Contacts of the helix formed by residues 178 - 202 (chain B) in PDB entry 2XGZ
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 THR 178 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ALA* 3.5 2.6 - - - +
177B LYS* 1.3 87.6 - - + +
179B PHE* 1.3 63.7 + - - +
180B ALA* 3.6 6.3 + - - +
181B GLU* 3.1 24.1 + - - +
182B ALA* 3.1 22.2 + - - +
416B GLU* 3.5 15.5 - - - +
425B PHE* 3.7 11.3 - - - -
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Residues in contact with PHE 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LEU* 4.1 15.9 - - + -
147B PRO* 3.3 29.8 - - + -
149B PRO* 3.9 22.7 - - + -
178B THR* 1.3 71.9 - - - +
180B ALA* 1.3 62.6 + - - +
182B ALA* 3.1 2.3 + - - +
183B LEU* 2.9 38.9 + - + +
409B LEU* 3.4 36.1 - - + -
412B LEU* 3.4 36.6 - - + -
413B LEU* 3.7 20.0 - - + -
416B GLU* 2.7 24.2 + - - +
425B PHE* 3.7 10.5 - + + -
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Residues in contact with ALA 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 4.4 2.3 + - - -
56A TRP* 5.7 0.9 - - - -
178B THR* 3.2 6.7 - - - +
179B PHE* 1.3 77.5 - - - +
181B GLU* 1.3 62.6 + - - +
183B LEU* 3.4 2.1 + - - +
184B ARG* 3.0 22.9 + - - +
413B LEU* 3.7 22.8 - - + +
416B GLU* 2.9 16.3 + - - +
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Residues in contact with GLU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ALA* 3.6 7.1 - - + +
177B LYS* 2.9 33.4 + - - +
178B THR* 3.1 20.8 + - - +
180B ALA* 1.3 77.1 - - - +
182B ALA* 1.3 57.0 + - - +
184B ARG* 3.3 27.8 + - - +
185B ILE* 2.9 40.3 + - + +
240B LYS* 2.9 28.6 + - - +
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Residues in contact with ALA 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B PRO* 4.3 11.0 - - + -
151B LEU* 4.8 0.3 - - - +
173B PRO* 3.4 23.6 - - + +
176B ALA* 3.5 11.0 - - + +
178B THR 3.1 8.1 + - - +
179B PHE* 3.4 8.5 - - - +
181B GLU* 1.3 77.7 - - - +
183B LEU* 1.3 57.0 + - - +
185B ILE* 3.6 0.8 - - - +
186B GLY* 3.0 24.1 + - - -
425B PHE* 3.5 35.4 - - + -
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 3.4 38.8 - - + +
149B PRO* 5.0 4.2 - - + +
151B LEU* 4.4 13.5 - - + -
179B PHE* 2.9 34.5 + - + +
180B ALA 3.9 3.8 - - - +
182B ALA* 1.3 75.3 - - - +
184B ARG* 1.3 59.1 + - - +
186B GLY* 3.8 0.6 - - - -
187B SER* 2.9 29.6 + - - -
400B PRO* 4.6 11.0 - - + -
406B LEU* 5.3 0.7 - - + -
409B LEU* 3.9 48.2 - - + +
413B LEU* 4.0 11.0 - - + -
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Residues in contact with ARG 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 3.1 17.0 + - - +
54A SER 4.0 11.9 + - - -
55A LYS* 3.8 29.7 - - - +
56A TRP* 3.4 41.4 - - + +
180B ALA 3.0 16.8 + - - +
181B GLU* 3.7 20.8 + - - +
183B LEU* 1.3 73.7 - - - +
185B ILE* 1.3 78.2 + - - +
187B SER* 2.8 20.3 + - - -
188B GLU* 3.0 51.8 + - - +
237B HIS* 4.6 4.0 - - - -
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Residues in contact with ILE 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B PRO* 3.9 13.7 - - + -
176B ALA* 4.2 16.4 - - + +
181B GLU* 2.9 34.7 + - + +
182B ALA 3.6 5.6 - - - +
184B ARG* 1.3 96.0 - - - +
186B GLY* 1.3 60.9 + - - +
188B GLU* 3.3 4.6 + - - +
189B VAL* 3.0 33.1 + - - +
237B HIS* 3.4 37.1 - - + +
240B LYS* 4.4 17.3 - - + -
241B ILE* 3.6 20.9 - - + -
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Residues in contact with GLY 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 3.8 22.4 - - - -
171B ILE* 3.7 14.1 - - - +
