Contacts of the helix formed by residues 211 - 241 (chain B) in PDB entry 6XPD
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 ASN 211 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLU* 3.6 26.6 + - - +
67B TYR* 4.9 2.1 - - - +
69B TYR* 6.0 0.2 - - - +
70B ALA* 3.4 26.7 - - + +
121B LEU* 5.6 5.5 - - + +
140B GLU* 5.3 7.2 - - - +
210B ALA* 1.3 77.6 - - - +
212B ALA* 1.3 66.6 + - - +
213B SER* 3.0 8.8 + - - +
214B VAL* 3.2 13.0 + - + +
215B ARG* 3.0 22.2 + - - +
310B MET* 5.1 2.5 - - - -
311B ASN* 4.9 7.6 - - - +
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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
----------------------------------------------------------
140B GLU* 4.1 21.9 + - + +
141B ILE* 4.4 15.3 - - + +
144B ALA* 3.9 3.4 - - - +
210B ALA 3.4 3.2 + - - -
211B ASN* 1.3 71.6 - - - +
213B SER* 1.3 62.0 + - - +
215B ARG* 4.6 2.9 - - - +
216B ALA* 3.2 23.2 + - - +
270B PHE* 3.4 33.1 - - + -
309B THR* 4.8 0.9 - - - -
310B MET* 3.8 20.5 - - + +
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Residues in contact with SER 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 3.8 7.1 - - - +
117B SER* 2.9 41.5 + - - -
120B SER* 4.6 3.3 - - - -
121B LEU* 4.0 24.6 + - - -
140B GLU* 4.7 16.5 + - - +
144B ALA* 5.4 0.4 - - - -
211B ASN* 3.0 4.9 + - - +
212B ALA* 1.3 76.6 - - - +
214B VAL* 1.3 67.4 + - - +
216B ALA* 3.1 8.4 + - - +
217B ALA* 3.1 19.6 + - - +
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Residues in contact with VAL 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ALA* 3.5 35.4 - - + -
73B LYS* 3.9 31.0 - - + +
74B LEU* 4.3 14.8 - - + -
196B LEU* 4.3 25.8 - - + +
198B GLN* 5.7 3.8 - - + +
210B ALA* 5.2 5.8 - - + -
211B ASN* 3.2 13.9 + - + +
213B SER* 1.3 73.6 - - - +
215B ARG* 1.3 59.0 + - - +
217B ALA* 2.7 25.8 + - - +
218B PHE* 2.8 13.7 + - - +
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Residues in contact with ARG 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B GLN* 5.4 13.7 - - + -
210B ALA* 4.9 20.9 + - + +
211B ASN 3.0 18.0 + - - +
212B ALA* 4.3 2.7 - - - +
214B VAL* 1.3 77.8 - - - +
216B ALA* 1.3 58.9 + - - +
218B PHE* 3.9 8.4 - - + +
219B VAL* 3.4 29.9 + - + +
265B THR* 4.9 14.3 - - - +
266B ILE* 3.6 25.4 - - + +
269B ASP* 2.5 39.5 + - - +
270B PHE* 4.4 9.2 - - - -
280B LYS* 5.0 8.1 - - - +
310B MET* 3.9 18.4 - - - +
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Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B SER* 5.1 6.3 - - - +
144B ALA* 3.5 33.0 - - + +
147B SER* 5.1 6.5 - - - -
148B ILE* 4.1 15.8 - - + +
212B ALA 3.2 19.2 + - - +
213B SER* 3.1 7.5 + - - +
214B VAL 3.0 0.8 - - - -
215B ARG* 1.3 77.2 - - - +
217B ALA* 1.3 61.3 + - - +
219B VAL* 5.0 0.2 - - - -
220B HIS* 3.3 21.4 + - - +
266B ILE* 5.5 2.2 - - - -
270B PHE* 4.8 4.0 - - + -
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Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 3.9 20.6 - - + -
113B SER* 5.3 0.7 - - - -
114B PHE* 3.7 24.8 - - + -
117B SER* 4.3 9.6 + - - +
196B LEU* 3.6 8.9 - - + +
213B SER 3.1 10.7 + - - +
214B VAL 2.7 14.6 + - - +
216B ALA* 1.3 71.3 - - - +
218B PHE* 1.3 58.9 + - - +
220B HIS* 3.4 7.8 + - - +
221B ALA* 2.8 28.4 + - - +
