Contacts of the helix formed by residues 208 - 237 (chain R) in PDB entry 3SN6
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 PHE 208 (chain R).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121R ILE* 4.0 7.5 - - + +
204R SER 2.8 6.4 + - - +
206R VAL 3.4 0.2 - - - -
207R SER* 1.3 80.3 - - - +
209R TYR* 1.3 81.7 + + - +
210R VAL 3.4 1.8 - - - -
211R PRO* 3.0 7.0 - - - +
212R LEU* 2.9 40.7 + - + +
282R PHE* 3.8 30.7 - + - -
283R THR* 5.5 0.4 - - - -
286R TRP* 3.4 34.8 - - + -
287R LEU* 3.5 46.0 - - + -
290R PHE* 3.4 39.7 - + + -
291R ILE* 5.3 0.2 - - + -
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Residues in contact with TYR 209 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204R SER* 3.2 48.8 + - - -
205R ILE* 3.5 22.4 - - + +
208R PHE* 1.3 91.2 - + - +
210R VAL* 1.3 64.2 + - - +
212R LEU* 3.0 12.1 + - + +
213R VAL* 2.9 28.7 + - + +
287R LEU* 5.8 0.2 - - + -
290R PHE* 2.6 30.9 + - + -
291R ILE* 3.1 26.5 - - + +
294R ILE* 3.3 19.5 - - + +
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Residues in contact with VAL 210 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122R GLU* 5.9 1.1 - - - +
205R ILE* 2.9 39.6 + - + +
206R VAL* 4.7 6.3 - - + +
209R TYR* 1.3 70.6 - - - +
211R PRO* 1.3 72.6 - - + +
213R VAL* 3.0 10.3 + - - +
214R ILE* 2.9 45.8 + - + +
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Residues in contact with PRO 211 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121R ILE* 3.8 24.0 - - + +
122R GLU* 4.0 15.5 - - - +
125R CYS* 3.7 31.9 - - + -
206R VAL 3.6 18.8 - - - +
207R SER 4.1 2.5 - - - +
208R PHE 3.0 15.0 - - - +
210R VAL* 1.3 97.4 - - + +
212R LEU* 1.3 56.2 + - - +
214R ILE* 3.8 1.2 - - + +
215R MET* 2.9 37.7 + - - +
282R PHE* 5.1 0.9 - - + -
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Residues in contact with LEU 212 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208R PHE* 2.9 42.1 + - + +
209R TYR* 3.0 17.9 + - + +
211R PRO* 1.3 77.6 - - - +
213R VAL* 1.3 60.1 + - + +
215R MET* 3.6 2.8 - - + +
216R VAL* 2.9 47.4 + - + +
279R MET* 5.6 3.4 - - - -
282R PHE* 3.7 28.7 - - + -
283R THR* 5.0 9.4 - - + +
287R LEU* 3.8 15.5 - - + -
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Residues in contact with VAL 213 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209R TYR* 2.9 23.2 + - + +
210R VAL* 3.0 8.0 + - - +
212R LEU* 1.3 76.1 - - + +
214R ILE* 1.3 68.9 + - + +
216R VAL* 3.0 9.7 + - + +
217R PHE* 3.0 26.2 + - + +
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Residues in contact with ILE 214 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125R CYS* 3.7 30.3 - - - +
129R VAL* 4.2 17.7 - - + -
210R VAL* 2.9 34.9 + - + +
211R PRO* 4.3 0.7 - - + -
213R VAL* 1.3 78.9 - - + +
215R MET* 1.3 64.0 + - - +
217R PHE* 3.4 5.4 + - - +
218R VAL* 2.9 35.5 + - + +
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Residues in contact with MET 215 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121R ILE 5.0 0.2 - - - +
124R LEU* 4.3 7.6 - - + +
125R CYS* 3.8 32.8 - - - -
128R ALA* 3.8 11.9 - - + -
211R PRO 2.9 26.6 + - - +
212R LEU* 3.6 4.3 - - + +
214R ILE* 1.3 77.4 - - - +
216R VAL* 1.3 62.8 + - - +
218R VAL* 3.1 5.3 + - - -
219R TYR* 2.9 40.6 + - + +
278R ILE 5.0 2.7 - - - +
279R MET* 3.1 36.9 - - + +
282R PHE* 3.9 40.2 - - + -
326R TYR* 5.2 3.4 - - - +
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Residues in contact with VAL 216 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212R LEU* 2.9 44.0 + - + +
213R VAL* 3.0 9.4 + - + +
215R MET* 1.3 75.0 - - - +
217R PHE* 1.3 62.0 + - - +
219R TYR* 4.5 0.3 - - - +
220R SER* 2.5 40.9 + - - +
279R MET* 3.6 12.8 - - + -
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Residues in contact with PHE 217 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132R TYR* 4.0 23.6 - + - -
213R VAL* 3.0 19.0 + - + +
214R ILE* 3.9 4.3 - - - +
216R VAL* 1.3 79.2 - - - +
218R VAL* 1.3 66.6 + - + +
220R SER* 3.3 6.4 - - - -
221R ARG* 2.9 37.3 + - + +
