Contacts of the helix formed by residues 213 - 241 (chain B) in PDB entry 3F9C
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 GLU 213 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ARG* 4.4 11.5 + - - -
208B THR 4.5 1.0 - - - +
209B LEU* 3.4 13.9 - - + +
210B LYS* 2.7 60.9 + - + +
212B GLU* 1.3 84.8 - - + +
214B GLU* 1.3 64.4 + - - +
215B THR 3.4 2.9 - - - -
216B HIS* 3.4 9.3 + - + +
217B ILE* 2.8 51.7 + - + +
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Residues in contact with GLU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B LEU* 3.9 22.5 + - + +
210B LYS 3.9 3.8 - - - +
211B GLN* 3.2 32.8 + - + +
213B GLU* 1.3 78.4 - - - +
215B THR* 1.3 58.1 + - - +
218B ARG* 2.9 77.7 + - - +
298B TRP* 4.5 5.2 - - - -
300B PHE* 3.8 18.4 - - + -
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Residues in contact with THR 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B GLN 4.8 1.0 + - - -
212B GLU 5.2 2.8 - - - -
213B GLU 3.4 0.6 - - - -
214B GLU* 1.3 77.9 - - - +
216B HIS* 1.3 63.6 + - + +
218B ARG* 4.6 1.0 - - - +
219B ASN* 3.6 19.2 + - - +
300B PHE* 3.8 27.1 - - + +
301B PRO 5.2 0.3 - - - +
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Residues in contact with HIS 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLU 5.9 0.4 - - - +
213B GLU* 3.4 11.9 + - + +
214B GLU 3.3 0.2 - - - -
215B THR* 1.3 79.2 - - + +
217B ILE* 1.3 81.5 + - + +
219B ASN* 3.2 5.6 + - - +
220B GLU* 3.0 47.8 + - + +
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Residues in contact with ILE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B ARG* 4.9 11.0 - - - +
209B LEU* 3.7 31.6 - - + -
213B GLU* 2.8 48.0 + - + +
216B HIS* 1.3 88.8 - - + +
218B ARG* 1.3 63.3 + - - +
220B GLU* 3.1 8.6 + - + +
221B GLN* 2.9 39.8 + - + +
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Residues in contact with ARG 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 3.4 41.3 - - - +
183B SER* 5.1 0.2 - - - +
206B LEU* 6.1 0.2 - - - +
207B ARG 4.9 7.5 + - - -
209B LEU* 3.5 22.4 - - - +
214B GLU* 2.9 57.5 + - - +
215B THR 4.6 0.9 - - - +
217B ILE* 1.3 72.4 - - - +
219B ASN* 1.3 57.6 + - - +
221B GLN* 2.9 30.6 + - - +
222B VAL 3.0 22.9 + - - -
274B PHE* 3.8 9.4 - - - -
298B TRP* 3.7 19.6 - - + -
300B PHE* 3.8 12.3 - - + -
301B PRO* 3.6 30.1 - - + +
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Residues in contact with ASN 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B THR 3.6 16.1 + - - +
216B HIS* 3.2 5.9 + - - +
217B ILE 3.2 0.8 - - - -
218B ARG* 1.3 76.4 - - - +
220B GLU* 1.3 68.0 + - - +
222B VAL* 3.4 7.6 - - - +
223B ARG* 2.7 59.6 + - - +
281B GLN* 5.1 0.6 + - - -
301B PRO 2.7 25.4 + - - +
302B LEU* 3.6 1.6 - - - +
303B GLY* 3.1 26.5 - - - +
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Residues in contact with GLU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B HIS* 3.0 36.7 + - - +
217B ILE* 3.5 11.9 - - + +
219B ASN* 1.3 79.1 + - - +
221B GLN* 1.3 55.0 + - + +
223B ARG* 3.3 21.2 + - - +
224B GLN* 2.9 27.8 + - - +
