + - - +
199B GLY* 3.1 4.1 + - - +
200B LYS* 3.0 19.4 + - - +
495B LEU* 5.3 2.5 - - + +
498B LEU* 4.4 22.9 - - + +
499B SER* 3.8 12.7 - - - +
523B LEU* 6.2 0.4 - - + -
526B GLN* 4.2 11.2 - - - +
527B PHE* 3.4 40.2 - - + -
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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
----------------------------------------------------------
173B PHE* 3.4 29.0 - - + -
176B GLU* 5.2 3.4 - - - +
180B LYS* 4.9 6.9 + - - -
193B ALA 2.9 15.5 + - - +
194B LEU* 3.4 17.5 + - - +
196B LEU* 1.3 71.8 - - - +
198B THR* 1.3 66.6 + - - +
200B LYS* 3.1 12.4 + - + +
201B PHE* 3.0 40.8 + - + -
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Residues in contact with THR 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 3.8 20.3 - - + +
149B GLY 4.3 7.2 - - - -
150B LEU* 4.1 12.5 - - + +
153B MET* 3.2 24.6 - - + +
173B PHE* 3.6 18.7 - - - -
177B ALA* 4.7 0.2 - - - +
194B LEU* 2.8 22.2 + - - +
195B THR* 3.3 12.6 - - - -
196B LEU 3.2 0.2 - - - -
197B GLU* 1.3 76.6 - - - +
199B GLY* 1.3 54.7 + - - +
201B PHE 3.3 0.5 + - - -
202B GLY 2.8 24.6 + - - -
492B ILE* 3.6 14.3 - - + +
495B LEU* 4.1 11.4 - - + -
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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 THR 3.1 11.7 + - - -
196B LEU* 3.1 5.3 + - - -
198B THR* 1.3 78.6 - - - +
200B LYS* 1.3 60.8 + - - +
202B GLY* 3.0 2.9 + - - -
203B VAL 3.0 17.8 + - - -
492B ILE* 4.6 0.9 - - - -
495B LEU* 3.4 34.7 - - - +
496B ALA* 3.4 9.5 - - - -
499B SER* 3.4 8.0 + - - -
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Residues in contact with LYS 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU 3.0 11.2 + - - +
197B GLU* 3.1 16.6 + - + +
199B GLY* 1.3 74.8 - - - +
201B PHE* 1.3 74.0 + - + +
203B VAL* 3.2 10.0 + - + +
204B SER* 3.1 22.1 + - - +
499B SER* 3.5 13.6 + - - +
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Residues in contact with PHE 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B MET* 3.7 13.9 - - + -
169B SER* 3.7 31.6 - - - -
170B LEU* 3.7 18.3 - - + +
173B PHE* 3.4 50.7 - + + -
197B GLU* 3.0 40.7 + - + +
198B THR 3.6 0.2 - - - -
200B LYS* 1.3 85.1 - - + +
202B GLY* 1.3 59.5 + - - +
204B SER* 3.2 15.3 + - - -
205B ALA* 2.8 29.1 + - - +
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Residues in contact with GLY 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B MET* 3.7 5.8 - - - +
156B TYR* 5.3 0.2 - - - -
198B THR 2.8 11.1 + - - -
199B GLY 3.0 6.0 + - - -
201B PHE* 1.3 72.7 - - - +
203B VAL* 1.3 64.7 + - - +
205B ALA* 3.2 2.3 + - - +
206B MET* 2.9 28.6 + - - +
492B ILE* 3.6 30.2 - - - +
496B ALA* 4.3 7.0 - - - -
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Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B GLY 3.0 14.1 + - - +
200B LYS* 3.2 9.6 + - + +
202B GLY* 1.3 74.8 - - - +
204B SER* 1.3 58.4 + - - +
206B MET* 3.2 8.8 + - + +
207B ALA* 2.8 29.8 + - + +
456B TYR* 4.2 18.3 - - + -
496B ALA* 3.7 19.9 - - + +
499B SER* 3.6 15.5 - - - +
500B LEU* 4.0 27.8 - - + -