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Residues in contact with VAL 218 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128R ALA* 3.2 30.1 - - + +
129R VAL* 4.8 7.9 - - + -
132R TYR* 3.2 42.4 - - + -
214R ILE* 2.9 38.1 + - + +
215R MET* 3.6 4.3 - - - +
216R VAL 3.1 0.2 - - - -
217R PHE* 1.3 78.7 - - + +
219R TYR* 1.3 76.4 + - + +
220R SER 3.0 1.1 - - - -
221R ARG* 3.0 4.9 + - - -
222R VAL* 2.9 25.5 + - + +
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Residues in contact with TYR 219 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124R LEU 4.4 1.0 + - - -
127R ILE* 4.3 2.1 - - - +
128R ALA* 3.2 44.9 + - + +
131R ARG* 4.3 17.6 - - + -
215R MET* 2.9 32.4 + - + +
218R VAL* 1.3 82.2 - - + +
220R SER* 1.3 56.2 + - - +
222R VAL* 3.6 14.1 - - + +
223R PHE* 2.9 28.9 + - - +
275R LEU* 4.2 16.9 - - + +
278R ILE* 3.4 41.9 - - + +
279R MET* 3.5 35.2 - - + -
326R TYR* 4.3 7.6 + - - -
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Residues in contact with SER 220 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216R VAL* 2.5 35.8 + - - +
217R PHE* 3.3 9.2 - - - -
219R TYR* 1.3 73.6 - - - +
221R ARG* 1.3 67.5 + - - +
223R PHE* 3.1 9.6 + - - +
224R GLN* 2.9 25.8 + - - +
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Residues in contact with ARG 221 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ARG* 5.5 2.8 - - - +
132R TYR* 3.1 43.4 + - + -
136R THR* 3.3 32.9 + - - +
217R PHE* 2.9 25.8 + - + +
218R VAL 3.0 1.3 + - - +
220R SER* 1.3 74.7 - - - +
222R VAL* 1.3 63.0 + - - +
224R GLN* 3.0 12.8 - - + +
225R GLU* 2.9 38.8 + - + +
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Residues in contact with VAL 222 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LEU* 4.8 0.7 - - + +
393A LEU* 3.7 17.5 - - + -
131R ARG* 4.2 2.5 - - + +
132R TYR* 3.8 31.6 - - + +
135R ILE* 3.6 34.5 - - + -
136R THR* 5.2 1.1 - - - +
218R VAL* 2.9 21.3 + - + +
219R TYR* 3.6 14.4 - - + +
221R ARG* 1.3 76.9 - - - +
223R PHE* 1.3 66.6 + - - +
225R GLU* 2.9 20.7 + - - +
226R ALA* 2.9 11.7 + - + +
275R LEU* 4.5 9.0 - - + -
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Residues in contact with PHE 223 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219R TYR 2.9 19.3 + - - +
220R SER* 3.1 8.0 + - - +
222R VAL* 1.3 78.6 - - - +
224R GLN* 1.3 74.1 + - - +
226R ALA* 3.1 9.8 + - + +
227R LYS* 2.9 46.4 + - + +
268R GLU* 5.7 1.1 - - + -
271R ALA* 5.0 6.3 - - + -
272R LEU* 4.7 18.4 - - + -
275R LEU* 3.4 30.5 - - + -
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Residues in contact with GLN 224 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220R SER 2.9 15.8 + - - +
221R ARG* 3.0 20.2 - - + +
223R PHE* 1.3 89.8 - - - +
225R GLU* 1.3 61.9 + - + +
227R LYS* 3.2 17.7 + - - +
228R ARG* 2.9 23.0 + - - +
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Residues in contact with GLU 225 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ARG* 4.5 3.6 + - - -
384A GLN* 3.0 22.2 + - - +
388A LEU* 4.7 0.4 - - - -
135R ILE* 3.7 31.7 - - + +
136R THR* 4.2 11.4 - - - +
221R ARG* 2.9 38.1 + - + +
222R VAL* 2.9 9.4 + - - +
224R GLN* 1.3 77.2 - - - +
226R ALA* 1.3 63.3 + - - +
228R ARG* 3.1 37.6 + - - +
229R GLN* 2.9 28.5 + - + +
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Residues in contact with ALA 226 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LEU* 3.5 24.6 - - + +
393A LEU* 3.8 27.8 - - + +
394A LEU* 5.6 0.2 - - + -
222R VAL 2.9 11.5 + - - +
223R PHE* 3.1 16.1 + - + +
225R GLU* 1.3 75.1 - - - +
227R LYS* 1.3 65.7 + - - +
229R GLN* 3.3 2.4 + - - +
230R LEU* 2.9 28.4 + - - +
271R ALA* 4.8 7.4 - - + +
275R LEU* 5.9 0.7 - - + -
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Residues in contact with LYS 227 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223R PHE* 2.9 37.7 + - + +
224R GLN* 3.5 21.4 + - - +
226R ALA* 1.3 75.7 - - - +
228R ARG* 1.3 63.5 + - - +
230R LEU* 3.3 11.4 + - - +
231R GLN* 2.9 24.7 + - + +
268R GLU* 6.1 5.6 - - + +
----------------------------------------------------------
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Residues in contact with ARG 228 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A ARG* 4.5 17.4 - - - +
