Contacts of the helix formed by residues 215 - 237 (chain B) in PDB entry 2PID
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 215 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A GLY 3.8 7.6 - - - -
191A GLY* 3.9 9.4 - - - -
193A PHE 3.2 11.0 - - - -
194A ARG* 3.4 22.4 - - - +
195A MET* 3.6 1.7 - - - +
128B GLU* 4.1 4.6 - - - -
214B MET* 1.3 80.7 - - - +
216B LEU* 1.3 64.9 + - - +
217B ALA* 3.4 6.8 + - - +
218B GLU* 2.8 38.1 + - - +
219B PHE* 3.2 17.8 + - - +
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Residues in contact with LEU 216 (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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185A PHE* 5.5 1.3 - - + -
186A LEU* 4.8 5.4 - - + -
190A GLY* 3.3 16.4 + - - +
193A PHE* 2.9 30.8 + - + -
195A MET* 4.1 16.5 - - - +
198A LEU* 4.1 16.2 - - + -
216A LEU* 6.3 0.2 - - + -
219A PHE* 4.3 10.3 - - + -
220A PHE* 3.8 34.1 - - + -
223A VAL* 3.9 26.7 - - + -
215B SER* 1.3 74.3 - - - +
217B ALA* 1.3 58.5 + - - +
219B PHE* 3.2 9.5 + - + +
220B PHE* 2.9 29.9 + - + +
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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
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186A LEU* 3.7 18.8 - - - +
190A GLY* 3.3 23.4 + - - -
191A GLY* 4.0 3.1 - - - +
119B LEU* 3.7 30.5 - - + +
215B SER* 3.2 4.4 - - - +
216B LEU* 1.3 82.3 - - - +
218B GLU* 1.3 63.0 + - + +
220B PHE* 3.4 5.7 + - - +
221B TYR* 3.1 18.5 + - - +
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Residues in contact with GLU 218 (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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119B LEU 5.9 2.2 - - - +
120B GLY 4.6 8.1 - - - +
122B PRO* 3.3 42.9 - - + +
125B ARG* 5.7 0.7 + - - -
127B LYS 4.6 1.0 - - - +
128B GLU* 3.1 34.1 - - + +
129B ARG* 4.5 7.1 + - + +
204B VAL* 5.9 0.7 - - - +
207B ARG* 2.8 33.5 + - - -
214B MET* 3.5 8.9 - - + +
215B SER* 2.8 35.7 + - - +
217B ALA* 1.3 78.4 - - + +
219B PHE* 1.3 62.9 + - - +
221B TYR* 3.4 11.0 - - - +
222B GLN* 4.5 1.2 + - - +
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Residues in contact with PHE 219 (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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195A MET* 3.4 34.8 - - + -
216A LEU* 4.1 20.9 - - + -
219A PHE* 4.4 3.1 - + - -
195B MET* 3.5 31.2 - - + -
198B LEU* 3.9 22.7 - - + -
199B LEU* 3.4 23.3 - - + -
204B VAL* 4.3 10.8 - - + -
214B MET* 3.9 12.3 - - - +
215B SER 3.2 13.3 + - - +
216B LEU* 3.4 16.2 - - + +
218B GLU* 1.3 78.7 - - - +
220B PHE* 1.3 66.7 + + - +
221B TYR 3.4 0.5 + - - -
222B GLN* 3.3 41.8 + - - +
223B VAL* 4.6 1.2 - - + +
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Residues in contact with PHE 220 (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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182A LEU* 4.1 6.7 - - + -
186A LEU* 3.4 36.6 - - + -
216A LEU* 3.8 28.5 - - + -
220A PHE* 3.8 36.1 - + - -
119B LEU* 4.9 0.9 - - + -
185B PHE* 4.0 16.2 - + - -
186B LEU* 4.0 14.6 - - + -
216B LEU* 2.9 20.6 + - + +
217B ALA 3.8 5.2 - - - +
218B GLU 3.3 0.2 - - - -
219B PHE* 1.3 76.7 - + - +
221B TYR* 1.3 66.9 + - - +
222B GLN 3.2 0.4 - - - -
223B VAL* 2.8 42.0 + - + +
224B LEU* 3.3 13.5 + - + +
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Residues in contact with TYR 221 (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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81B ASP* 2.5 24.1 + - - -
116B THR* 3.4 36.5 - - + -
119B LEU* 4.2 12.3 - - + +
120B GLY 3.2 21.3 - - - +
121B ASP* 3.2 36.6 - - + +
122B PRO* 3.8 6.7 - - + -
217B ALA 3.1 11.8 + - - +
218B GLU 3.4 14.6 - - - +
219B PHE 3.2 0.8 - - - -
220B PHE* 1.3 75.4 - - - +
222B GLN* 1.3 68.8 + - - +
224B LEU* 3.0 17.6 + - - +
225B GLN* 3.1 22.5 + - + -
250B ASN* 4.2 3.1 - - - -
384B YSA 2.8 32.3 + - - +
