Contacts of the helix formed by residues 230 - 254 (chain B) in PDB entry 2QVS
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 230 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ALA* 5.0 1.3 - - + -
99B GLU* 2.5 37.0 + - + +
169B GLY 3.2 17.6 + - - -
170B ASP* 2.9 35.2 + - - +
206B ALA 2.6 38.9 + - - +
207B LEU* 3.6 21.9 - - - +
208B MET 3.7 26.2 - - - -
209B TYR 3.9 5.1 + - - -
210B ASN* 3.4 26.9 - - - +
228B LEU 3.7 1.0 + - - -
229B ASP* 1.3 72.3 + - - +
231B VAL* 1.3 60.5 + - + +
233B PHE* 2.9 4.2 + - - +
234B ARG* 2.7 39.3 + - + +
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Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLU* 3.6 37.2 - - + +
229B ASP* 3.4 15.0 + - - +
230B ARG* 1.3 81.9 - - + +
232B THR* 1.3 61.9 + - - +
234B ARG* 4.2 4.0 - - - +
235B ARG* 2.9 53.7 + - + +
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Residues in contact with THR 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B VAL* 4.3 18.3 - - + +
150B ALA* 3.7 32.1 - - + +
228B LEU* 4.5 4.5 - - + -
229B ASP* 2.8 36.4 + - - +
231B VAL* 1.3 75.0 - - - +
233B PHE* 1.3 63.7 + - - +
235B ARG* 3.9 4.2 - - - +
236B ILE* 3.0 29.9 + - + +
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Residues in contact with PHE 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 4.0 33.9 - - + -
136B PHE* 4.2 17.5 - + - -
139B LEU* 4.7 5.2 - - + -
147B VAL* 4.0 16.6 - - + -
207B LEU* 3.7 38.6 - - + -
228B LEU* 3.6 32.3 - - + +
229B ASP 2.9 11.3 + - - +
230B ARG 2.9 7.6 + - - +
232B THR* 1.3 76.2 - - - +
234B ARG* 1.3 76.3 + - + +
236B ILE* 3.4 5.6 + - - +
237B ILE* 3.3 45.5 + - + +
212E SER* 5.7 3.1 - - - -
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Residues in contact with ARG 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ALA* 3.6 21.0 - - - +
99B GLU* 4.4 10.2 + - + +
101B PHE* 5.6 0.4 - - - -
207B LEU 3.6 23.8 - - - +
208B MET 4.4 3.1 - - - -
230B ARG* 2.7 30.1 + - + +
231B VAL* 4.2 4.5 - - - +
233B PHE* 1.3 80.8 - - + +
235B ARG* 1.3 60.4 + - + +
237B ILE* 3.2 4.9 + - - +
238B VAL* 2.9 42.9 + - + +
196E TRP 3.7 12.3 + - - -
197E TPO 4.0 2.8 - - - -
198E LEU* 3.0 51.9 - - - +
209E ILE 4.8 1.2 + - - -
212E SER* 3.0 31.7 + - - +
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Residues in contact with ARG 235 (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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101B PHE* 3.5 50.5 - - + -
106B GLU* 3.1 25.9 + - - +
231B VAL* 2.9 45.7 + - + +
232B THR* 3.9 4.7 - - - +
234B ARG* 1.3 76.9 - - + +
236B ILE* 1.3 61.9 + - - +
239B LYS* 3.1 45.7 + - - +
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Residues in contact with ILE 236 (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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114B VAL* 5.6 4.3 - - + -
143B GLN* 4.4 3.8 - - - +
146B GLN* 3.4 60.1 + - + +
147B VAL* 3.9 21.8 - - + -
150B ALA* 3.6 21.8 - - + -
228B LEU* 5.7 0.2 - - + -
232B THR* 3.0 25.0 + - + +
233B PHE* 3.8 5.4 - - - +
235B ARG* 1.3 76.7 - - + +
237B ILE* 1.3 63.8 + - + +
239B LYS* 3.9 4.4 - - - +
240B ASN* 3.1 27.1 + - + +
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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
----------------------------------------------------------
139B LEU* 3.7 24.7 - - + -
143B GLN* 3.6 29.5 - - + +
147B VAL* 4.0 17.0 - - + -
233B PHE* 3.3 38.3 + - + +
234B ARG* 3.2 5.1 + - - +
236B ILE* 1.3 75.2 - - + +
238B VAL* 1.3 61.3 + - - +
240B ASN 3.3 0.5 + - - -
241B ASN* 2.9 48.1 + - - +
211E LEU 4.5 3.6 - - - +
212E SER* 3.9 20.0 - - - +
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Residues in contact with VAL 238 (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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101B PHE* 3.9 15.9 - - + -
