Contacts of the helix formed by residues 184 - 205 (chain B) in PDB entry 3OX4
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 PRO 184 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B GLY 3.3 9.4 - - - +
183B MET* 1.3 87.3 - - + +
185B LYS* 1.3 67.4 + - - +
186B GLY 3.1 5.5 + - - +
187B LEU* 3.2 15.6 + - + +
188B THR* 3.0 19.4 + - - -
1385B NAD 3.6 17.7 - - + +
339C ASN* 5.6 1.8 - - - +
341C THR* 5.3 3.6 - - + -
342C GLU* 3.5 50.7 - - + +
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Residues in contact with LYS 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B MET 3.8 0.4 + - - -
184B PRO* 1.3 72.0 - - - +
186B GLY* 1.3 56.4 + - - +
188B THR* 3.7 7.0 - - - -
189B ALA* 3.0 29.1 + - - +
231B CYS* 3.5 40.5 - - + +
232B ASP* 4.1 14.3 + - - +
333B SER 4.4 3.4 + - - -
334B ILE* 3.3 37.7 + - - +
335B GLY* 5.1 0.8 - - - -
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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
----------------------------------------------------------
184B PRO* 3.1 4.3 - - - +
185B LYS* 1.3 80.0 - - - +
187B LEU* 1.3 55.2 + - - +
189B ALA* 3.6 5.0 + - - +
190B ALA* 3.0 28.7 + - - +
279B VAL* 5.3 1.4 - - - +
334B ILE 6.0 0.2 - - - -
336B ILE* 5.7 0.2 - - - +
342C GLU* 6.1 0.6 - - - -
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Residues in contact with LEU 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B THR* 3.5 11.9 - - + -
183B MET* 3.0 35.4 - - + -
184B PRO* 3.2 23.2 + - + +
186B GLY* 1.3 73.4 - - - +
188B THR* 1.3 64.7 + - - +
190B ALA* 4.3 7.4 - - + -
191B THR* 2.8 51.1 + - + -
276B PRO* 6.5 0.9 - - + -
1385B NAD 3.6 41.5 - - + +
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Residues in contact with THR 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ALA* 5.0 1.4 - - + +
183B MET* 3.4 16.6 + - + +
184B PRO 3.0 17.0 + - - -
185B LYS* 3.7 7.9 - - - -
187B LEU* 1.3 78.4 - - - +
189B ALA* 1.3 57.3 + - - +
191B THR* 3.5 4.4 + - - -
192B GLY* 3.0 28.1 + - - -
227B LEU* 3.7 6.3 - - + +
230B ALA* 3.9 22.8 + - + +
231B CYS* 3.7 17.9 - - - -
240B ARG* 2.8 32.6 + - - +
243B MET* 5.9 1.1 - - + -
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LYS 3.0 17.9 + - - +
186B GLY* 3.7 4.7 - - - +
188B THR* 1.3 78.6 - - - +
190B ALA* 1.3 57.4 + - - +
192B GLY* 3.9 0.3 - - - -
193B MET* 3.0 35.7 + - - +
227B LEU* 4.5 0.9 - - - -
231B CYS* 3.6 13.0 - - - -
334B ILE* 3.6 40.4 - - + +
335B GLY 5.8 0.2 - - - -
336B ILE* 4.1 9.2 - - + -
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Residues in contact with ALA 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLY 3.0 19.4 + - - +
187B LEU* 3.8 10.1 - - + +
188B THR 3.3 0.2 - - - -
189B ALA* 1.3 74.4 - - - +
191B THR* 1.3 63.3 + - + +
193B MET* 3.2 3.0 + - - +
194B ASP* 3.0 25.6 + - - +
276B PRO* 5.9 2.0 - - + -
278B GLY* 3.6 15.8 - - - +
279B VAL* 3.8 31.4 - - + +
336B ILE* 4.5 8.2 - - + +
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Residues in contact with THR 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B THR* 3.6 12.8 - - - +
140B ALA* 3.4 17.1 + - - +
141B GLY* 2.8 36.3 - - - -
142B THR* 5.4 1.3 - - - +
183B MET* 3.8 4.9 - - - +
187B LEU* 2.8 47.9 + - + +
188B THR* 3.5 3.3 + - - -
190B ALA* 1.3 70.8 - - + +
192B GLY* 1.3 66.5 + - - +
194B ASP* 3.2 8.3 + - - +
195B ALA 3.0 9.4 + - - -
278B GLY* 5.0 2.0 - - - -
1385B NAD 3.7 20.6 - - - +
