Contacts of the helix formed by residues 203 - 228 (chain B) in PDB entry 1W59
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 203 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B ASN 4.1 5.2 - - - +
202B MET* 1.3 88.6 - - - +
204B LEU* 1.3 64.9 + - - +
205B LYS* 4.3 8.1 - - + +
206B LEU* 2.9 29.4 + - + +
207B ALA* 2.9 20.8 + - - +
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Residues in contact with LEU 204 (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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164B MET* 2.9 45.7 - - + -
165B GLU* 5.9 0.4 - - + -
202B MET 3.8 0.6 + - - -
203B PRO* 1.3 72.0 - - - +
205B LYS* 1.3 69.5 + - + +
206B LEU 3.1 0.9 + - - -
207B ALA* 3.3 6.8 + - - +
208B PHE* 3.0 58.2 + - + -
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Residues in contact with LYS 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B PRO* 3.2 7.5 - - + +
204B LEU* 1.3 87.4 - - + +
206B LEU* 1.3 88.1 + - + +
208B PHE* 4.4 5.4 + - - +
209B LYS* 3.4 45.3 + - - +
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Residues in contact with LEU 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B VAL* 5.4 5.6 - - + -
201B ASN 5.8 0.2 - - - +
202B MET* 3.6 24.2 - - + -
203B PRO* 2.9 29.3 + - + +
205B LYS* 1.3 106.8 - - + +
207B ALA* 1.3 59.0 + - - +
208B PHE 3.3 2.2 - - - -
209B LYS* 3.0 10.1 + - + +
210B VAL* 2.9 37.5 + - + +
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Residues in contact with ALA 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B PHE* 3.2 35.5 - - + -
164B MET* 3.8 15.9 - - + -
195B LEU* 4.1 0.7 - - - +
196B PHE* 4.3 3.1 - - + -
202B MET* 3.8 23.3 - - + +
203B PRO 2.9 11.2 + - - +
204B LEU 3.3 8.7 + - - +
206B LEU* 1.3 77.2 - - - +
208B PHE* 1.3 56.3 + - - +
210B VAL* 3.3 2.9 + - - +
211B ALA 2.8 23.2 + - - -
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Residues in contact with PHE 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B PHE* 3.6 17.9 - + - -
165B GLU* 3.2 39.9 - - + -
192B ASN* 5.7 0.7 - - - -
204B LEU* 3.0 56.1 + - + +
205B LYS* 4.7 5.2 - - - +
206B LEU 3.3 0.4 - - - -
207B ALA* 1.3 73.2 - - - +
209B LYS* 1.3 66.6 + - - +
211B ALA* 3.6 7.2 - - + +
212B ASP* 2.9 29.3 + - - +
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Residues in contact with LYS 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LYS* 3.4 43.9 + - - +
206B LEU* 3.0 15.8 + - + +
208B PHE* 1.3 78.7 - - + +
210B VAL* 1.3 57.6 + - + +
212B ASP* 3.1 13.9 + - + +
213B GLU* 3.0 29.2 + - - +
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Residues in contact with VAL 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B LEU* 4.0 20.0 - - + -
199B VAL* 4.3 17.7 - - + -
202B MET* 3.3 21.5 - - - -
206B LEU* 2.9 26.5 + - + +
207B ALA 3.6 6.3 - - - +
209B LYS* 1.3 75.5 - - + +
211B ALA* 1.3 60.0 + - - +
213B GLU* 3.1 9.5 + - + +
214B VAL* 2.9 34.4 + - + +
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Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B THR* 5.1 4.5 - - + +
162B PHE* 4.0 4.3 - - + -
192B ASN* 3.7 23.3 + - - +
195B LEU* 3.5 21.5 - - + +
207B ALA 2.8 17.4 + - - +
208B PHE* 3.6 10.1 - - + +
209B LYS 3.3 0.2 - - - -
210B VAL* 1.3 75.0 - - - +
212B ASP* 1.3 65.3 + - - +
214B VAL* 3.2 3.1 + - - +
215B LEU* 3.0 24.9 + - - +
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Residues in contact with ASP 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ALA* 4.1 18.9 - - - +
51B ASN* 3.2 40.7 + - + +
52B THR* 4.7 2.4 + - - -
208B PHE* 2.9 19.0 + - - +
209B LYS* 3.1 15.0 + - + +
211B ALA* 1.3 77.3 - - - +
213B GLU* 1.3 62.6 + - - +
215B LEU* 4.0 5.2 - - - +
216B ILE* 2.8 42.1 + - + +
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Residues in contact with GLU 213 (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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55B ARG* 2.8 37.9 + - - -