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Residues in contact with GLN 222 (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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122B PRO* 5.7 0.2 - - - +
198B LEU* 3.2 38.3 + - + +
201B ARG* 3.4 18.5 - - - +
204B VAL* 3.3 21.5 - - + +
218B GLU 4.5 1.2 + - - +
219B PHE* 3.3 31.9 + - - +
221B TYR* 1.3 81.1 - - - +
223B VAL* 1.3 61.7 + - + +
224B LEU 3.3 0.2 - - - -
225B GLN* 3.8 2.6 - - - +
226B ALA* 3.0 29.1 + - - +
249B GLY 5.6 0.2 - - - -
250B ASN* 3.4 27.4 - - - +
253B SER* 3.1 26.5 + - - +
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Residues in contact with VAL 223 (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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216A LEU* 3.7 26.9 - - + -
185B PHE* 4.0 11.7 - - + -
193B PHE* 3.8 27.2 - - + -
198B LEU* 4.2 20.0 - - + -
219B PHE* 4.6 1.8 - - + +
220B PHE* 2.8 44.7 + - + +
222B GLN* 1.3 79.7 - - + +
224B LEU* 1.3 59.5 + - - +
226B ALA* 3.4 6.4 + - - +
227B TYR* 2.9 27.5 + - - +
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Residues in contact with LEU 224 (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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182A LEU* 3.8 20.0 - - + -
183A VAL* 4.2 18.8 - - + -
186A LEU* 4.7 2.9 - - + -
116B THR* 3.7 26.5 - - + +
119B LEU* 4.0 27.4 - - + -
177B TYR* 2.7 46.4 + - + +
185B PHE* 4.7 2.7 - - + -
220B PHE* 3.3 23.8 + - + +
221B TYR* 3.0 9.6 + - - +
223B VAL* 1.3 79.5 - - - +
225B GLN* 1.3 57.4 + - - +
227B TYR* 3.1 0.6 + - - -
228B ASP* 2.8 22.5 + - - -
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Residues in contact with GLN 225 (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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77B TYR* 3.5 2.8 + - - -
116B THR* 4.7 1.0 - - - +
221B TYR* 3.1 19.1 + - + +
222B GLN* 4.0 6.1 - - - +
224B LEU* 1.3 76.0 - - - +
226B ALA* 1.3 63.3 + - - +
228B ASP* 3.4 4.1 + - - +
229B PHE* 3.2 18.5 + - - +
241B GLN* 2.9 26.4 + - - +
247B GLN* 2.9 20.8 + - - +
250B ASN* 3.3 34.1 + - + +
251B ILE* 4.3 5.5 - - - +
384B YSA 2.8 60.6 + - + -
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Residues in contact with ALA 226 (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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193B PHE* 3.7 23.1 - - + -
222B GLN 3.0 19.3 + - - +
223B VAL 3.6 4.5 - - - +
224B LEU 3.2 0.2 - - - -
225B GLN* 1.3 77.6 - - - +
227B TYR* 1.3 62.2 + - - +
229B PHE* 3.2 6.6 + - - +
230B TYR* 3.2 18.5 + - - +
250B ASN 4.7 1.1 + - - -
253B SER* 3.8 6.1 - - - -
254B GLY* 3.7 34.2 - - - +
257B PHE* 4.2 5.4 - - + -
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Residues in contact with TYR 227 (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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176B TRP* 4.2 15.0 - + + -
177B TYR* 3.5 27.6 - + - +
180B GLN* 4.2 19.3 + - + -
185B PHE* 3.7 31.9 - + + -
189B VAL* 4.2 16.6 - - + -
193B PHE* 4.6 2.4 - - + -
223B VAL 2.9 18.1 + - - +
226B ALA* 1.3 75.0 - - - +
228B ASP* 1.3 54.2 + - - +
230B TYR* 3.1 34.2 + + - +
231B TYR* 2.7 54.4 + + + +
257B PHE* 4.3 11.4 - + - -
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Residues in contact with ASP 228 (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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77B TYR* 3.8 2.2 - - - +
111B LEU* 3.5 9.3 - - + +
116B THR* 4.5 0.2 - - - +
173B ASN* 2.9 27.5 + - - +
176B TRP* 3.0 25.3 + - + +
177B TYR* 3.0 22.5 + - - -
224B LEU 2.8 14.8 + - - +
225B GLN* 3.4 4.8 - - - +
227B TYR* 1.3 77.1 - - - +
229B PHE* 1.3 56.2 + - - +
231B TYR* 3.2 2.3 + - - +
232B LEU* 2.9 35.6 + - - +
384B YSA 2.5 33.9 + - - +
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Residues in contact with PHE 229 (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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77B TYR* 3.6 18.1 + + - +
225B GLN 3.2 9.2 + - - +