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Residues in contact with GLY 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ALA 3.5 10.8 - - - -
188B THR 3.0 19.1 + - - -
189B ALA 3.9 1.1 - - - -
191B THR* 1.3 80.4 + - - +
193B MET* 1.3 54.8 + - - +
195B ALA* 3.3 4.7 + - - +
196B LEU* 3.1 24.8 + - - +
223B ILE* 4.2 4.3 - - - +
227B LEU* 3.8 14.2 - - - +
243B MET* 3.8 15.5 - - - -
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Residues in contact with MET 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ALA 3.0 21.7 + - - +
190B ALA 3.2 2.0 + - - +
192B GLY* 1.3 72.6 - - - +
194B ASP* 1.3 55.3 + - - +
196B LEU* 3.7 17.4 - - + +
197B THR* 2.7 36.0 + - - -
227B LEU* 4.2 13.5 - - - -
278B GLY 5.0 1.1 - - - -
282B ALA* 3.6 29.2 - - + +
285B LEU* 4.1 24.7 - - + -
327B VAL* 4.2 12.6 - - + +
330B LEU* 4.2 9.9 - - + -
331B ALA* 4.2 21.1 - - + -
334B ILE* 3.9 17.3 - - + -
336B ILE* 4.0 12.1 - - + -
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Residues in contact with ASP 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLY 3.4 6.8 - - - +
142B THR* 3.6 9.5 + - - -
190B ALA 3.0 13.7 + - - +
191B THR* 3.4 14.6 - - - +
192B GLY 3.2 0.2 - - - -
193B MET* 1.3 76.1 - - - +
195B ALA* 1.3 59.6 + - - +
197B THR* 3.2 6.1 + - - -
198B HIS* 2.9 40.3 + - - -
263B HIS* 3.3 5.7 + - - -
277B HIS* 3.2 21.7 + - - -
278B GLY* 4.1 12.1 - - - +
281B ASN* 3.9 5.2 - - - +
501B FE2 2.1 32.2 - - - -
1385B NAD 5.5 1.0 + - - -
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Residues in contact with ALA 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ALA 4.3 2.5 - - - +
141B GLY* 3.5 29.6 + - - +
191B THR 3.0 5.4 + - - +
192B GLY* 3.3 9.4 + - - +
194B ASP* 1.3 78.3 - - - +
196B LEU* 1.3 61.1 + - - +
198B HIS* 3.2 9.7 + - - +
199B ALA* 3.1 18.5 + - - +
223B ILE* 3.8 14.5 - - + +
243B MET* 5.2 0.9 - - + -
247B GLN* 4.0 19.7 - - + -
250B ALA* 3.4 9.0 - - + +
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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 GLY 3.1 13.6 + - - +
193B MET* 3.7 26.5 - - + +
194B ASP 3.2 0.2 - - - -
195B ALA* 1.3 73.6 - - - +
197B THR* 1.3 65.7 + - - +
199B ALA* 3.2 3.7 + - + +
200B PHE* 3.0 50.5 + - + -
220B ALA* 4.1 28.9 - - + +
223B ILE* 3.5 20.3 - - + +
285B LEU* 4.4 5.8 - - + -
307B MET* 4.3 14.1 - - + -
327B VAL* 4.6 5.2 - - + -
330B LEU* 4.2 25.6 - - + -
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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
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193B MET 2.7 20.4 + - - -
194B ASP* 3.2 10.7 + - - -
196B LEU* 1.3 78.1 - - - +
198B HIS* 1.3 56.5 + - - +
200B PHE* 3.4 0.3 + - - +
201B GLU* 2.8 32.9 + - + +
262B VAL* 3.5 31.6 - - + -
263B HIS* 3.4 25.1 - - + +
281B ASN* 3.8 14.8 + - - +
285B LEU* 3.6 25.4 - - + +
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Residues in contact with HIS 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLY 3.1 27.0 + - - -
142B THR* 3.6 17.0 + - - -
143B ALA* 5.2 0.6 - - - +
194B ASP* 2.9 19.9 + - - -
195B ALA* 3.2 9.3 + - - +
197B THR* 1.3 77.4 - - - +
199B ALA* 1.3 56.7 + - - +
201B GLU* 4.0 0.2 - - - -
202B ALA* 2.8 34.6 + - - +
250B ALA* 3.9 11.1 - - + +
254B PHE* 3.5 33.0 - + + +
259B LEU* 3.8 14.3 - - + +
263B HIS* 3.1 18.3 + + - -
501B FE2 2.2 31.2 - - - -
1385B NAD 3.9 6.2 - + - -