173B PRO* 4.3 4.0 - - - -
182B ALA 3.0 19.0 + - - -
183B LEU 3.8 0.9 - - - -
185B ILE* 1.3 75.6 - - - +
187B SER* 1.3 63.1 + - - +
189B VAL* 3.3 4.5 + - - +
190B TYR* 3.0 22.5 + - - +
241B ILE* 5.2 0.4 - - - -
400B PRO* 4.4 1.4 - - - +
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Residues in contact with SER 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 3.7 17.8 - - - -
15A GLY 3.8 19.2 + - - -
56A TRP* 3.9 9.0 - - - -
183B LEU 2.9 17.9 + - - -
184B ARG* 2.8 19.8 + - - -
186B GLY* 1.3 73.1 - - - +
188B GLU* 1.3 57.6 + - - +
190B TYR* 3.3 2.1 + - - +
191B HIS* 2.9 39.3 + - - -
400B PRO* 4.0 22.1 - - - +
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Residues in contact with GLU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A SER 4.4 5.3 - - - +
55A LYS* 3.6 4.0 - - - -
56A TRP* 2.8 38.5 + - - +
57A MET* 4.1 19.3 - - - +
184B ARG* 3.0 43.8 + - - +
185B ILE* 3.5 5.8 - - - +
187B SER* 1.3 79.3 + - - +
189B VAL* 1.3 62.3 + - - +
191B HIS* 3.5 1.6 + - - +
192B ASN* 3.0 30.4 + - - +
235B ALA* 4.0 10.6 - - + +
237B HIS* 2.8 30.6 + - - +
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Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL* 5.3 2.0 - - + -
171B ILE* 3.5 31.0 - - + -
185B ILE 3.0 19.7 + - - +
186B GLY 3.7 1.1 - - - +
187B SER 3.3 0.2 - - - -
188B GLU* 1.3 76.4 - - - +
190B TYR* 1.3 56.7 + - - +
192B ASN* 3.4 3.5 + - - +
193B LEU* 2.9 28.4 + - + +
228B ILE* 5.0 0.9 - - + +
231B ALA* 3.7 7.3 - - + +
232B ILE* 4.0 32.1 - - + +
235B ALA* 4.0 18.6 - - + -
237B HIS* 4.1 4.0 - - + -
241B ILE* 4.0 26.9 - - + -
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Residues in contact with TYR 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG 4.6 3.8 - - - -
152B ASN 4.2 1.6 - - - -
153B VAL* 4.2 27.6 - - + -
171B ILE* 4.6 0.2 - - - +
186B GLY 3.0 16.0 + - - +
187B SER 3.3 3.6 + - - +
189B VAL* 1.3 79.2 - - - +
191B HIS* 1.3 77.2 + + - +
193B LEU* 3.2 9.1 + - + +
194B LYS* 2.8 52.7 + - + +
208B VAL* 3.5 13.9 - - - +
212B GLY 2.7 29.7 + - - -
213B GLY* 4.5 6.0 - - - -
214B VAL* 5.0 1.6 - - + -
399B ALA* 3.8 8.3 - - + -
400B PRO* 3.6 30.5 - - + -
401B ALA* 3.3 24.9 - - + +
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Residues in contact with HIS 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG 3.1 24.0 + - - -
15A GLY* 2.9 26.6 - - - -
16A ASN* 3.3 19.8 + - - -
17A PRO* 6.1 0.2 - - + -
56A TRP* 5.8 1.7 - + - -
57A MET* 3.9 36.0 - - + +
187B SER* 2.9 33.2 + - - +
188B GLU 4.0 0.9 - - - +
190B TYR* 1.3 86.9 - + - +
192B ASN* 1.3 58.4 + - - +
194B LYS* 3.2 9.3 + - + +
195B SER* 2.9 29.7 + - - -
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Residues in contact with ASN 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A MET* 3.6 23.8 - - - +
188B GLU* 3.0 26.2 + - - +
189B VAL 3.6 3.6 - - - +
191B HIS* 1.3 76.9 - - - +
193B LEU* 1.3 55.9 + - - +
195B SER* 3.4 7.8 + - - -
196B LEU* 2.8 34.4 + - - +
231B ALA* 3.7 17.3 - - - +
234B ALA* 3.6 19.8 + - + +
235B ALA* 3.4 28.0 - - - +
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Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B VAL* 3.4 51.8 - - + +
154B LEU* 4.6 4.3 - - + -
189B VAL* 2.9 16.0 + - + +
190B TYR* 3.4 11.2 - - + +
192B ASN* 1.3 74.5 - - - +
194B LYS* 1.3 57.4 + - - +
196B LEU* 3.8 1.7 - - - -
197B THR* 2.7 44.1 + - - +
214B VAL* 4.2 8.1 - - + -
227B LEU* 3.5 46.4 - - + +
228B ILE* 4.5 7.4 - - + -
