Contacts of the helix formed by residues 203 - 233 (chain B) in PDB entry 3L6D
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).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLU* 5.9 2.7 - - - +
198B ASP* 5.2 4.7 - - - +
201B GLY 3.6 9.5 - - - +
202B LEU* 1.3 83.6 - - + +
204B VAL* 1.3 68.0 + - - +
205B SER* 3.0 13.0 + - - +
206B LYS* 3.0 23.0 + - + +
207B THR* 2.8 29.5 + - - +
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LEU* 3.6 34.5 - - + +
233A GLN* 5.2 5.4 - - - +
290A THR* 3.8 13.2 - - + -
194B VAL* 3.5 41.5 - - + +
195B GLY* 4.9 0.7 - - - -
198B ASP* 4.1 20.5 + - + +
202B LEU 3.3 2.1 + - - -
203B PRO* 1.3 71.2 - - - +
205B SER* 1.3 57.0 + - - +
207B THR* 4.7 2.2 - - - +
208B ALA* 3.0 32.1 + - - +
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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
----------------------------------------------------------
230A LEU 3.6 22.9 + - - -
231A GLU* 3.4 36.7 - - - +
233A GLN* 4.7 7.8 - - - +
203B PRO* 4.3 10.4 - - - +
204B VAL* 1.3 78.9 - - - +
206B LYS* 1.3 59.1 + - - +
208B ALA* 4.8 0.7 - - - -
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Residues in contact with LYS 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B PRO* 3.0 22.3 + - + +
205B SER* 1.3 80.2 + - - +
207B THR* 1.3 66.1 + - - +
208B ALA 3.4 1.3 + - - -
209B ARG* 3.9 5.8 + - - +
210B LEU* 3.7 17.4 + - + +
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Residues in contact with THR 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PHE* 4.0 25.8 - - + -
178A VAL* 5.1 2.9 - - + -
194B VAL* 5.3 6.5 - - - +
197B GLY* 5.4 3.6 - - - -
202B LEU* 3.4 34.0 - - + +
203B PRO* 2.8 23.0 + - - +
204B VAL* 4.3 2.2 - - - -
206B LYS* 1.3 78.2 - - - +
208B ALA* 1.3 55.9 + - - +
210B LEU* 3.3 5.4 + - + +
211B LEU* 2.8 43.4 + - + +
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Residues in contact with ALA 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A VAL* 3.8 17.3 - - + +
230A LEU* 3.8 31.9 - - + -
231A GLU* 5.7 0.9 - - + -
190B PHE* 3.5 8.8 - - - -
194B VAL* 4.1 19.5 - - + +
204B VAL* 3.0 19.3 + - - +
205B SER* 5.4 1.8 - - - -
206B LYS 3.4 0.2 - - - -
207B THR* 1.3 76.3 - - - +
209B ARG* 1.3 63.6 + - - +
211B LEU* 3.7 0.4 - - - +
212B LEU* 3.1 20.4 + - - +
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Residues in contact with ARG 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A GLU 5.1 3.4 + - - -
227A VAL* 3.7 23.8 - - + +
228A ARG* 4.9 9.7 - - - +
231A GLU* 2.9 47.2 + - - +
206B LYS* 3.9 7.3 + - - +
207B THR 3.3 0.4 - - - -
208B ALA* 1.3 79.8 - - - +
210B LEU* 1.3 58.1 + - - +
212B LEU* 3.4 2.4 + - + +
213B GLU* 2.9 59.1 + - + +
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Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A HIS* 6.2 0.2 - - + -
165A VAL* 4.7 23.3 - - + -
167A LEU* 4.4 20.9 - - + -
175A PHE* 3.5 31.6 - - + -
206B LYS 3.7 12.2 + - - +
207B THR* 3.3 9.3 + - + +
209B ARG* 1.3 79.1 - - - +
211B LEU* 1.3 63.3 + - - +
213B GLU* 4.8 5.6 - - + +
214B THR* 2.7 45.6 + - - +
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PHE* 3.8 14.5 - - + -
178A VAL* 3.9 33.0 - - + +
179A LEU* 3.5 26.6 - - + +
182A HIS* 3.7 31.0 - - + -