209B LYS 3.0 15.0 + - - +
210B VAL* 3.1 15.2 + - + +
212B ASP* 1.3 79.4 - - - +
214B VAL* 1.3 62.9 + - + +
216B ILE* 3.7 3.7 - - - +
217B ASN* 2.9 45.4 + - - +
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Residues in contact with VAL 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ILE* 4.4 14.1 - - + -
192B ASN* 6.1 0.4 - - - +
195B LEU* 4.0 21.5 - - + -
198B ILE* 5.9 3.1 - - + -
210B VAL* 2.9 24.0 + - + +
211B ALA* 3.2 4.0 + - - +
213B GLU* 1.3 74.9 - - + +
215B LEU* 1.3 55.3 + - - +
217B ASN* 3.3 5.9 + - - +
218B ALA* 2.7 33.8 + - - +
251B ILE* 4.3 5.4 - - + -
253B ILE* 4.1 13.9 - - + +
274B LEU* 3.6 29.2 - - + -
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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
----------------------------------------------------------
48B ALA* 4.5 10.3 - - + +
52B THR* 3.5 22.2 - - + +
128B THR* 3.1 29.2 - - + +
129B CYS 4.2 16.8 - - - +
130B GLY 4.9 0.4 - - - +
157B VAL* 3.7 20.4 - - + +
159B THR* 3.6 25.1 - - + -
190B ILE* 4.4 6.0 - - + +
211B ALA 3.0 16.5 + - - +
212B ASP* 4.0 5.2 - - - +
214B VAL* 1.3 75.6 - - - +
216B ILE* 1.3 56.1 + - - +
218B ALA* 3.0 3.2 + - - +
219B VAL* 2.8 44.7 + - + +
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Residues in contact with ILE 216 (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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51B ASN 4.3 4.3 - - - +
52B THR* 3.9 28.9 - - + +
55B ARG* 3.2 62.8 - - + +
56B LEU* 4.0 12.1 - - + +
59B GLU* 4.4 7.9 - - - +
212B ASP* 2.8 38.1 + - + +
213B GLU* 3.7 6.1 - - - +
215B LEU* 1.3 75.9 - - - +
217B ASN* 1.3 64.1 + - - +
220B LYS* 2.9 36.1 + - + +
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Residues in contact with ASN 217 (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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213B GLU* 2.9 40.9 + - - +
214B VAL* 3.7 6.0 - - - +
216B ILE* 1.3 81.1 - - - +
218B ALA* 1.3 61.0 + - - +
220B LYS* 3.9 7.0 - - - +
221B GLY* 2.8 28.8 + - - -
253B ILE* 4.8 11.7 - - + -
332B ARG* 4.1 29.0 + - - -
334B LEU* 4.3 2.0 - - - +
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Residues in contact with ALA 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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157B VAL* 4.4 8.7 - - + -
190B ILE* 4.0 15.5 - - + -
214B VAL 2.7 22.1 + - - +
215B LEU* 3.4 4.3 - - - +
217B ASN* 1.3 74.2 - - - +
219B VAL* 1.3 64.0 + - - +
222B LEU* 3.0 24.4 + - - +
251B ILE* 3.9 26.0 - - + -
253B ILE* 4.9 1.1 - - - +
334B LEU* 3.6 17.6 - - + +
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Residues in contact with VAL 219 (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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42B VAL* 4.0 17.0 - - + -
52B THR* 4.7 3.8 - - + -
56B LEU* 3.6 26.9 - - + -
126B PHE* 5.2 4.5 - - + -
128B THR* 3.5 32.1 - - + +
157B VAL* 3.9 17.9 - - + -
215B LEU* 2.8 29.9 + - + +
216B ILE 4.2 1.8 - - - +
218B ALA* 1.3 72.8 - - - +
220B LYS* 1.3 63.1 + - - +
222B LEU* 3.9 4.2 - - - +
223B VAL* 3.0 39.3 + - + +
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Residues in contact with LYS 220 (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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56B LEU* 4.0 12.5 - - + +
59B GLU* 3.7 36.3 + - + +
60B GLY 5.1 2.0 - - - -
61B ILE* 3.6 30.1 - - + +
216B ILE* 2.9 24.4 + - + +
217B ASN* 3.9 7.6 - - - +
219B VAL* 1.3 76.7 - - - +
221B GLY* 1.3 58.2 + - - +
224B GLU* 2.9 63.5 + - - +
324B ASP* 5.3 6.5 + - - -
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Residues in contact with GLY 221 (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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217B ASN 2.8 17.1 + - - -
220B LYS* 1.3 72.9 - - - +
222B LEU* 1.3 60.9 + - - +
