Contacts of the helix formed by residues 198 - 227 (chain B) in PDB entry 4DTZ
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 TYR 198 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B ARG* 3.5 59.7 + - + +
191B ALA* 3.2 27.8 + - + +
192B ASN 3.8 15.7 - - - -
193B PRO 3.3 22.4 - - - +
195B ASP* 2.8 21.8 + - + +
197B ALA* 1.3 81.8 - - + +
199B ASP* 1.3 56.6 + - - -
201B ASN* 3.3 16.2 - - - +
202B LYS* 3.2 27.5 + - - +
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Residues in contact with ASP 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B PRO* 3.2 30.7 - - + +
197B ALA 3.1 3.4 - - - -
198B TYR* 1.3 75.8 - - - +
200B GLU* 1.3 65.1 + - - +
201B ASN 3.3 1.1 - - - -
202B LYS* 3.6 18.6 - - + +
203B ARG* 3.3 19.4 + - - +
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Residues in contact with GLU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B PRO 4.9 0.2 + - - -
197B ALA 4.3 4.3 + - - +
199B ASP* 1.3 75.7 - - - +
201B ASN* 1.3 70.9 + - - +
203B ARG* 2.8 44.8 + - - +
204B GLN* 2.9 27.0 + - + +
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Residues in contact with ASN 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLU* 3.4 25.2 + - - +
186B ASN* 5.7 2.6 - - - +
190B ARG* 3.2 23.5 - - - +
197B ALA 3.6 6.4 - - - +
198B TYR* 3.3 31.0 - - - +
200B GLU* 1.3 79.2 + - - +
202B LYS* 1.3 56.5 + - - +
204B GLN* 3.2 7.8 + - - +
205B PHE* 2.9 31.0 + - - +
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Residues in contact with LYS 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLU* 4.5 4.9 + - - +
187B LYS* 6.2 3.1 - - - -
190B ARG* 5.4 2.7 - - - +
193B PRO 4.2 13.5 - - - -
194B ASP* 4.8 4.4 - - - +
195B ASP 3.3 31.3 + - - +
196B PRO* 4.3 1.0 - - - +
198B TYR* 3.2 17.6 + - - +
199B ASP* 3.6 21.6 + - + +
200B GLU 3.3 0.2 - - - -
201B ASN* 1.3 79.4 - - - +
203B ARG* 1.3 61.9 + - - +
205B PHE* 3.4 7.3 + - - +
206B GLN* 3.2 28.2 + - + +
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Residues in contact with ARG 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ASP 3.3 7.5 + - - +
200B GLU* 2.8 43.1 + - - +
202B LYS* 1.3 78.0 - - - +
204B GLN* 1.3 79.9 + - - +
206B GLN* 3.3 7.8 + - + +
207B GLU* 3.0 49.3 + - - +
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Residues in contact with GLN 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ARG* 3.4 40.6 + - + +
200B GLU* 2.9 20.1 + - - +
201B ASN* 3.6 6.7 - - - +
203B ARG* 1.3 94.2 - - - +
205B PHE* 1.3 58.0 + - - +
207B GLU* 2.9 31.7 + - - +
208B ASP* 2.9 46.5 + - - +
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Residues in contact with PHE 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE 4.3 4.7 - - - -
80B ASP* 3.7 24.9 - - + -
81B PHE* 3.9 18.2 - + - -
180B ALA* 3.6 33.7 - - + -
183B GLU* 3.4 31.4 - - + +
184B ALA* 4.7 3.1 - - + -
187B LYS* 3.7 24.9 - - - -
201B ASN 2.9 17.0 + - - +
202B LYS* 3.6 8.5 - - - +
204B GLN* 1.3 75.8 - - - +
206B GLN* 1.3 75.3 + - - +
208B ASP* 3.3 6.9 + - - +
209B ILE* 3.0 47.8 + - + +
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Residues in contact with GLN 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASP* 6.2 0.2 - - - +
202B LYS* 3.2 13.8 + - + +
203B ARG* 3.8 8.7 - - + +
205B PHE* 1.3 97.3 - - - +
207B GLU* 1.3 61.4 + - - +
209B ILE* 3.4 20.5 + - - +
210B LYS* 3.2 21.5 + - - +
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Residues in contact with GLU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ARG* 4.5 5.7 + - - -
203B ARG* 3.0 40.8 + - - +
204B GLN* 2.9 32.6 + - - +
206B GLN* 1.3 75.6 - - - +
208B ASP* 1.3 60.5 + - - +
210B LYS* 3.3 10.1 + - - +
211B VAL* 2.9 36.3 + - + +
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Residues in contact with ASP 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B SER* 2.7 43.3 + - - +