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Residues in contact with GLN 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B ASP* 2.9 47.2 + - + +
182B ARG* 3.8 18.6 + - - +
183B SER* 3.8 1.6 - - - +
207B ARG* 5.2 5.3 - - - +
209B LEU* 5.3 1.0 - - - +
217B ILE* 2.9 33.3 + - + +
218B ARG* 2.9 45.7 + - - +
220B GLU* 1.3 76.4 - - + +
222B VAL* 1.3 51.0 + - - +
224B GLN* 3.3 4.4 + - - +
225B ARG* 2.8 38.3 + - - +
274B PHE* 3.6 9.6 - - + -
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Residues in contact with VAL 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ARG 3.0 13.4 + - - +
219B ASN* 3.4 16.4 + - - +
221B GLN* 1.3 72.1 - - - +
223B ARG* 1.3 61.8 + - + +
225B ARG* 3.7 6.4 - - - +
226B ALA* 3.0 27.9 + - - +
274B PHE* 3.9 5.0 - - + -
277B ALA* 3.7 39.5 - - + +
278B THR* 3.9 12.3 - - - +
281B GLN* 3.8 23.2 - - + +
301B PRO* 3.8 22.7 - - + +
302B LEU* 4.0 9.2 - - + -
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Residues in contact with ARG 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B ASN* 2.7 43.3 + - - +
220B GLU* 3.5 23.9 + - - +
222B VAL* 1.3 72.7 - - + +
224B GLN* 1.3 65.4 + - - +
226B ALA* 3.3 6.6 + - - +
227B LYS* 2.9 24.5 + - - +
281B GLN* 3.1 33.5 - - - +
285B GLU* 3.9 12.8 + - - +
303B GLY* 5.0 0.4 - - - -
305B GLU* 2.6 34.7 + - - -
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Residues in contact with GLN 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ASN 5.0 3.8 + - - -
180B ARG* 3.6 19.3 + - - +
181B ASP* 3.7 21.5 - - + +
220B GLU 2.9 16.9 + - - +
221B GLN* 3.3 8.6 + - - +
223B ARG* 1.3 71.6 - - - +
225B ARG* 1.3 51.8 + - - +
227B LYS* 3.2 12.5 + - + +
228B GLU* 2.8 67.0 + - + +
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Residues in contact with ARG 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B SER* 3.2 11.3 + - - -
151B HIS* 2.9 43.4 + - - -
152B GLY 3.7 5.5 + - - -
179B HIS* 3.6 24.7 - - + +
181B ASP* 2.9 27.8 + - - +
183B SER* 2.9 20.0 + - - -
221B GLN 2.8 22.9 + - - +
222B VAL* 3.7 4.5 - - - +
224B GLN* 1.3 73.4 - - - +
226B ALA* 1.3 55.9 + - - +
228B GLU* 3.1 3.4 + - - +
229B CYS* 2.9 31.5 + - - -
274B PHE* 3.3 40.7 + - - +
278B THR* 3.0 35.6 + - - +
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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
----------------------------------------------------------
222B VAL 3.0 18.2 + - - +
223B ARG 3.3 2.2 + - - +
225B ARG* 1.3 72.1 - - - +
227B LYS* 1.3 67.1 + - - +
229B CYS* 3.1 3.3 + - - +
230B SER* 3.0 27.2 + - - +
278B THR* 4.2 1.4 - - - +
281B GLN* 3.7 22.0 - - + -
282B THR* 3.3 29.8 + - - +
285B GLU* 3.7 17.3 - - + +
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Residues in contact with LYS 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LYS* 5.1 6.7 + - - +
223B ARG 2.9 14.8 + - - +
224B GLN* 3.3 15.0 - - + +
226B ALA* 1.3 75.5 - - - +
228B GLU* 1.3 60.8 + - + +
230B SER* 3.3 6.0 + - - -
231B GLN* 2.9 49.8 + - + +
285B GLU* 4.5 5.1 + - - +
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Residues in contact with GLU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ASN 4.7 2.4 - - - +
78B GLY 5.1 7.0 - - - +