103B PRO* 3.6 30.3 - - + -
234B ARG* 2.9 38.1 + - + +
237B ILE* 1.3 71.4 - - - +
239B LYS* 1.3 59.6 + - - +
241B ASN* 3.1 2.3 + - - +
242B ALA* 2.8 28.9 + - - +
196E TRP* 3.6 41.1 - - + +
212E SER* 4.4 15.0 - - - -
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Residues in contact with LYS 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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101B PHE* 3.0 27.5 - - + -
103B PRO 4.0 17.6 - - - +
105B GLU* 4.6 17.0 + - + +
106B GLU* 3.3 35.0 + - - +
108B GLU* 5.6 4.5 - - - +
235B ARG* 3.1 37.2 + - - +
236B ILE* 3.9 4.5 - - - +
238B VAL* 1.3 79.0 - - - +
240B ASN* 1.3 57.4 + - - +
242B ALA* 3.4 1.9 + - - +
243B LYS* 3.0 36.3 + - - +
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Residues in contact with ASN 240 (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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140B ASP* 3.9 5.7 - - - +
142B GLU* 4.1 15.6 - - - +
143B GLN* 3.3 33.3 - - + +
146B GLN* 3.9 21.8 + - - +
236B ILE* 3.1 17.6 + - + +
237B ILE 3.7 2.9 - - - +
239B LYS* 1.3 81.3 - - - +
241B ASN* 1.3 58.2 + - - +
243B LYS* 3.3 9.2 + - - +
244B LYS* 3.0 34.0 + - - +
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Residues in contact with ASN 241 (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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139B LEU* 5.9 0.8 - - - +
143B GLN* 3.2 25.1 + - - +
237B ILE* 2.9 30.9 + - - +
240B ASN* 1.3 76.1 - - - +
242B ALA* 1.3 57.6 + - - +
244B LYS* 3.6 17.8 + - - +
245B ARG* 2.9 32.2 + - - +
196E TRP* 3.6 19.1 - - + -
211E LEU 4.5 0.8 + - - -
212E SER 2.9 25.0 + - - +
213E LYS* 4.1 22.7 + - - +
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Residues in contact with ALA 242 (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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103B PRO* 4.0 22.7 - - + +
104B ASP* 4.7 9.9 - - - +
105B GLU 5.8 0.2 - - - +
238B VAL 2.8 16.6 + - - +
239B LYS 3.8 3.8 - - - +
241B ASN* 1.3 74.5 - - - +
243B LYS* 1.3 63.2 + - - +
245B ARG* 3.8 4.4 - - - +
246B LYS* 3.3 21.3 + - - +
196E TRP* 3.4 28.2 - - + +
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Residues in contact with LYS 243 (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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105B GLU* 2.9 40.3 + - - +
108B GLU* 3.3 22.4 + - - -
239B LYS* 3.0 24.3 + - - +
240B ASN* 3.6 10.8 - - - +
241B ASN 3.2 0.2 - - - -
242B ALA* 1.3 76.7 - - - +
244B LYS* 1.3 64.4 + - - +
246B LYS* 3.3 9.4 + - + +
247B MET* 3.0 24.0 + - + +
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Residues in contact with LYS 244 (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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140B ASP* 2.8 31.5 + - - +
143B GLN* 4.1 2.4 - - - +
240B ASN* 3.0 25.4 + - - +
241B ASN* 3.6 20.4 + - - +
243B LYS* 1.3 77.5 - - - +
245B ARG* 1.3 55.5 + - + +
247B MET* 3.2 14.7 + - + +
248B PHE* 2.8 69.2 + - + -
275B GLU* 4.6 9.4 + - - +
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Residues in contact with ARG 245 (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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241B ASN 2.9 14.3 + - - +
242B ALA* 3.8 5.6 - - - +
244B LYS* 1.3 77.0 - - + +
246B LYS* 1.3 57.7 + - - +
248B PHE* 3.7 2.9 - - + +
249B GLU* 2.8 31.3 + - - +
267B MET* 4.3 9.9 + - + +
270B VAL* 3.8 30.5 - - + +
271B ASP* 2.6 37.7 + - - +
194E ARG* 3.4 27.0 - - - +
196E TRP* 3.6 27.9 - - - -
213E LYS* 2.9 30.7 + - - +
214E GLY* 3.4 17.4 + - - -
277E LEU* 6.2 0.2 - - - +
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Residues in contact with LYS 246 (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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104B ASP* 5.1 14.6 + - - +