381A ASP* 4.3 4.4 + - - -
384A GLN* 3.9 17.0 + - - +
224R GLN 2.9 13.4 + - - +
225R GLU* 3.1 38.2 + - - +
227R LYS* 1.3 75.8 - - - +
229R GLN* 1.3 63.8 + - - +
231R GLN* 2.9 23.3 + - - +
232R LYS* 2.9 50.6 + - + +
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Residues in contact with GLN 229 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ASP* 3.6 18.0 + - - +
384A GLN* 2.8 47.6 + - + +
385A ARG* 3.4 32.1 + - + +
388A LEU* 3.9 22.9 - - + -
394A LEU* 5.0 2.9 - - + -
135R ILE* 6.2 0.2 - - + -
225R GLU* 2.9 19.2 + - + +
226R ALA 3.7 6.3 - - - +
228R ARG* 1.3 81.6 - - - +
230R LEU* 1.3 57.3 + - - +
232R LYS* 3.3 15.1 + - - +
233R ILE* 2.9 35.7 + - - +
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Residues in contact with LEU 230 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A LEU* 3.5 29.4 - - + +
226R ALA 2.9 15.1 + - - +
227R LYS* 3.5 11.9 - - - +
229R GLN* 1.3 75.4 - - - +
231R GLN* 1.3 58.6 + - - +
233R ILE* 3.4 15.4 + - + +
234R ASP* 2.9 29.3 + - - +
267R LYS* 4.8 13.9 - - + +
268R GLU* 4.0 38.8 - - + +
271R ALA* 4.3 16.6 - - + -
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Residues in contact with GLN 231 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227R LYS* 2.9 15.7 + - + +
228R ARG* 2.9 14.7 + - - +
230R LEU* 1.3 73.5 - - - +
232R LYS* 1.3 68.4 + - + +
234R ASP* 3.0 20.7 + - - +
235R LYS* 2.9 26.1 + - + +
----------------------------------------------------------
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Residues in contact with LYS 232 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ASN* 6.1 1.6 - - - +
381A ASP* 3.1 31.6 + - - +
385A ARG* 4.2 10.5 - - - +
228R ARG* 2.9 47.5 + - + +
229R GLN* 3.6 22.0 - - - +
231R GLN* 1.3 76.3 - - + +
233R ILE* 1.3 63.7 + - - +
235R LYS* 3.0 13.0 + - - +
236R SER* 2.9 25.2 + - - -
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Residues in contact with ILE 233 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A TYR* 3.4 39.0 - - + +
385A ARG* 3.4 27.3 - - - +
394A LEU* 4.3 17.0 - - + -
229R GLN 2.9 23.9 + - - +
230R LEU* 3.5 17.5 - - + +
232R LYS* 1.3 75.9 - - - +
234R ASP* 1.3 52.6 + - - +
236R SER* 2.9 8.2 + - - +
237R GLU* 2.6 60.3 + - + +
----------------------------------------------------------
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Residues in contact with ASP 234 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230R LEU 2.9 15.1 + - - +
231R GLN* 3.0 22.2 + - - +
233R ILE* 1.3 76.8 - - - +
235R LYS* 1.3 63.5 + - - +
237R GLU* 2.8 30.6 - - - +
----------------------------------------------------------
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Residues in contact with LYS 235 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A ASP* 3.8 28.8 - - - +
325A THR* 6.0 6.3 - - - +
342A ARG* 4.5 9.4 + - - -
231R GLN* 2.9 16.8 + - + +
232R LYS* 3.0 15.2 + - - +
234R ASP* 1.3 81.8 + - - +
236R SER* 1.3 60.1 + - - +
237R GLU 5.1 0.5 - - - -
----------------------------------------------------------
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Residues in contact with SER 236 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ARG* 4.5 12.8 + - - +
346A LEU* 3.8 32.2 - - - +
359A CYS 5.4 3.1 - - - -
360A TYR* 6.1 0.7 - - - -
361A PRO* 5.0 11.9 - - - +
232R LYS* 2.9 10.3 + - - +
233R ILE* 2.9 10.5 + - - -
235R LYS* 1.3 79.3 - - - +
237R GLU* 1.3 57.9 + - - +
239R ARG* 4.0 5.0 + - - -
----------------------------------------------------------
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Residues in contact with GLU 237 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A THR* 4.5 13.4 - - + +
358A TYR* 5.5 3.1 - - - -
233R ILE* 2.6 37.3 + - + +
234R ASP* 2.8 28.4 + - - +
235R LYS 5.0 0.4 - - - -
236R SER* 1.3 74.4 - - - +
238R GLY* 1.3 57.9 + - - +
239R ARG* 3.3 46.1 + - + +
----------------------------------------------------------
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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