231B ALA* 3.6 12.3 - - + +
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Residues in contact with LYS 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 6.2 0.2 - - - +
210A ASP* 4.2 16.0 + - - -
190B TYR* 2.8 39.3 + - + +
191B HIS* 3.6 11.7 - - + +
193B LEU* 1.3 72.3 - - - +
195B SER* 1.3 63.5 + - - +
197B THR* 3.4 5.5 + - - -
198B LYS* 3.0 43.0 + - + +
206B GLY* 2.7 31.9 + - - +
207B ASN* 5.3 0.6 - - - +
208B VAL* 3.9 20.7 - - - +
214B VAL* 3.7 17.7 - - + -
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Residues in contact with SER 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A MET* 6.1 2.2 - - - -
191B HIS 2.9 17.3 + - - -
192B ASN* 3.4 9.6 - - - -
194B LYS* 1.3 75.8 - - - +
196B LEU* 1.3 64.5 + - - +
198B LYS* 3.3 8.2 + - - +
199B LYS* 3.1 23.4 + - - +
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Residues in contact with LEU 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B ASN* 2.8 23.9 + - - +
193B LEU 3.9 3.4 - - - +
195B SER* 1.3 72.7 - - - +
197B THR* 1.3 58.0 + - - +
199B LYS* 3.3 6.0 + - + -
200B ARG* 2.8 59.2 + - + +
227B LEU* 3.9 16.2 - - + +
230B ASP* 3.9 17.3 - - + +
231B ALA* 3.7 33.2 - - + +
234B ALA* 4.7 7.2 - - + -
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Residues in contact with THR 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LEU* 2.7 34.0 + - - +
194B LYS* 3.7 6.3 - - - -
196B LEU* 1.3 73.4 - - - +
198B LYS* 1.3 58.1 + - - +
201B TYR* 2.8 39.2 + - + +
202B GLY 3.8 0.7 + - - +
205B ALA* 3.5 36.6 - - + +
206B GLY 4.6 0.2 - - - +
214B VAL* 3.9 8.7 - - + +
216B PRO* 3.8 21.5 - - + -
227B LEU* 3.8 18.2 - - - +
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Residues in contact with LYS 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A SER 5.8 0.2 + - - -
159A HIS* 5.2 16.2 - - - +
194B LYS* 3.0 34.1 + - + +
195B SER* 3.9 5.6 - - - +
197B THR* 1.3 76.5 - - - +
199B LYS* 1.3 59.8 + - - +
202B GLY* 3.0 33.9 + - - +
203B ALA* 3.8 27.3 + - - +
206B GLY* 3.7 27.3 - - - -
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Residues in contact with LYS 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B SER 3.1 16.4 + - - +
196B LEU* 3.3 9.4 + - + +
198B LYS* 1.3 79.9 - - - +
200B ARG* 1.3 61.9 + - + +
202B GLY 4.6 1.0 + - - -
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Residues in contact with ARG 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU* 2.8 39.9 + - + +
199B LYS* 1.3 81.0 - - + +
201B TYR* 1.3 80.8 + - + +
202B GLY 3.7 0.2 - - - -
226B ASP* 5.2 0.4 - - - +
227B LEU* 3.7 30.6 - - - +
230B ASP* 2.9 38.5 + - - +
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Residues in contact with TYR 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B THR* 2.8 23.1 + - + +
200B ARG* 1.3 100.8 + - + +
202B GLY* 1.3 61.1 + - - +
204B SER* 5.3 2.1 + - - -
205B ALA* 3.6 19.0 + - + +
216B PRO* 3.7 15.0 - - + -
217B ASN* 3.8 21.5 - - + +
218B ILE* 3.9 12.2 - - + +
223B GLU* 2.6 40.1 + - - +
227B LEU* 4.0 23.5 - - + +
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Residues in contact with GLY 202 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LYS* 3.0 28.0 + - - -
199B LYS 4.5 1.0 + - - -
200B ARG 3.7 1.2 - - - -
201B TYR* 1.3 80.7 - - - +
203B ALA* 1.3 65.4 + - - -
204B SER* 3.4 3.6 - - - -
205B ALA* 3.2 13.1 + - - +
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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