79B THR* 4.8 1.6 + - - +
177B VAL* 4.3 10.2 - - + +
178B GLU 5.0 1.6 - - - -
179B HIS* 3.0 36.0 + - + +
180B ARG* 3.3 30.4 + - - +
181B ASP 4.0 0.3 + - - -
224B GLN* 2.8 53.8 + - + +
225B ARG* 3.1 6.3 + - - +
227B LYS* 1.3 78.5 - - + +
229B CYS* 1.3 57.0 + - - +
231B GLN* 3.8 8.7 - - - +
232B ALA* 2.9 30.7 + - - +
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Residues in contact with CYS 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B VAL* 3.9 25.2 - - + +
150B SER* 4.2 10.5 - - - -
177B VAL* 4.6 3.1 - - - -
179B HIS* 4.2 10.8 - - - -
225B ARG 2.9 20.7 + - - -
226B ALA 3.8 0.2 - - - +
228B GLU* 1.3 73.0 - - - +
230B SER* 1.3 57.5 + - - +
232B ALA* 3.4 3.7 + - - +
233B LEU* 3.0 27.9 + - - +
269B VAL* 4.3 7.4 - - + -
278B THR* 3.6 23.1 - - - -
282B THR* 3.8 22.9 - - + +
289B PHE* 3.8 6.7 - - + -
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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 ALA 3.0 13.6 + - - -
227B LYS* 3.5 11.9 - - - -
229B CYS* 1.3 73.4 - - - +
231B GLN* 1.3 60.4 + - - +
233B LEU* 3.3 3.2 + - - +
234B SER* 2.8 26.3 + - - -
282B THR* 4.4 2.4 - - - +
285B GLU* 5.5 2.9 - - - +
286B ASP* 2.5 39.4 + - - +
288B ARG* 3.1 12.9 + - - +
289B PHE* 4.6 1.1 - - - -
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Residues in contact with GLN 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PHE 4.8 1.2 + - - -
77B LYS 3.2 22.4 + - - +
78B GLY* 3.2 4.8 + - - -
79B THR* 2.7 36.7 + - - +
227B LYS* 2.9 39.3 + - + +
228B GLU* 3.9 9.5 - - - +
230B SER* 1.3 69.1 - - - +
232B ALA* 1.3 60.8 + - - +
234B SER* 3.7 7.3 - - - -
235B LEU* 2.8 30.9 + - + +
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Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B THR* 3.8 22.5 + - + -
81B LEU* 4.2 6.1 - - + -
148B VAL* 4.7 5.4 - - + -
175B ALA* 5.5 0.4 - - + -
177B VAL* 3.3 34.3 - - + -
228B GLU 2.9 13.0 + - - +
229B CYS 3.6 4.3 - - - +
231B GLN* 1.3 75.9 - - - +
233B LEU* 1.3 58.0 + - - +
235B LEU* 3.5 2.0 + - - +
236B ILE* 3.0 37.3 + - + +
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Residues in contact with LEU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LEU* 3.4 29.8 - - + -
148B VAL* 4.5 5.7 - - + +
229B CYS 3.0 15.7 + - - +
230B SER 3.6 7.6 - - - +
232B ALA* 1.3 73.5 - - - +
234B SER* 1.3 66.4 + - - +
236B ILE* 3.3 3.9 + - - -
237B LEU* 3.0 47.5 + - + +
267B ILE* 3.7 24.2 - - + -
288B ARG* 3.8 32.3 - - + +
289B PHE* 3.5 31.6 - - + -
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Residues in contact with SER 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B SER 2.8 16.8 + - - -
231B GLN* 3.7 9.5 - - - -
233B LEU* 1.3 70.6 - - - +
235B LEU* 1.3 56.1 + - - +
237B LEU* 3.4 3.0 + - - +
238B ASP* 2.9 42.3 + - - +
288B ARG* 3.0 33.8 + - - +
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Residues in contact with LEU 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 3.9 24.5 - - + -
72B PHE* 3.6 40.8 - - + +
79B THR* 3.9 28.5 - - + +
81B LEU* 5.1 1.8 - - + -
231B GLN* 2.8 21.6 + - + +
232B ALA* 3.7 4.7 - - - +
234B SER* 1.3 72.1 - - - +
236B ILE* 1.3 62.6 + - - +