226B ALA 3.4 10.5 - - - +
227B TYR 3.2 0.2 - - - -
228B ASP* 1.3 79.4 - - - +
230B TYR* 1.3 57.6 + - - +
232B LEU* 3.2 1.4 + - - -
233B PHE* 2.8 27.5 + - - +
238B CYS* 3.9 21.8 - - - -
239B ARG 4.0 1.6 - - - -
240B VAL 3.8 13.2 - - - -
241B GLN* 3.2 33.9 - - + +
251B ILE* 4.3 11.0 - - + -
254B GLY* 4.0 18.4 - - - -
255B TYR* 4.2 1.6 - - + -
258B ILE* 3.7 13.7 - - + -
266B VAL* 3.8 24.2 - - + -
267B PHE 3.5 23.1 - - - -
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Residues in contact with TYR 230 (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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189B VAL* 5.3 3.8 - - + -
226B ALA 3.2 1.8 + - - +
227B TYR* 3.1 37.6 + + - +
229B PHE* 1.3 77.0 - - - +
231B TYR* 1.3 60.4 + - - +
233B PHE* 3.2 3.8 + + - +
234B GLN* 2.9 74.4 + - + +
257B PHE* 3.6 32.3 - + + -
258B ILE* 3.7 23.8 - - + +
261B LEU* 4.1 24.4 - - + +
262B THR* 4.2 15.9 - - + -
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Residues in contact with TYR 231 (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* 5.8 0.2 - - - +
176B TRP* 3.1 68.4 - + + +
227B TYR* 2.7 42.0 + - + +
228B ASP* 3.2 5.6 + - - +
230B TYR* 1.3 78.5 - - - +
232B LEU* 1.3 70.9 + - + +
234B GLN* 3.8 4.4 - - - +
235B ARG* 2.8 74.2 + - + +
236B TYR* 4.4 2.9 + + - -
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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
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77B TYR* 3.5 50.3 - - + -
109B ILE* 4.4 9.4 - - + -
111B LEU* 4.5 9.0 - - + -
171B LEU* 4.0 13.2 - - + -
176B TRP* 4.0 6.7 - - + -
228B ASP 2.9 20.7 + - - +
229B PHE 3.9 2.7 - - - +
231B TYR* 1.3 83.8 - - + +
233B PHE* 1.3 62.1 + - - +
236B TYR* 2.8 56.8 + - + +
237B GLY 3.3 3.8 + - - -
238B CYS* 3.3 20.2 + - + -
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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
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229B PHE* 2.8 18.6 + - + +
230B TYR* 3.5 6.7 - + - +
232B LEU* 1.3 77.4 - - - +
234B GLN* 1.3 79.7 + - + +
237B GLY* 2.8 30.4 + - - -
238B CYS 3.2 26.6 + - - +
239B ARG* 3.4 36.1 - - + -
258B ILE* 4.2 16.6 - - + -
262B THR* 4.4 12.1 - - + -
264B GLU* 3.2 37.2 - - + -
266B VAL* 3.9 13.5 - - + -
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Residues in contact with GLN 234 (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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230B TYR* 2.9 65.7 + - + +
231B TYR* 3.8 4.5 - - - +
233B PHE* 1.3 96.6 - - + +
235B ARG* 1.3 62.5 + - - +
237B GLY 4.3 0.9 + - - -
262B THR* 4.6 7.2 - - - +
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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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231B TYR* 2.8 66.0 + - + +
234B GLN* 1.3 76.7 - - - +
236B TYR* 1.3 93.9 + - + +
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Residues in contact with TYR 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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75B THR* 4.0 14.7 + - + -
109B ILE* 4.3 18.4 - - + -
169B THR* 6.3 1.6 - - + -
171B LEU* 3.6 37.3 - - + +
176B TRP* 6.0 0.2 - - - -
231B TYR* 4.4 3.8 - + - -
232B LEU* 2.8 36.8 + - + +
235B ARG* 1.3 120.2 + - + +
237B GLY* 1.3 64.9 + - - +
238B CYS* 3.4 2.6 + - + +
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Residues in contact with GLY 237 (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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74B GLN* 5.2 2.1 - - - +
75B THR* 4.1 8.9 + - - -
233B PHE* 2.8 24.0 + - - -
234B GLN 4.3 1.2 + - - -
235B ARG 3.6 1.4 - - - -
236B TYR* 1.3 79.0 - - - +
238B CYS* 1.3 63.6 + - - +
239B ARG* 3.3 12.7 + - - +
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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
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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