Contacts of the helix formed by residues 184 - 205 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A GLY 3.4 9.6 - - - +
183A MET* 1.3 86.1 - - + +
185A LYS* 1.3 67.4 + - - +
186A GLY* 3.1 2.9 + - - +
187A LEU* 3.2 19.5 + - + +
188A THR* 3.0 19.8 + - - -
1385A NAD 3.8 15.9 - - + +
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Residues in contact with LYS 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A MET 3.7 0.6 + - - -
184A PRO* 1.3 71.9 - - - +
186A GLY* 1.3 58.8 + - - +
188A THR* 3.5 7.2 - - - -
189A ALA* 2.9 25.7 + - + +
230A ALA 5.7 0.2 - - - -
231A CYS* 3.2 45.5 + - + +
232A ASP* 4.2 12.5 + - - -
333A SER 4.6 2.8 + - - -
334A ILE* 3.0 40.6 + - - +
335A GLY* 5.1 0.6 - - - -
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Residues in contact with GLY 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A PRO* 3.1 3.8 + - - +
185A LYS* 1.3 82.5 - - - +
187A LEU* 1.3 56.4 + - - +
189A ALA* 3.5 4.0 + - - +
190A ALA* 3.0 30.7 + - - +
279A VAL* 5.5 0.5 - - - +
336A ILE* 5.7 0.2 - - - +
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A THR* 3.8 9.2 - - + -
183A MET* 3.8 21.5 - - + -
184A PRO* 3.2 19.9 + - + +
186A GLY* 1.3 73.1 - - - +
188A THR* 1.3 56.1 + - - +
190A ALA* 4.6 4.5 - - + +
191A THR* 2.7 63.3 + - + +
1385A NAD 3.3 66.2 - - + +
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Residues in contact with THR 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ALA* 5.1 1.6 - - + +
183A MET* 3.2 18.7 + - + +
184A PRO 3.0 16.8 + - - -
185A LYS* 3.5 7.6 - - - -
187A LEU* 1.3 78.6 - - - +
189A ALA* 1.3 57.5 + - - +
191A THR* 3.4 4.9 + - - -
192A GLY* 3.0 25.8 + - - -
227A LEU* 3.6 6.5 - - + +
230A ALA* 3.9 23.3 - - + +
231A CYS* 3.8 15.7 - - - -
240A ARG* 3.0 32.1 + - - +
243A MET* 5.5 1.3 - - + +
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Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LYS* 2.9 18.1 + - + +
186A GLY* 4.0 4.5 - - - +
188A THR* 1.3 77.0 - - - +
190A ALA* 1.3 59.0 - - - +
192A GLY 3.9 0.5 - - - -
193A MET* 3.0 35.3 + - - +
227A LEU* 4.4 1.3 - - - +
231A CYS* 3.7 16.6 - - - -
334A ILE* 3.5 36.6 - - + +
336A ILE* 4.1 9.4 - - + -
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Residues in contact with ALA 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A GLY 3.0 18.8 + - - +
187A LEU* 4.1 5.8 - - + +
189A ALA* 1.3 74.6 - - - +
191A THR* 1.3 63.2 + - + +
193A MET* 3.4 1.7 + - - +
194A ASP* 3.1 26.2 + - - +
276A PRO* 6.2 0.7 - - + -
278A GLY* 3.5 15.3 - - - +
279A VAL* 3.6 34.3 - - + +
336A ILE* 4.2 9.6 - - + +
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Residues in contact with THR 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A THR* 3.9 12.8 - - - +
140A ALA* 3.5 27.4 + - - +
141A GLY* 2.9 25.7 - - - -
142A THR* 5.7 0.9 - - - +
183A MET* 3.9 4.3 - - - +
187A LEU* 2.7 50.3 + - + +
188A THR* 3.4 4.3 + - - -
190A ALA* 1.3 75.8 - - + +
192A GLY* 1.3 62.8 + - - +
194A ASP* 3.2 6.8 + - - +
195A ALA 3.0 14.7 + - - -
278A GLY* 5.1 2.0 - - - -
1385A NAD 3.8 16.8 - - - +
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Residues in contact with GLY 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ALA 3.6 11.2 - - - -
188A THR 3.0 18.8 + - - -
190A ALA 3.3 0.2 - - - -
191A THR* 1.3 78.8 + - - +
193A MET* 1.3 55.7 + - - +