190B PHE* 4.1 7.9 - - + -
193B ALA* 4.1 12.6 - - + +
194B VAL* 4.1 18.2 - - + +
207B THR* 2.8 24.1 + - + +
208B ALA* 3.7 4.7 - - - +
210B LEU* 1.3 73.1 - - - +
212B LEU* 1.3 62.8 + - - +
215B SER* 2.9 28.4 + - - -
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Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A HIS* 5.6 0.9 - - - +
220A ALA* 5.7 1.1 - - - +
223A LEU* 3.7 51.8 - - + +
224A GLU* 4.0 26.0 - - + +
227A VAL* 4.1 9.6 - - + -
190B PHE* 3.8 14.9 - - + -
208B ALA 3.1 16.7 + - - +
209B ARG* 3.8 4.5 - - + +
211B LEU* 1.3 77.4 - - - +
213B GLU* 1.3 65.1 + - + +
215B SER* 3.4 6.6 + - - +
216B ARG* 3.0 54.3 + - + +
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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
----------------------------------------------------------
140A HIS* 3.5 20.3 - - - +
209B ARG* 2.9 51.3 + - + +
210B LEU* 4.3 6.9 - - + +
212B LEU* 1.3 80.8 - - + +
214B THR* 1.3 61.5 + - - +
215B SER 3.5 0.3 + - - -
216B ARG* 3.8 35.7 + - - +
217B PHE 5.0 0.9 + - - -
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Residues in contact with THR 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 4.2 14.6 - - + +
140A HIS* 3.7 45.9 + - + +
141A SER 5.5 0.9 - - - +
142A ILE* 4.8 7.4 - - + -
165A VAL* 5.5 4.0 - - + +
175A PHE* 4.1 9.8 - - + -
179A LEU* 3.9 26.9 - - + -
210B LEU* 2.7 41.0 + - - +
213B GLU* 1.3 77.3 - - - +
215B SER* 1.3 59.1 + - - +
217B PHE 5.4 0.6 + - - -
218B PHE* 4.8 3.1 + - - +
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Residues in contact with SER 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 5.4 0.7 - - - -
179A LEU* 3.6 15.7 - - - -
182A HIS* 3.7 27.0 + - - -
183A ALA* 4.5 6.7 - - - -
211B LEU 2.9 21.0 + - - -
212B LEU* 3.4 6.8 + - - +
214B THR* 1.3 78.7 - - - +
216B ARG* 1.3 67.0 + - - +
217B PHE 3.4 2.0 - - - -
218B PHE* 3.3 8.7 + - - +
219B VAL* 3.0 33.0 + - - +
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Residues in contact with ARG 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ALA* 5.1 11.0 + - + +
224A GLU* 3.8 22.8 + - - +
212B LEU* 3.0 44.5 + - + +
213B GLU* 3.8 38.9 + - - +
214B THR 3.7 1.0 - - - -
215B SER* 1.3 77.8 - - - +
217B PHE* 1.3 64.7 + - - +
219B VAL* 4.0 3.4 - - - +
220B ALA* 3.0 28.0 + - + +
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Residues in contact with PHE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL 6.0 1.1 - - - -
133A ASN* 4.0 21.3 - - + -
136A HIS* 3.6 37.7 - + - -
138A GLU* 3.6 47.6 - - + +
139A SER* 4.0 14.8 - - - -
140A HIS* 5.5 3.3 + - + +
213B GLU 5.0 1.4 + - - -
214B THR 5.4 0.6 + - - -
216B ARG* 1.3 78.9 - - - +
218B PHE* 1.3 70.3 + - + +
220B ALA* 3.2 5.1 + - + -
221B ASP* 2.8 53.3 + - + +
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Residues in contact with PHE 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 3.4 42.4 - - + +
129A ALA* 3.9 19.5 - - - -
130A TYR* 3.6 39.8 - + - -
180A HIS* 5.0 5.4 - + - -
183A ALA* 3.8 30.1 - - + -
184A PHE* 4.0 27.8 - + - -
187A MSE 4.7 6.5 - - - -
214B THR 4.8 2.2 + - - +
215B SER* 3.3 10.6 + - - +
217B PHE* 1.3 84.6 - - + +
219B VAL* 1.3 59.5 + - + +
221B ASP* 3.9 3.6 - - - +
222B ALA* 2.9 30.8 + - - +