224B GLU* 5.0 0.2 - - - -
225B LEU* 3.1 8.0 + - - +
288B HIS* 2.8 32.5 + - - -
290B MET* 5.0 9.9 - - - -
334B LEU* 3.4 22.4 - - - -
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Residues in contact with LEU 222 (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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126B PHE* 4.1 16.8 - - + -
155B VAL* 4.8 0.4 - - + -
157B VAL* 4.0 27.1 - - + -
188B VAL* 4.5 15.5 - - + -
218B ALA 3.0 16.4 + - - +
219B VAL* 3.9 4.0 - - - +
221B GLY* 1.3 74.0 - - - +
223B VAL* 1.3 65.2 + - - +
225B LEU* 3.4 19.8 + - + +
226B ILE* 3.7 14.4 + - + +
243B MET* 4.2 16.2 - - + -
251B ILE* 6.1 0.9 - - + -
286B LEU* 3.8 31.2 - - + -
334B LEU* 3.5 4.7 - - + +
336B VAL* 4.2 27.4 - - + -
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Residues in contact with VAL 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B ILE* 4.3 9.0 - - + -
42B VAL* 3.9 13.9 - - + -
61B ILE* 4.0 25.4 - - + -
62B GLU 4.3 5.8 - - - +
64B ALA* 4.0 19.3 - - + -
126B PHE* 3.7 37.2 - - + -
219B VAL* 3.0 22.2 + - + +
220B LYS 4.0 2.0 - - - +
222B LEU* 1.3 75.8 - - - +
224B GLU* 1.3 59.3 + - - +
226B ILE* 3.1 7.4 + - - +
227B THR* 3.1 25.7 + - + +
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Residues in contact with GLU 224 (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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60B GLY 4.2 2.4 - - - +
61B ILE* 3.6 13.7 - - + -
62B GLU* 3.1 35.0 + - - +
220B LYS* 2.9 51.6 + - - +
221B GLY* 5.0 0.2 - - - -
223B VAL* 1.3 68.5 - - - +
225B LEU* 1.3 60.4 + - - +
226B ILE 2.9 5.6 - - - -
227B THR* 3.5 8.7 - - - +
228B LYS* 2.7 57.5 + - + +
288B HIS* 3.9 12.3 - - + -
322B THR* 4.6 0.7 - - - +
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Residues in contact with LEU 225 (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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221B GLY 3.1 13.8 + - - +
222B LEU* 3.4 13.0 - - + +
223B VAL 3.2 0.4 - - - -
224B GLU* 1.3 75.9 - - - +
226B ILE* 1.3 60.2 + - + +
228B LYS 5.0 1.6 - - - +
234B VAL* 2.9 30.0 - - + +
286B LEU* 4.1 34.8 - - + -
287B ILE 3.3 27.4 - - - +
288B HIS* 3.2 33.8 + - + +
318B ILE* 4.8 9.4 - - + -
319B TRP 4.0 2.5 - - - -
320B GLY* 3.4 23.7 - - - +
322B THR* 5.4 2.7 - - + +
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Residues in contact with ILE 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LYS* 4.3 12.1 - - + +
38B ALA* 5.8 1.1 - - + -
40B ILE* 5.0 6.7 - - + -
124B MET* 3.9 19.7 - - + -
126B PHE* 4.7 5.4 - - + -
222B LEU* 3.8 14.1 - - + +
223B VAL 3.1 7.3 + - - +
224B GLU 2.9 0.4 - - - -
225B LEU* 1.3 89.5 - - + +
227B THR* 1.3 67.5 + - + +
228B LYS 3.8 0.6 - - - +
234B VAL* 4.2 18.7 - - + +
236B PHE* 4.1 25.1 - - + -
239B VAL* 3.3 43.1 - - + -
243B MET* 5.2 3.6 - - + -
286B LEU* 5.4 3.8 - - + -
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Residues in contact with THR 227 (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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37B LYS* 3.0 32.9 + - + +
38B ALA 5.6 1.1 - - - +
40B ILE* 4.0 20.4 - - + -
62B GLU* 2.5 42.9 + - - +
63B GLY* 3.8 19.3 - - - +
223B VAL* 3.1 20.4 + - + +
224B GLU* 3.5 6.1 - - - -
226B ILE* 1.3 84.2 - - + +
228B LYS* 1.3 60.6 + - - +
229B ASP* 3.8 0.5 + - - -
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Residues in contact with LYS 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LYS* 5.4 0.4 - - - -
62B GLU* 3.0 28.0 + - - +
224B GLU* 2.7 53.4 + - + +
225B LEU 5.0 3.3 - - - +
227B THR* 1.3 73.9 + - - +
229B ASP* 1.3 73.8 + - - +
230B GLY 3.3 2.9 + - - -
234B VAL* 5.2 6.1 - - - +
322B THR* 3.8 28.9 + - + +
323B ILE 3.3 29.0 + - - +
324B ASP* 4.3 13.5 + - - +
325B GLU 5.3 0.4 - - - +
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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