195A ALA* 3.3 5.1 + - - +
196A LEU* 3.0 25.3 + - - +
223A ILE* 4.1 4.0 - - - +
227A LEU* 3.8 14.3 - - - +
243A MET* 3.8 16.2 - - - -
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Residues in contact with MET 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ALA 3.0 24.5 + - - +
190A ALA 3.9 2.7 - - - +
191A THR 3.3 0.2 - - - -
192A GLY* 1.3 73.8 - - - +
194A ASP* 1.3 60.3 + - - +
196A LEU* 3.7 14.7 - - + +
197A THR* 2.8 31.9 + - - -
227A LEU* 4.1 6.1 - - - -
278A GLY 5.0 0.9 - - - -
282A ALA* 3.5 39.9 - - + +
285A LEU* 4.4 5.6 - - + -
327A VAL* 4.3 20.6 - - + +
330A LEU* 3.9 25.6 - - - -
331A ALA* 3.9 23.3 - - + -
334A ILE* 3.9 15.3 - - + -
336A ILE* 4.0 5.6 - - + -
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Residues in contact with ASP 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLY 3.3 8.0 - - - +
142A THR* 4.0 3.8 + - - -
190A ALA 3.1 14.6 + - - +
191A THR* 3.3 12.8 - - - +
192A GLY 3.2 0.2 - - - -
193A MET* 1.3 77.1 - - - +
195A ALA* 1.3 64.1 + - - +
197A THR* 3.1 5.5 + - - -
198A HIS* 2.9 42.3 + - - -
263A HIS* 3.3 6.8 + - - -
277A HIS* 3.3 19.7 + - - -
278A GLY* 4.2 10.5 - - - -
281A ASN* 3.6 6.7 - - - +
501A FE2 2.1 32.0 - - - -
1385A NAD 3.9 4.0 - - - -
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Residues in contact with ALA 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ALA 4.3 2.7 - - - +
141A GLY* 3.7 20.4 + - - +
191A THR 3.0 12.9 + - - +
192A GLY* 3.3 10.3 + - - +
194A ASP* 1.3 77.8 - - - +
196A LEU* 1.3 61.0 + - - +
198A HIS* 3.1 10.4 + - - +
199A ALA* 3.1 19.8 + - - +
223A ILE* 3.6 17.2 - - + +
243A MET* 5.0 0.7 - - + -
247A GLN* 4.2 18.6 - - + -
250A ALA* 3.5 8.5 - - + +
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Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A GLY 3.0 13.8 + - - +
193A MET* 3.7 24.5 - - + +
195A ALA* 1.3 76.4 - - - +
197A THR* 1.3 62.8 + - - +
199A ALA* 3.1 5.7 + - - +
200A PHE* 3.0 47.3 + - + -
220A ALA* 4.0 32.1 - - + +
223A ILE* 3.5 18.1 - - + +
285A LEU* 4.5 6.1 - - + -
307A MET* 4.6 8.3 - - + -
327A VAL* 4.5 8.7 - - + -
330A LEU* 3.8 28.5 - - + -
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Residues in contact with THR 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A MET 2.8 21.3 + - - -
194A ASP* 3.1 10.1 + - - -
196A LEU* 1.3 78.2 - - - +
198A HIS* 1.3 57.5 + - - +
200A PHE* 3.3 1.0 + - - +
201A GLU* 2.8 33.0 + - + +
262A VAL* 3.6 26.9 - - + -
263A HIS* 3.3 30.7 - - + +
281A ASN* 3.8 16.8 + - - +
285A LEU* 3.7 23.1 - - + +
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Residues in contact with HIS 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLY 3.1 19.8 + - - -
142A THR 3.7 15.4 + - - -
143A ALA* 5.3 0.6 - - - +
194A ASP* 2.9 33.4 + - - -
195A ALA* 3.1 9.0 + - - +
197A THR* 1.3 75.8 - - - +
199A ALA* 1.3 58.5 + - - +
202A ALA* 2.9 34.7 + - - +
250A ALA* 3.8 13.0 - - + +
251A GLY 5.3 0.2 + - - -
254A PHE* 3.6 29.8 - + + +
259A LEU* 3.8 17.4 - - + +
263A HIS* 3.4 14.4 - + - -
501A FE2 2.2 28.8 - - - -
1385A NAD 3.8 6.0 - + - -
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Residues in contact with ALA 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A ALA 3.1 11.6 + - - +
196A LEU* 3.3 10.8 - - + +
198A HIS* 1.3 76.5 - - - +
200A PHE* 1.3 56.8 + - - +
202A ALA* 4.8 0.4 - - - -
203A TYR* 2.9 33.2 + - - +