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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
----------------------------------------------------------
182A HIS* 5.0 5.2 - - - +
183A ALA* 3.7 40.8 - - + +
186A ALA* 4.2 19.5 - - + -
187A MSE 4.9 4.7 - - + -
215B SER* 3.0 25.7 + - - +
216B ARG* 4.0 3.4 - - - +
218B PHE* 1.3 74.3 - - + +
220B ALA* 1.3 60.7 + - - +
222B ALA* 3.2 5.8 + - - +
223B LEU* 2.9 49.1 + - + +
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Residues in contact with ALA 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A LEU* 5.1 2.9 - - - +
216A ARG* 6.5 0.9 - - - -
216B ARG* 3.0 21.2 + - + +
217B PHE* 3.8 6.5 - - + +
219B VAL* 1.3 77.4 - - - +
221B ASP* 1.3 63.6 + - - +
223B LEU* 3.4 7.7 + - - +
224B GLU* 3.0 25.0 + - - +
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Residues in contact with ASP 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A TYR* 5.1 1.7 - - - -
132A ARG* 2.7 34.9 + - - -
133A ASN* 2.9 29.8 + - - +
217B PHE* 2.8 42.2 + - + +
218B PHE* 4.0 3.2 - - - +
220B ALA* 1.3 74.3 - - - +
222B ALA* 1.3 56.9 + - - +
224B GLU* 3.5 6.2 + - - +
225B GLU* 3.0 27.3 + - - +
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Residues in contact with ALA 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A TYR* 4.3 14.1 - - + -
132A ARG* 4.2 10.1 - - - +
187A MSE 3.8 36.8 - - + +
191A PHE* 6.4 0.4 - - - -
218B PHE* 2.9 20.1 + - + +
219B VAL* 3.2 4.7 + - - +
221B ASP* 1.3 75.3 + - - +
223B LEU* 1.3 60.1 + - - +
225B GLU* 3.4 2.6 + - - +
226B ALA* 2.9 29.9 + - - +
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Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A ALA* 4.6 1.3 - - + +
187A MSE 4.0 23.1 - - + +
190A PHE* 3.6 35.7 - - + -
191A PHE* 5.3 3.1 - - + -
212A LEU* 3.6 33.0 - - + -
182B HIS* 4.5 17.7 - - + +
219B VAL* 2.9 38.0 + - + +
220B ALA* 3.9 5.4 - - - +
222B ALA* 1.3 69.8 - - - +
224B GLU* 1.3 61.4 + - - +
226B ALA* 3.3 4.9 + - - +
227B VAL* 2.9 33.3 + - - +
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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
----------------------------------------------------------
209A ARG* 2.8 37.1 + - - -
212A LEU* 3.5 20.9 - - + +
213A GLU* 5.0 2.6 - - - +
220B ALA 3.0 17.8 + - - +
221B ASP* 3.7 7.6 - - - +
223B LEU* 1.3 75.5 - - - +
225B GLU* 1.3 64.1 + - - +
227B VAL* 3.3 4.8 + - - +
228B ARG* 3.0 22.3 + - + +
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Residues in contact with GLU 225 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ARG* 3.5 38.3 + - - +
221B ASP* 3.0 18.3 + - - +
222B ALA 3.8 2.9 - - - +
224B GLU* 1.3 77.4 - - - +
226B ALA* 1.3 61.4 + - - +
228B ARG* 2.7 52.9 + - - +
229B ARG* 3.0 44.4 + - - +
239B GLN* 5.4 2.1 + - - -
285B ASP* 5.6 1.1 - - - +
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Residues in contact with ALA 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PHE* 4.9 5.2 - - + -
191A PHE* 3.6 33.9 - - + -
222B ALA 2.9 17.4 + - - +
223B LEU* 3.3 8.3 + - - +
225B GLU* 1.3 76.5 - - - +
227B VAL* 1.3 51.7 + - - +
229B ARG* 3.3 5.6 + - - +
230B LEU* 2.8 41.9 + - + +
285B ASP* 5.4 0.7 - - - +
286B ILE* 6.2 0.9 - - + -
287B ALA* 4.0 14.9 - - + +