179B ARG* 2.7 51.6 + - - +
180B ALA* 4.2 10.0 + - + -
204B GLN* 2.9 25.8 + - - +
205B PHE* 3.7 7.2 - - - +
207B GLU* 1.3 73.6 - - - +
209B ILE* 1.3 64.7 + - - +
211B VAL* 3.3 2.4 + - - +
212B MET* 3.1 31.0 + - - +
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Residues in contact with ILE 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ASP* 3.8 18.8 - - + +
81B PHE* 3.7 22.2 - - + -
205B PHE* 3.0 50.7 + - + +
206B GLN* 3.6 26.9 - - - +
207B GLU 3.4 0.2 - - - -
208B ASP* 1.3 75.9 - - + +
210B LYS* 1.3 58.2 + - - +
212B MET* 3.2 10.1 + - + +
213B ASN* 2.8 55.8 + - - +
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Residues in contact with LYS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLN 3.2 12.7 + - - +
207B GLU* 3.3 11.4 + - - +
209B ILE* 1.3 77.2 - - - +
211B VAL* 1.3 57.9 + - + +
213B ASN* 4.5 5.4 - - + +
214B ASP* 2.8 70.1 + - - +
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Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B PRO* 4.0 19.3 - - + +
173B PHE* 4.1 11.4 - - + +
176B SER* 3.5 31.4 - - - +
207B GLU* 2.9 29.5 + - + +
208B ASP 3.3 2.6 + - - +
210B LYS* 1.3 74.4 - - + +
212B MET* 1.3 63.4 + - - +
214B ASP* 4.0 4.6 - - - +
215B LEU* 3.2 24.9 + - + +
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Residues in contact with MET 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PHE* 3.7 41.3 - - + -
173B PHE* 3.6 39.1 - - + +
176B SER* 4.5 1.8 - - - +
177B MET* 3.7 31.0 - - - +
180B ALA* 3.8 19.3 - - + -
208B ASP 3.1 23.8 + - - +
209B ILE* 3.6 6.3 - - - +
211B VAL* 1.3 77.2 - - - +
213B ASN* 1.3 65.5 + - - +
216B VAL* 3.2 28.8 + - - +
259B ILE* 4.1 16.4 - - + -
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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
----------------------------------------------------------
81B PHE* 4.8 1.7 - - - +
209B ILE* 2.8 43.5 + - - +
210B LYS* 4.0 4.8 - - + +
212B MET* 1.3 73.4 - - - +
214B ASP* 1.3 68.1 + - - +
217B ASP* 2.9 35.2 + - - +
255B ARG* 3.5 41.3 + - - +
256B TYR* 4.7 5.3 + - - -
259B ILE* 3.5 19.1 - - - +
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Residues in contact with ASP 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B LYS* 2.8 68.3 + - - +
211B VAL* 4.0 4.8 - - - +
213B ASN* 1.3 75.4 - - - +
215B LEU* 1.3 62.5 + - - +
217B ASP* 4.0 4.3 - - - +
218B LYS* 3.0 26.4 + - - +
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Residues in contact with LEU 215 (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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158B PHE* 4.4 9.0 - - + -
160B TYR* 4.0 38.4 - - + +
162B PHE* 4.2 4.5 - - + -
171B HIS* 4.0 13.7 - - + -
173B PHE* 3.7 36.3 - - + -
211B VAL* 3.2 16.0 + - + +
212B MET 4.1 2.0 - - - +
214B ASP* 1.3 77.5 - - - +
216B VAL* 1.3 59.3 + - - +
218B LYS* 3.2 14.3 + - + +
219B ILE* 2.9 37.9 + - + +
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Residues in contact with VAL 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B PHE* 4.2 15.9 - - + -
173B PHE* 3.7 22.9 - - + -
212B MET 3.2 17.1 + - - +
215B LEU* 1.3 72.8 - - - +
217B ASP* 1.3 65.5 + - - +
219B ILE* 3.8 1.1 - - - +
220B ILE* 2.9 25.3 + - + +
255B ARG* 3.7 37.0 - - + +
258B ILE* 3.7 39.9 - - + -
259B ILE* 4.2 7.4 - - + -
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Residues in contact with ASP 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213B ASN* 2.9 27.6 + - - +
214B ASP* 4.0 4.6 - - - +
216B VAL* 1.3 74.8 - - - +
218B LYS* 1.3 57.2 + - - +
220B ILE* 3.4 8.2 + - - +
221B ALA* 2.9 30.9 + - - +
251B ASP 4.9 1.7 - - - +
252B GLU* 5.5 0.9 - - - -
255B ARG* 2.8 51.9 + - - +