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Residues in contact with SER 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B GLU* 4.4 16.1 - - - +
170B LEU* 4.7 4.5 - - - -
200B LYS* 3.1 15.7 + - - +
201B PHE* 3.2 26.4 + - - -
203B VAL* 1.3 77.8 - - - +
205B ALA* 1.3 57.5 + - - +
207B ALA* 3.3 6.6 + - - +
208B LEU* 2.9 29.5 + - - +
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Residues in contact with ALA 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B MET* 3.9 29.2 - - + +
156B TYR* 4.3 13.8 - - + +
157B ALA* 4.5 2.6 - - - +
160B ALA* 5.3 0.2 - - - +
170B LEU* 3.8 23.8 - - + +
201B PHE 2.8 16.5 + - - +
202B GLY* 3.2 4.7 + - - +
204B SER* 1.3 75.0 - - - +
206B MET* 1.3 58.3 + - - +
208B LEU* 3.3 3.9 + - - +
209B LEU* 3.0 29.3 + - - +
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Residues in contact with MET 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B TYR* 3.7 23.6 - - + -
202B GLY 2.9 19.5 + - - +
203B VAL* 3.7 7.0 - - + +
205B ALA* 1.3 75.4 - - - +
207B ALA* 1.3 57.5 + - - +
209B LEU* 3.4 6.0 + - - +
210B ASP* 2.9 30.5 + - - +
453B ASN* 3.6 21.7 - - - +
455B SER* 4.2 5.4 - - - -
456B TYR* 3.6 39.6 - - + +
459B ALA* 5.6 4.3 - - + -
492B ILE* 5.6 1.8 - - + -
493B VAL* 4.0 29.2 - - + -
496B ALA* 4.3 21.1 - - + -
497B LEU* 6.2 3.1 - - + -
500B LEU* 6.2 1.6 - - + -
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Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B VAL* 2.8 19.3 + - + +
204B SER* 3.6 7.9 - - - +
205B ALA 3.3 0.2 - - - -
206B MET* 1.3 72.3 - - - +
208B LEU* 1.3 60.9 + - - +
210B ASP* 3.4 2.6 + - - +
211B ALA* 3.0 28.8 + - - +
456B TYR* 3.5 33.9 - - + +
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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
----------------------------------------------------------
157B ALA* 5.3 3.6 - - + +
160B ALA* 3.9 13.0 - - + -
165B LYS* 3.8 33.9 - - + +
166B HIS* 4.0 7.2 - - - +
167B GLU* 3.7 41.1 - - + +
170B LEU* 4.1 18.6 - - + -
204B SER 2.9 16.9 + - - +
205B ALA 3.6 4.9 - - - +
207B ALA* 1.3 78.0 - - - +
209B LEU* 1.3 55.7 + - - +
211B ALA* 3.3 8.9 + - + +
212B ALA* 2.9 27.5 + - - +
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Residues in contact with LEU 209 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B TYR* 3.8 30.3 - - + +
159B HIS* 3.6 32.5 - - + +
160B ALA* 3.7 16.1 - - - +
205B ALA 3.0 15.5 + - - +
206B MET* 3.8 5.4 - - - +
208B LEU* 1.3 75.1 - - - +
210B ASP* 1.3 60.0 + - - +
212B ALA* 4.3 2.0 - - + -
213B ASN* 2.8 54.9 + - - +
451B GLN* 5.7 0.2 - - - +
453B ASN* 3.7 35.7 - - + +
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Residues in contact with ASP 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B MET 2.9 18.3 + - - +
207B ALA 3.6 5.5 - - - +
209B LEU* 1.3 76.1 - - - +
211B ALA* 1.3 60.0 + - - +
213B ASN* 4.0 4.9 - - - +
214B THR* 2.9 47.2 + - - +
370B ALA* 5.7 0.7 - - - +
371B HIS* 2.8 40.3 + - - -
453B ASN 5.9 0.2 - - - +
454B ASP* 4.4 12.6 - - - +
456B TYR* 3.6 23.6 - - + +
457B SER* 3.9 5.9 + - - -
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Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B LYS* 5.4 4.5 - - + -