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Residues in contact with PHE 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B THR* 3.5 33.2 - - + -
196B LEU* 3.2 40.3 - - + +
197B HIS* 4.3 11.0 - - + -
198B GLN* 4.6 26.2 - - + +
214B VAL 2.8 12.5 + - - +
215B ARG* 4.1 8.5 - - + +
216B ALA 3.4 0.2 - - - -
217B ALA* 1.3 72.5 - - - +
219B VAL* 1.3 68.8 + - + +
220B HIS 3.0 1.1 - - - -
221B ALA* 2.7 5.9 + - - +
222B LEU* 2.6 61.8 + - + +
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Residues in contact with VAL 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B ILE* 4.2 7.0 - - + -
151B ILE* 5.3 2.1 - - - +
215B ARG* 3.4 23.1 + - + +
216B ALA 4.4 2.9 - - - +
218B PHE* 1.3 89.2 - - + +
220B HIS* 1.3 61.0 + - - +
222B LEU* 4.3 6.2 - - + +
223B GLY* 3.1 20.6 + - - -
259B VAL* 5.7 0.5 - - - +
262B SER* 4.1 18.9 + - - +
263B THR* 4.0 21.1 - - + +
266B ILE* 3.9 35.9 - - + -
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Residues in contact with HIS 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 3.9 21.1 + - + +
110B ASN* 4.0 18.2 + - + -
113B SER* 2.9 38.9 - - - +
114B PHE* 4.6 2.5 - + - -
147B SER* 4.0 15.4 + - - -
148B ILE* 4.9 1.5 - - + +
150B CYS* 5.4 4.0 - - + -
151B ILE* 3.1 45.4 - - + +
154B VAL* 6.5 0.2 - - + -
216B ALA 3.3 19.6 + - - +
217B ALA* 3.4 9.0 - - - +
218B PHE 3.0 0.8 - - - -
219B VAL* 1.3 81.8 - - - +
221B ALA* 1.3 54.2 + - - +
223B GLY 3.9 0.2 + - - -
224B ASN* 2.6 34.4 + - - +
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Residues in contact with ALA 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ASN* 5.1 2.9 - - - +
114B PHE* 4.3 12.1 - - + -
189B ASN* 4.8 2.4 + - - -
192B LEU* 4.0 10.5 - - + +
193B THR* 3.7 17.2 + - - +
196B LEU* 3.7 19.3 - - + -
217B ALA 2.8 16.1 + - - +
218B PHE* 2.7 12.0 + - - +
220B HIS* 1.3 69.4 - - - +
222B LEU* 1.3 65.9 + - - +
223B GLY 3.1 1.3 - - - -
224B ASN* 2.8 20.5 + - - +
225B LEU* 3.2 7.4 + - - +
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Residues in contact with LEU 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B THR* 3.5 14.4 + - + +
218B PHE* 2.6 50.0 + - + +
219B VAL* 4.3 5.8 - - + +
221B ALA* 1.3 72.3 - - - +
223B GLY* 1.3 63.4 + - - +
225B LEU* 2.8 37.0 + - + +
226B PHE* 3.3 37.6 + - + -
262B SER* 4.8 16.6 - - - +
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Residues in contact with GLY 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B ILE* 5.7 3.4 - - - -
219B VAL 3.1 18.7 + - - -
220B HIS 4.2 2.0 - - - -
221B ALA 3.1 0.4 - - - -
222B LEU* 1.3 79.8 - - - +
224B ASN* 1.3 62.0 + - - +
226B PHE* 3.4 4.8 + - - -
227B GLN* 3.1 20.3 + - - +
259B VAL* 3.7 33.6 - - - +
262B SER* 5.3 3.1 + - - -
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Residues in contact with ASN 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B HIS* 3.9 22.8 + - + +
109B ILE* 5.7 1.0 - - - +
110B ASN* 2.6 41.4 + - - +
151B ILE* 4.5 6.4 - - - +
189B ASN* 3.0 21.4 + - - +
220B HIS* 2.6 28.2 + - - +
221B ALA 2.8 12.9 + - - +
223B GLY* 1.3 72.1 - - - +
225B LEU* 1.3 51.7 + - - +
227B GLN* 3.1 12.2 + - - +
228B SER* 2.4 33.3 + - - -
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Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B VAL* 4.1 18.8 - - + +
189B ASN* 3.3 25.4 - - + +