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Residues in contact with LYS 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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136A ASP* 2.2 45.3 + - - -
214B ASP 3.0 19.9 + - - +
215B LEU* 3.5 13.5 - - + +
217B ASP* 1.3 77.4 - - - +
219B ILE* 1.4 61.9 + - + +
221B ALA* 3.2 6.0 + - - +
222B ASP* 2.7 57.1 + - - +
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Residues in contact with ILE 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ASN* 6.2 0.2 - - + -
158B PHE* 3.6 51.8 - - + +
160B TYR* 3.6 28.9 - - + -
215B LEU* 2.9 30.0 + - + +
216B VAL 3.2 1.5 + - - +
218B LYS* 1.4 80.3 - - - +
220B ILE* 1.3 65.5 + - - +
222B ASP* 3.3 18.5 + - + +
223B ARG* 3.0 26.0 + - + +
234B LEU* 4.2 9.6 - - + -
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Residues in contact with ILE 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B VAL* 2.9 27.2 + - + +
217B ASP* 3.7 7.2 - - - +
219B ILE* 1.3 75.7 - - - +
221B ALA* 1.3 57.9 + - - +
223B ARG* 3.2 7.6 + - - +
224B LYS* 2.9 36.6 + - + +
234B LEU* 3.9 20.6 - - + -
238B LEU* 4.5 11.0 - - + -
251B ASP* 3.8 36.1 - - + +
254B ILE* 3.8 9.4 - - + -
255B ARG* 3.5 38.6 - - + +
258B ILE* 4.2 6.5 - - + -
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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
----------------------------------------------------------
217B ASP 2.9 21.0 + - - +
218B LYS* 3.6 6.7 - - - +
220B ILE* 1.3 74.3 - - - +
222B ASP* 1.3 64.5 + - - +
224B LYS* 3.4 9.1 + - - +
225B ALA* 3.0 24.9 + - - +
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Residues in contact with ASP 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ALA* 5.6 5.0 - - - +
136A ASP* 5.0 2.3 - - - +
218B LYS* 2.7 56.0 + - - +
219B ILE* 3.7 17.4 - - + +
220B ILE 3.2 0.4 - - - -
221B ALA* 1.3 73.7 - - - +
223B ARG* 1.4 56.2 + - - +
225B ALA* 3.3 7.2 + - - +
226B SER* 2.9 30.5 + - - -
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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
----------------------------------------------------------
158B PHE 3.4 17.2 + - - -
159B ASN* 3.6 13.3 - - - +
219B ILE* 3.0 20.8 + - + +
220B ILE 3.5 4.0 - - - +
222B ASP* 1.4 73.0 - - - +
224B LYS* 1.3 67.1 + - - +
226B SER* 3.2 5.5 + - - -
227B GLY* 3.2 21.1 + - - -
228B GLU* 3.2 42.6 + - - +
230B SER* 4.0 8.7 + - - -
232B ASP* 2.8 29.7 + - - -
234B LEU* 3.7 16.4 - - + +
235B THR* 3.0 32.5 + - - +
238B LEU* 3.4 20.8 - - + +
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Residues in contact with LYS 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B ILE* 2.9 23.0 + - + +
221B ALA* 3.7 8.1 - - - +
223B ARG* 1.3 78.8 - - - +
225B ALA* 1.3 60.9 + - - +
227B GLY* 3.8 7.8 + - - -
238B LEU* 4.0 24.7 - - + -
251B ASP* 2.8 41.1 + - - +
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Residues in contact with ALA 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B ALA 3.0 17.7 + - - +
222B ASP* 3.7 6.7 - - - +
223B ARG 3.3 0.2 - - - -
224B LYS* 1.3 78.4 - - - +
226B SER* 1.3 58.0 + - - +
227B GLY 3.6 0.2 - - - -
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Residues in contact with SER 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ASP 2.9 15.6 + - - -
223B ARG* 3.2 12.0 + - - -
225B ALA* 1.3 77.1 - - - +
227B GLY* 1.3 60.5 + - - +
228B GLU* 3.2 34.2 + - - +
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Residues in contact with GLY 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ARG 3.2 8.9 + - - -
224B LYS 3.8 5.8 + - - -
225B ALA 3.6 2.2 - - - -
226B SER* 1.3 77.4 + - - +
228B GLU* 1.3 63.3 + - - +
229B GLN* 3.3 17.9 + - - +
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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