207B ALA 3.0 17.2 + - - +
208B LEU* 3.6 10.8 - - + +
210B ASP* 1.3 78.9 + - - +
212B ALA* 1.3 57.8 + - - +
214B THR* 3.9 5.2 - - - -
215B GLY* 2.9 29.1 + - - -
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Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ALA* 4.0 12.8 - - - -
163B LEU* 3.9 22.6 - - + +
165B LYS* 3.8 28.4 - - + +
208B LEU 2.9 17.7 + - - +
209B LEU* 3.2 4.0 + - - +
211B ALA* 1.3 78.5 - - - +
213B ASN* 1.3 61.2 + - - +
216B THR* 2.7 33.0 + - - -
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Residues in contact with ASN 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LEU* 3.3 21.5 - - - +
209B LEU* 2.8 44.8 + - - +
210B ASP* 4.0 4.6 - - - +
212B ALA* 1.3 74.3 - - - +
214B THR* 1.3 58.4 + - + +
217B TYR* 2.9 37.1 + - - +
242B LEU* 3.5 21.9 - - + +
271B TYR* 3.4 25.1 + - + +
451B GLN* 4.2 6.9 - - - +
453B ASN* 3.8 15.4 - - - +
454B ASP* 5.2 2.2 + - - +
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Residues in contact with THR 214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ASP* 2.9 37.9 + - - +
211B ALA* 3.7 5.4 + - - -
213B ASN* 1.3 75.6 - - + +
215B GLY* 1.3 63.5 + - - +
218B GLY* 2.8 36.1 + - - -
219B HIS* 3.6 41.4 + - + -
220B PRO* 3.9 18.6 - - + -
271B TYR* 4.5 4.0 - - + +
370B ALA* 6.3 0.7 - - + -
371B HIS* 5.1 0.7 - - + +
----------------------------------------------------------
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Residues in contact with GLY 215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ALA 2.9 20.8 + - - -
214B THR* 1.3 78.0 + - - +
216B THR* 1.3 61.5 + - - +
218B GLY 4.9 0.3 + - - -
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Residues in contact with THR 216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LEU* 4.0 21.6 + - + +
165B LYS* 4.9 4.2 + - - -
212B ALA* 2.7 23.2 + - - -
215B GLY* 1.3 80.6 - - - +
217B TYR* 1.3 97.5 + - + +
218B GLY 3.6 0.8 + - - -
246B GLU* 4.9 3.6 - - - +
273B ALA* 4.6 2.4 - - - +
----------------------------------------------------------
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Residues in contact with TYR 217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LEU* 3.6 25.1 - - + +
213B ASN* 2.9 18.7 + - - +
216B THR* 1.3 92.1 - - + +
218B GLY* 1.3 60.5 + - - +
242B LEU* 3.7 30.5 - - + -
243B ARG* 3.3 19.9 - - - -
246B GLU* 2.7 38.7 + - + +
271B TYR* 3.7 17.7 - - + +
272B PRO* 3.4 8.4 - - - +
273B ALA* 3.0 43.5 + - + -
274B PHE* 3.5 27.4 - + + -
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Residues in contact with GLY 218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B THR* 2.8 26.4 + - - -
215B GLY 4.7 0.6 + - - -
216B THR 3.6 1.2 - - - -
217B TYR* 1.3 79.3 - - - +
219B HIS* 1.3 61.8 + - - -
271B TYR* 3.1 23.4 - - - -
272B PRO* 3.8 10.1 - - - -
----------------------------------------------------------
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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).
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