238B ASP* 3.3 5.6 + - - +
239B ILE* 3.1 34.3 + - + +
243B LYS* 4.5 9.2 - - + +
245B VAL* 3.8 17.9 - - + -
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Residues in contact with ILE 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 5.5 4.3 - - + -
81B LEU* 3.6 27.6 - - + -
83B LEU* 5.0 10.1 - - + -
146B LEU* 3.8 19.5 - - + -
148B VAL* 5.8 0.7 - - + -
173B ILE* 5.8 0.9 - - + -
175B ALA* 3.9 17.5 - - + -
232B ALA 3.0 31.9 + - - +
233B LEU* 3.3 4.5 + - - +
235B LEU* 1.3 78.3 - - + +
237B LEU* 1.3 58.0 + - - +
239B ILE* 3.5 11.7 + - + +
240B ASP* 3.0 25.5 + - - +
258B LEU* 5.7 12.4 - - + +
262B ILE* 3.7 32.9 - - + +
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Residues in contact with LEU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLU 5.6 2.0 - - - +
287A GLN* 6.6 0.2 - - + -
146B LEU* 5.2 0.7 - - + -
233B LEU* 3.0 39.0 + - + +
234B SER* 3.8 4.5 - - - +
236B ILE* 1.3 74.2 - - - +
238B ASP* 1.3 67.7 + - - +
240B ASP* 3.4 1.3 + - - -
241B HIS* 3.2 13.0 + - - +
262B ILE* 4.2 15.9 - - + -
264B ARG* 2.7 73.3 + - + +
267B ILE* 4.7 6.7 - - + -
288B ARG* 3.6 34.5 - - - +
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Residues in contact with ASP 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B SER* 2.9 27.9 + - - +
235B LEU* 3.3 7.1 + - - +
237B LEU* 1.3 76.9 - - - +
239B ILE* 1.3 55.1 + - - +
241B HIS* 3.3 13.6 + - - +
242B GLY 3.3 1.0 + - - -
243B LYS* 2.7 61.0 + - + +
264B ARG* 5.6 1.7 + - - -
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Residues in contact with ILE 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B LEU* 4.1 21.8 - - + -
235B LEU* 3.1 26.8 + - + +
236B ILE* 3.7 9.2 - - + +
238B ASP* 1.3 72.7 - - - +
240B ASP* 1.3 60.6 + - - +
241B HIS 3.1 1.1 - - - -
242B GLY* 3.0 17.2 + - - -
243B LYS* 3.9 13.4 - - + +
245B VAL* 3.7 36.3 - - + -
255B MET* 3.6 33.2 - - + +
256B GLU* 5.3 1.9 - - - -
258B LEU* 4.0 19.5 - - + -
259B LYS* 3.5 12.6 - - - +
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Residues in contact with ASP 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LYS* 3.8 5.7 + - - -
236B ILE 3.0 18.4 + - - +
237B LEU* 3.5 7.4 - - - +
239B ILE* 1.3 76.6 - - - +
241B HIS* 1.3 64.7 + - - +
242B GLY 3.3 2.1 + - - -
258B LEU* 3.6 10.3 - - - +
259B LYS* 3.6 2.3 - - - +
260B ASP* 2.7 30.0 + - - +
261B SER 2.9 14.2 + - - -
262B ILE* 2.7 46.9 + - + +
264B ARG* 3.4 31.6 + - - +
----------------------------------------------------------
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Residues in contact with HIS 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A SER* 3.0 25.4 + - - -
285A GLU* 4.7 10.8 - - + -
309A ARG* 3.3 64.6 + - + +
143B LYS* 5.8 1.6 - - - -
237B LEU 3.2 9.9 + - - +
238B ASP* 3.3 8.0 + - - +
239B ILE 3.1 0.4 - - - -
240B ASP* 1.3 82.7 + - - +
242B GLY* 1.3 57.9 - - - +
243B LYS 3.8 0.5 + - - -
259B LYS* 4.6 0.9 - - - -
260B ASP* 4.6 2.3 + - - -
264B ARG* 3.3 46.0 + - - -
----------------------------------------------------------
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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