190B ILE* 4.3 24.2 - - + +
193B THR* 4.6 10.8 - - + +
221B ALA 3.2 5.1 + - - +
222B LEU* 2.8 32.7 + - + +
224B ASN* 1.3 75.8 - - - +
226B PHE* 1.3 67.6 + - + +
228B SER* 2.7 17.0 + - - -
229B ILE* 2.9 30.2 + - + +
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Residues in contact with PHE 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LEU* 3.3 43.3 + - + -
223B GLY* 3.8 6.5 - - - +
225B LEU* 1.3 84.0 - - + +
227B GLN* 1.3 62.8 + - - +
229B ILE* 3.5 15.3 - - + +
230B SER* 3.1 22.7 + - - -
255B PHE* 3.3 20.9 - + + +
258B LEU* 4.1 34.8 - - + -
259B VAL* 4.2 20.0 - - + -
262B SER* 5.5 4.0 - - - -
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Residues in contact with GLN 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B HIS* 5.9 9.6 - - + -
158B LEU* 3.5 35.7 - - + +
223B GLY 3.1 13.8 + - - +
224B ASN* 3.4 15.0 - - - +
226B PHE* 1.3 77.1 - - - +
228B SER* 1.3 63.3 + - - +
230B SER* 2.2 42.2 + - - -
231B VAL* 4.0 11.7 + - - +
252B THR* 4.6 15.1 - - - +
255B PHE* 5.3 0.9 - - - -
256B SER* 4.2 17.0 + - - -
259B VAL* 4.7 6.8 - - + +
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Residues in contact with SER 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B HIS* 5.0 5.6 + - - -
182B SER* 4.8 0.9 - - - -
185B ALA* 2.9 42.0 + - - +
186B VAL* 3.1 12.4 + - - +
189B ASN* 3.3 14.3 + - - -
224B ASN 2.4 29.3 + - - -
225B LEU* 2.7 11.3 + - - -
227B GLN* 1.3 67.9 - - - +
229B ILE* 1.3 62.4 + - - -
231B VAL* 3.1 25.3 - - - +
232B LEU* 3.8 1.0 + - - +
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Residues in contact with ILE 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B VAL* 3.5 33.4 - - + -
225B LEU* 2.9 18.6 + - + +
226B PHE* 3.5 20.4 - - + +
228B SER* 1.3 69.6 - - - +
230B SER* 1.3 55.4 + - - +
231B VAL 2.7 8.4 + - - -
232B LEU* 2.7 33.8 + - + -
233B ILE* 2.8 22.8 + - + +
255B PHE* 3.5 28.3 - - + -
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Residues in contact with SER 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B PHE 3.1 16.0 + - - -
227B GLN* 2.2 47.3 + - - -
228B SER 3.0 0.4 - - - -
229B ILE* 1.3 74.5 - - - +
231B VAL* 1.3 59.4 + - - +
233B ILE* 4.2 0.2 - - - -
234B SER* 3.5 7.3 - - - -
248B ASP 4.9 0.2 - - - +
251B CYS* 3.0 25.2 - - - +
252B THR* 4.5 12.7 - - - +
255B PHE* 3.4 27.8 - - - -
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Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178B MET* 5.2 18.6 - - + +
182B SER* 3.8 19.3 - - - -
185B ALA* 6.2 1.3 - - + -
227B GLN* 4.7 10.5 - - - +
228B SER* 3.1 18.4 + - - +
229B ILE 2.7 4.2 + - - -
230B SER* 1.3 84.1 + - - +
232B LEU* 1.3 53.9 + - - +
234B SER* 2.4 12.3 + - - +
235B ALA* 2.3 39.2 + - - +
248B ASP* 5.9 0.4 - - - +
252B THR* 5.5 4.9 - - + -
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Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ILE* 4.6 12.3 - - + -
182B SER* 3.2 28.5 - - - +
183B SER* 4.2 20.0 - - - -
186B VAL* 4.4 11.2 - - + -
229B ILE* 2.7 27.2 + - + +
231B VAL* 1.3 76.0 - - - +
233B ILE* 1.3 73.8 + - + +
235B ALA* 2.6 26.2 + - - +
236B LEU* 2.9 30.9 + - + +
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Residues in contact with ILE 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ILE* 2.8 26.9 + - + +