216A ALA* 3.5 33.8 - - - +
219A ALA* 4.3 7.6 - - + -
220A ALA* 4.2 20.4 - - + +
250A ALA* 4.4 4.2 - - + +
253A ALA* 5.5 0.2 - - - -
303A VAL* 5.9 1.3 - - - -
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Residues in contact with PHE 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A LEU* 3.0 42.3 + - + +
197A THR 3.7 6.1 - - - +
199A ALA* 1.3 77.8 - - + +
201A GLU* 1.3 58.3 + - + +
203A TYR* 3.4 4.2 + - - +
204A SER* 2.9 34.6 + - - -
285A LEU* 4.2 19.3 - - + -
289A LEU* 3.7 29.4 - - + -
300A LEU* 4.2 13.0 - - + -
303A VAL* 3.4 44.3 - - + +
307A MET* 4.1 3.4 - - - -
323A THR* 3.7 18.2 - - + -
327A VAL* 3.6 32.1 - - + -
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Residues in contact with GLU 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A THR* 2.8 28.1 + - + +
200A PHE* 1.3 72.3 - - + +
202A ALA* 1.3 61.7 + - - +
204A SER* 3.3 6.3 + - - -
205A SER* 2.8 29.6 + - - -
258A SER 4.1 2.4 - - - +
259A LEU* 3.4 13.1 - - + +
260A GLY* 2.8 35.3 + - - +
261A TYR 3.0 0.9 + - - -
262A VAL* 2.7 42.3 + - + +
263A HIS* 2.7 35.2 + - - -
285A LEU* 5.4 0.2 - - + -
288A VAL* 4.8 0.7 - - - +
289A LEU* 6.4 0.7 - - + -
292A ASN* 5.5 0.7 + - - -
366A ASN* 4.3 1.9 - - - +
367A PRO* 5.8 0.3 - - - +
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Residues in contact with ALA 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A HIS 2.9 19.7 + - - +
199A ALA 4.0 1.3 - - - +
201A GLU* 1.3 76.3 - - - +
203A TYR* 1.3 64.1 + - - +
205A SER* 3.4 15.1 + - - -
208A ALA* 3.8 8.0 - - - +
212A THR* 4.5 3.0 + - - -
216A ALA* 4.7 0.9 - - + -
253A ALA* 3.6 20.0 - - + +
254A PHE* 3.6 29.8 - - - +
257A ALA* 3.6 10.4 - - + +
258A SER 3.6 10.9 + - - +
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Residues in contact with TYR 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A ALA 2.9 19.5 + - - +
200A PHE 3.8 3.6 - - - +
202A ALA* 1.3 77.8 - - - +
204A SER* 1.3 59.8 + - - +
205A SER 3.8 0.3 + - - +
208A ALA* 4.3 1.0 - - - +
213A ASP* 3.4 45.6 + - + +
216A ALA* 4.0 7.8 - - + +
217A LEU* 3.5 28.5 - - + +
299A ARG* 2.8 81.2 + - + -
302A ASP* 2.7 31.5 + - + +
303A VAL* 3.6 22.2 - - + -
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Residues in contact with SER 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A PHE* 2.9 21.2 + - - -
201A GLU* 3.8 6.5 - - - -
203A TYR* 1.3 79.1 - - - +
205A SER* 1.3 65.6 + - - +
206A THR* 4.6 0.2 - - - -
289A LEU* 5.2 2.4 - - - +
292A ASN* 5.1 5.9 + - - +
296A VAL* 4.3 12.9 - - - +
299A ARG* 4.7 6.3 - - - +
300A LEU* 3.9 22.9 - - - +
303A VAL* 6.1 0.3 - - - +
367A PRO* 3.5 41.3 - - - +
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Residues in contact with SER 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLU 2.8 16.7 + - - -
202A ALA 3.4 13.5 + - - -
203A TYR 4.6 0.3 - - - +
204A SER* 1.3 80.2 - - - +
206A THR* 1.3 61.9 + - - +
207A ALA 2.9 13.5 + - - -
208A ALA* 3.2 16.8 + - - +
257A ALA* 2.5 32.4 + - - -
258A SER 4.2 3.1 - - - -
259A LEU 4.3 1.6 - - - -
299A ARG* 5.6 0.9 + - - -
365A THR* 3.3 19.0 - - - -
367A PRO* 4.9 0.2 - - - -
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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) + - + + + + + -
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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