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Residues in contact with VAL 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PHE* 3.7 27.8 - - + -
208A ALA* 3.7 12.1 - - + +
209A ARG* 3.7 43.7 - - - +
212A LEU* 3.9 15.3 - - + -
223B LEU 2.9 17.4 + - - +
224B GLU* 3.6 8.5 - - - +
225B GLU 3.3 0.2 - - - -
226B ALA* 1.3 75.3 - - - +
228B ARG* 1.3 57.3 + - - +
230B LEU* 3.2 8.6 + - - +
231B GLU* 2.9 41.6 + - + +
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Residues in contact with ARG 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ARG* 4.7 6.3 - - - +
224B GLU* 3.0 14.3 + - - +
225B GLU* 2.7 46.9 + - - +
227B VAL* 1.3 75.7 - - - +
229B ARG* 1.3 81.7 + - - +
231B GLU* 3.5 10.2 + - - +
232B THR* 2.9 54.4 + - + +
234B ASP* 4.5 10.7 + - - -
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Residues in contact with ARG 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B GLU* 3.0 38.8 + - - +
226B ALA* 3.7 8.1 - - - +
227B VAL 3.2 0.2 - - - -
228B ARG* 1.3 94.4 - - - +
230B LEU* 1.3 55.7 + - - +
232B THR* 3.6 4.9 - - - -
233B GLN* 2.6 32.2 + - - -
234B ASP* 2.9 47.8 + - + +
235B PHE* 4.4 4.9 - - + -
236B LYS 3.2 23.4 + - - +
238B ASP* 3.3 30.1 + - - -
239B GLN* 4.5 9.9 - - - +
285B ASP* 3.2 36.9 + - - +
287B ALA* 4.6 7.9 - - + -
----------------------------------------------------------
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Residues in contact with LEU 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PHE* 4.4 10.8 - - + -
191A PHE* 5.4 0.7 - - + -
194A VAL* 4.1 14.6 - - + -
204A VAL* 3.6 26.7 - - + +
205A SER* 4.7 4.2 - - - -
208A ALA* 3.6 28.3 - - + -
226B ALA* 2.8 30.6 + - + +
227B VAL* 3.7 4.3 - - - +
229B ARG* 1.3 73.0 - - - +
231B GLU* 1.3 61.9 + - - +
233B GLN* 3.3 24.5 + - - +
235B PHE* 3.9 25.1 - - + -
287B ALA* 4.1 4.3 - - + +
290B THR* 3.8 31.2 - - + +
291B LYS* 6.0 0.2 - - + -
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Residues in contact with GLU 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL 5.2 1.6 - - - +
205A SER* 3.6 34.2 - - - +
208A ALA* 5.9 0.7 - - + -
209A ARG* 3.0 55.5 + - + +
227B VAL* 2.9 23.0 + - + +
228B ARG* 3.7 7.2 - - - +
230B LEU* 1.3 78.6 - - + +
232B THR* 1.3 61.7 + - + +
233B GLN* 3.7 2.6 + - - +
----------------------------------------------------------
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Residues in contact with THR 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B ARG* 2.9 36.7 + - + +
229B ARG* 3.4 5.7 + - - -
231B GLU* 1.3 79.3 - - + +
233B GLN* 1.3 71.1 + - - +
234B ASP* 3.2 19.4 + - - +
----------------------------------------------------------
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Residues in contact with GLN 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A VAL* 4.6 10.5 - - - +
229B ARG 2.6 15.5 + - - -
230B LEU* 3.3 21.7 + - - +
231B GLU 3.3 3.2 - - - +
232B THR* 1.3 76.2 - - - +
234B ASP* 1.3 56.6 + - - +
235B PHE* 3.6 38.3 + - - -
291B LYS* 5.1 6.8 - - - +
----------------------------------------------------------
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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).
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