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Residues in contact with ALA 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B ALA 3.1 11.7 + - - +
196B LEU* 3.2 11.0 + - - +
198B HIS* 1.3 76.7 - - - +
200B PHE* 1.3 57.8 + - + +
202B ALA* 4.6 0.7 - - - -
203B TYR* 2.9 33.1 + - - +
216B ALA* 3.5 35.5 - - - +
219B ALA* 4.2 12.3 - - + -
220B ALA* 4.3 13.7 - - + +
250B ALA* 4.3 4.4 - - + +
303B VAL* 5.8 1.3 - - + -
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Residues in contact with PHE 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU* 3.0 44.7 + - + +
197B THR 3.8 2.9 - - - +
199B ALA* 1.3 76.5 - - + +
201B GLU* 1.3 58.4 + - + +
203B TYR* 3.2 4.6 + - - +
204B SER* 2.8 34.0 + - - -
285B LEU* 4.3 10.5 - - + -
289B LEU* 3.8 37.0 - - + -
300B LEU* 3.9 16.8 - - + -
303B VAL* 3.3 41.0 - - + +
307B MET* 4.0 4.5 - - - -
323B THR* 3.6 26.7 - - + -
327B VAL* 3.8 24.5 - - + -
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Residues in contact with GLU 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 29.1 + - + +
200B PHE* 1.3 74.6 - - + +
202B ALA* 1.3 58.0 + - - +
204B SER* 3.7 5.5 - - - -
205B SER* 2.9 29.8 + - - -
258B SER 4.1 2.9 - - - +
259B LEU* 3.6 15.9 - - + +
260B GLY* 3.0 29.7 + - - +
261B TYR 3.1 1.7 + - - -
262B VAL* 2.8 41.3 + - + +
263B HIS* 2.8 35.5 + - - -
288B VAL* 4.8 0.5 - - - +
289B LEU* 6.2 1.3 - - + -
292B ASN* 5.2 1.4 + - - -
366B ASN* 4.2 2.8 - - - +
367B PRO* 5.9 0.2 - - - +
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Residues in contact with ALA 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B HIS 2.8 20.9 + - - +
199B ALA 3.7 2.5 - - - +
201B GLU* 1.3 76.3 - - - +
203B TYR* 1.3 63.3 + - - +
204B SER 3.4 0.3 + - - -
205B SER* 3.4 14.8 + - - -
208B ALA* 3.8 12.0 - - - +
212B THR* 4.9 3.1 + - - +
216B ALA* 4.4 1.1 - - + -
253B ALA* 3.6 34.1 - - + +
254B PHE* 3.7 14.4 - - - +
257B ALA* 3.9 5.8 - - + +
258B SER 3.7 11.3 + - - -
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Residues in contact with TYR 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ALA 2.9 17.8 + - - +
200B PHE 3.7 3.6 - - - +
202B ALA* 1.3 77.5 - - - +
204B SER* 1.3 56.1 + - - +
208B ALA* 4.5 0.7 - - - +
213B ASP* 3.4 39.6 + - + +
216B ALA* 4.1 6.9 - - + +
217B LEU* 3.3 40.8 - - + +
299B ARG* 2.6 90.5 + - + +
302B ASP* 2.8 30.7 + - + +
303B VAL* 3.7 15.5 - - + -
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Residues in contact with SER 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B PHE* 2.8 22.6 + - - +
201B GLU* 3.9 6.3 - - - -
203B TYR* 1.3 76.9 - - - +
205B SER* 1.3 65.8 + - - +
206B THR* 4.9 0.2 - - - +
289B LEU* 5.2 2.3 - - - +
292B ASN* 5.2 5.2 + - - +
296B VAL* 4.2 15.6 - - - +
299B ARG* 4.6 5.8 - - - +
300B LEU* 3.8 22.9 - - - +
367B PRO* 3.4 40.6 - - - +
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Residues in contact with SER 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B GLU 2.9 17.4 + - - -
202B ALA 3.4 11.7 + - - -
203B TYR 4.5 0.5 - - - +
204B SER* 1.3 80.8 - - - +
206B THR* 1.3 63.7 + - - +
207B ALA* 2.9 9.7 + - - -
208B ALA* 3.3 16.8 + - - +
257B ALA* 2.5 31.5 + - - -
258B SER 4.1 4.9 - - - -
259B LEU 4.3 1.8 - - - -
299B ARG* 5.4 1.4 + - - -
365B THR* 3.3 19.0 - - - -
367B PRO* 4.9 0.7 - - - -
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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