105B GLU* 3.1 26.1 + - - +
242B ALA 3.3 11.9 + - - +
243B LYS* 3.3 11.8 + - + +
245B ARG* 1.3 79.6 - - - +
247B MET* 1.3 57.3 + - - +
249B GLU* 3.4 8.7 - - + +
250B SER* 3.1 26.7 + - - -
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Residues in contact with MET 247 (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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243B LYS* 3.0 14.7 + - + +
244B LYS* 3.4 15.9 - - + +
246B LYS* 1.3 76.4 - - - +
248B PHE* 1.3 73.4 + - + +
250B SER* 3.4 7.1 + - - -
251B PHE* 3.3 48.4 + - + -
275B GLU* 4.5 7.0 - - - +
298B GLU* 3.6 26.2 - - - +
354B LYS* 5.3 6.5 - - + +
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Residues in contact with PHE 248 (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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244B LYS* 2.8 52.7 + - + +
245B ARG* 3.7 4.7 - - + +
247B MET* 1.3 81.0 - - + +
249B GLU* 1.3 63.5 + - - +
251B PHE* 3.2 11.1 + - - +
252B ILE* 3.1 22.8 + - + +
270B VAL* 3.7 27.1 - - + -
273B ILE* 3.7 32.8 - - + -
275B GLU* 3.4 38.1 - - + -
298B GLU* 4.4 2.2 - - - -
356B LEU* 3.3 31.4 - - + -
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Residues in contact with GLU 249 (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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245B ARG 2.8 18.3 + - - +
246B LYS* 3.4 11.7 - - + +
248B PHE* 1.3 77.4 - - - +
250B SER* 1.3 56.5 + - - +
252B ILE* 3.3 2.9 + - - +
253B GLU* 3.0 32.1 + - + +
263B MET* 4.5 9.4 - - - +
266B ARG* 2.7 56.8 + - - +
267B MET* 4.4 13.3 + - + +
270B VAL* 3.5 16.0 - - + +
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Residues in contact with SER 250 (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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246B LYS 3.1 13.8 + - - -
247B MET* 3.6 11.7 - - - -
248B PHE 3.2 0.2 - - - -
249B GLU* 1.3 78.5 - - - +
251B PHE* 1.3 59.2 + - - +
253B GLU* 3.2 6.5 + - - +
254B SER* 3.0 32.8 + - - -
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Residues in contact with PHE 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B MET* 3.3 40.9 + - + -
248B PHE 3.2 7.8 + - - +
250B SER* 1.3 81.3 - - - +
252B ILE* 1.3 59.3 + - - +
254B SER* 3.6 9.5 + - - -
255B VAL* 2.9 25.5 - - - +
296B ILE* 3.9 10.3 - - + +
297B ILE 3.8 12.6 - - - -
298B GLU* 3.4 46.9 - - + -
328B LYS* 4.3 16.4 - - + -
329B GLY* 4.0 20.1 - - - +
356B LEU* 3.8 20.0 - - + -
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Residues in contact with ILE 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B PHE* 3.1 20.4 - - + +
249B GLU* 3.7 8.1 - - - +
250B SER 3.1 0.4 - - - -
251B PHE* 1.3 75.9 - - - +
253B GLU* 1.3 66.7 + - - +
255B VAL* 3.2 24.9 + - - +
258B PHE* 3.8 29.1 - - + +
261B LEU* 4.6 4.7 - - + -
266B ARG* 4.3 23.8 - - + -
269B ILE* 4.4 14.1 - - + -
270B VAL* 4.6 10.3 - - + -
273B ILE* 4.0 22.2 - - + -
294B PHE* 6.0 0.4 - - + -
296B ILE* 3.6 23.8 - - + -
356B LEU* 4.6 4.9 - - + -
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Residues in contact with GLU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B GLU* 3.0 20.7 + - + +
250B SER* 3.2 8.0 + - - +
252B ILE* 1.3 78.7 - - - +
254B SER* 1.3 63.8 + - - +
255B VAL 3.1 2.1 + - - +
258B PHE* 5.9 1.3 - - - -
259B LYS* 3.3 32.8 - - - +
266B ARG* 4.0 33.7 + - - +
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Residues in contact with SER 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B SER* 3.0 17.4 + - - -
251B PHE* 3.6 15.4 + - - -
253B GLU* 1.3 78.2 + - - +
255B VAL* 1.3 62.0 + - - +
256B PRO* 3.1 14.0 - - - +
259B LYS* 4.5 7.8 - - - +
329B GLY* 4.8 8.7 + - - +
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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