232B LEU* 1.3 84.7 - - + +
234B SER* 1.3 60.0 + - - +
236B LEU* 4.2 7.7 + - + +
237B ILE* 3.1 30.0 + - + +
251B CYS* 3.5 23.3 - - - -
255B PHE* 3.6 28.3 - - + -
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Residues in contact with SER 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B SER 3.5 16.6 - - - -
231B VAL* 2.4 30.0 + - - +
232B LEU 2.9 0.4 - - - -
233B ILE* 1.3 81.7 - - - +
235B ALA* 1.3 64.4 + - - +
237B ILE* 3.1 7.9 + - - +
238B ILE* 2.9 17.8 + - - +
247B ALA* 5.2 2.0 - - - -
248B ASP* 3.0 48.6 + - - +
251B CYS* 4.3 6.7 - - - -
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Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ALA* 4.4 3.1 - - - +
178B MET* 4.4 23.3 - - + +
179B ILE* 3.7 26.9 - - + -
231B VAL 2.3 30.6 + - - +
232B LEU* 2.6 13.1 + - - +
234B SER* 1.3 66.6 + - - +
236B LEU* 1.3 53.4 + - - +
238B ILE* 2.7 10.7 + - - +
239B TYR* 2.7 34.1 + - - +
248B ASP* 5.2 0.7 - - - -
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Residues in contact with LEU 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ILE* 3.5 33.4 - - + -
232B LEU* 2.9 34.5 + - + +
233B ILE* 4.4 8.1 - - + +
235B ALA* 1.3 74.6 - - - +
237B ILE* 1.3 62.1 + - + +
239B TYR* 3.2 1.0 + - - +
240B PHE* 2.7 61.8 + - + +
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Residues in contact with ILE 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B ILE* 3.1 23.1 - - + +
234B SER* 3.1 8.8 + - - +
236B LEU* 1.3 82.4 - - + +
238B ILE* 1.3 62.8 + - - +
240B PHE* 4.9 5.6 - - + -
241B LYS* 3.3 24.3 + - + +
244B TYR* 5.2 11.7 - - + +
247B ALA* 4.0 27.4 - - + -
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Residues in contact with ILE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B TYR* 6.0 0.7 - - - +
173B ILE* 5.0 10.5 - - + +
175B ALA* 3.5 20.0 - - + -
234B SER 2.9 6.6 + - - +
235B ALA* 2.7 11.6 + - - +
237B ILE* 1.3 76.8 - - - +
239B TYR* 1.3 66.2 + - - +
241B LYS 4.6 0.7 - - - +
242B PRO* 2.9 38.3 - - + +
244B TYR* 5.5 0.7 - - + -
245B LYS* 3.5 42.2 - - + +
247B ALA* 5.3 3.8 - - + +
248B ASP* 3.2 33.7 - - - +
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Residues in contact with TYR 239 (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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175B ALA* 3.2 29.6 - - + +
176B THR* 3.5 30.7 - - + -
179B ILE* 4.4 10.1 - - + -
235B ALA 2.7 14.3 + - - +
236B LEU 3.8 0.7 - - - +
238B ILE* 1.3 75.9 - - - +
240B PHE* 1.3 110.6 + + - +
241B LYS 3.2 1.0 + - - -
242B PRO* 3.4 13.4 - - - +
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Residues in contact with PHE 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LEU* 2.7 52.3 + - + +
237B ILE* 4.8 5.6 - - + +
239B TYR* 1.3 108.5 - + - +
241B LYS* 1.3 67.1 + - + +
242B PRO* 4.1 0.9 - - - -
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Residues in contact with LYS 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B ILE* 3.3 15.5 + - + +
238B ILE* 3.2 4.3 + - - -
239B TYR 3.2 0.6 - - - -
240B PHE* 1.3 84.1 - - - +
242B PRO* 1.3 63.2 - - + +
243B GLU* 2.8 33.1 + - + +
244B TYR* 3.0 44.4 + - + +
245B LYS 4.6 0.5 + - - -
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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