Contacts of the helix formed by residues 232 - 256 (chain B) in PDB entry 2R8K
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 ASP 232 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B SER* 2.7 27.1 + - - -
3B LYS* 3.3 38.2 + - - +
4B PHE* 3.7 11.4 - - + -
208B ILE* 3.5 9.3 + - - +
231B THR* 1.3 83.5 + - - +
233B TRP* 1.3 80.6 + - - +
234B ASP* 3.4 15.5 - - - +
235B ASP* 3.2 15.3 + - - +
236B VAL* 3.2 13.2 + - - +
289B ASP* 5.9 1.8 - - - +
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Residues in contact with TRP 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B SER* 3.2 25.4 - - - -
4B PHE* 5.1 2.2 - + + -
9B LEU* 5.6 2.0 - - + -
23B LEU* 4.0 12.3 - - + -
169B LEU* 3.7 26.5 - - + -
187B LEU* 3.7 28.0 - - + -
190B ILE* 3.3 40.2 - - + -
205B LEU* 3.8 26.7 - - + +
206B PRO* 2.7 28.1 + - + -
207B LEU 4.5 1.6 - - - -
208B ILE* 3.5 23.6 - - + +
209B PRO* 3.8 10.8 - - + -
232B ASP* 1.3 78.8 + - - +
234B ASP* 1.3 60.0 + - - +
235B ASP 3.0 1.8 - - - -
236B VAL* 2.8 35.2 + - + +
237B ILE* 2.8 18.3 + - + +
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Residues in contact with ASP 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LYS* 6.1 0.2 - - - -
4B PHE* 3.6 28.8 - - + -
22B SER 4.6 0.2 - - - +
23B LEU* 3.3 27.5 - - + +
24B ALA 5.3 2.9 - - - +
232B ASP* 3.4 20.3 - - - +
233B TRP* 1.3 75.0 - - - +
235B ASP* 1.3 79.8 + - - +
237B ILE* 4.0 1.4 - - - +
238B LEU* 3.1 24.6 + - - +
288B ASN* 3.4 36.6 + - - +
289B ASP* 4.9 5.2 - - - +
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Residues in contact with ASP 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B PHE* 3.6 11.8 - - + -
229B LEU 3.6 22.4 - - - +
230B ILE* 4.1 8.3 - - - -
231B THR* 2.7 27.5 + - - -
232B ASP* 3.2 14.2 + - - +
233B TRP 3.0 0.6 - - - -
234B ASP* 1.3 95.5 + - - +
236B VAL* 1.3 65.3 + - - +
238B LEU* 3.4 6.5 + - - +
239B ALA* 3.0 19.6 + - - +
287B LYS* 3.4 33.1 + - - +
288B ASN 4.7 0.3 + - - -
289B ASP* 4.5 7.2 - - - +
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B LEU* 4.4 20.9 - - + -
187B LEU* 5.3 0.2 - - + -
208B ILE* 3.8 16.2 - - + -
212B ILE* 3.7 28.0 - - + -
215B LEU* 3.7 12.8 - - + -
230B ILE* 4.0 17.3 - - + -
232B ASP 3.2 16.4 - - - +
233B TRP* 2.8 21.8 + - + +
235B ASP* 1.3 77.2 - - - +
237B ILE* 1.3 63.4 + - + +
239B ALA* 3.1 14.5 + - - +
240B LEU* 3.1 17.7 + - + +
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Residues in contact with ILE 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 4.5 2.0 - - + -
12B LEU* 4.3 17.5 - - + -
23B LEU* 3.7 26.9 - - + +
24B ALA 5.6 0.2 - - - +
25B CYS* 3.9 17.5 - - + -
165B CYS* 3.5 30.3 - - + +
169B LEU* 3.2 44.0 - - + -
233B TRP* 2.8 23.9 + - + +
234B ASP 4.0 3.6 - - - +
236B VAL* 1.3 71.6 - - + +
238B LEU* 1.3 62.7 + - - +
240B LEU* 3.3 9.9 + - + +
241B GLY 2.9 17.5 + - - -
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA 5.5 0.9 - - - +
25B CYS* 3.8 21.7 - - + +
217B PHE* 4.3 6.1 - - + -
234B ASP 3.1 18.0 + - - +
235B ASP* 3.6 7.0 - - - +
236B VAL 3.2 0.2 - - - -
237B ILE* 1.3 78.3 - - - +
239B ALA* 1.3 63.7 + - - +
241B GLY* 2.9 3.3 + - - -
242B SER* 2.9 20.6 + - - -
264B LEU* 3.8 26.5 - - + +
265B SER* 4.2 14.6 - - - +
285B ILE* 3.6 27.6 - - + -
286B VAL 4.1 6.1 - - - +
287B LYS* 4.0 25.8 - - + -
288B ASN* 5.2 2.5 - - - +
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Residues in contact with ALA 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 3.6 24.2 - - + +
216B LYS 4.3 4.7 - - - +
217B PHE* 4.0 28.4 - - + -
230B ILE* 4.8 0.2 - - + -
235B ASP 3.0 13.3 + - - +
236B VAL* 3.2 10.1 - - - +
238B LEU* 1.3 74.3 - - - +
240B LEU* 1.3 66.4 + - - +
242B SER* 2.6 30.0 + - - -
243B GLN* 3.0 9.1 + - - +
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Residues in contact with LEU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B CYS* 4.0 17.0 - - + +
168B MET* 3.6 30.2 - - + +
169B LEU* 3.9 38.8 - - + +
175B TYR* 4.7 5.6 - - + -
183B LEU* 4.0 19.1 - - + -
187B LEU* 5.7 0.4 - - + -
215B LEU* 4.2 19.0 - - + +
236B VAL* 3.1 17.0 + - + +
237B ILE* 3.3 13.7 + - - +
239B ALA* 1.3 78.9 - - - +
241B GLY* 1.3 57.7 + - - +
243B GLN* 3.2 9.3 - - + +
244B VAL* 3.0 31.9 + - - +
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Residues in contact with GLY 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B CYS* 4.0 10.1 - - - -
161B LEU* 3.7 6.6 - - - +
165B CYS* 3.5 19.0 - - - -
237B ILE 2.9 10.0 + - - -
238B LEU 3.3 4.9 - - - -
239B ALA 2.8 2.6 + - - -
240B LEU* 1.3 74.3 - - - +
242B SER* 1.3 54.1 + - - +
244B VAL* 3.2 3.4 + - - +
245B CYS* 2.6 37.8 + - - +
264B LEU* 3.8 5.6 - - - -
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Residues in contact with SER 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B PHE* 3.8 1.0 - - - -
218B GLU* 2.9 42.6 + - - +
238B LEU 2.9 7.8 + - - -
239B ALA* 2.6 28.1 + - - -
241B GLY* 1.3 71.0 - - - -
243B GLN* 1.3 57.1 + - - +
245B CYS* 4.0 0.2 - - - -
246B LYS* 2.8 30.3 + - - +
264B LEU* 3.3 14.6 - - - +
283B GLN* 3.2 11.5 + - - +
285B ILE* 3.5 15.0 - - - +
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Residues in contact with GLN 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B MET* 5.5 4.9 - - + -
175B TYR* 2.9 42.3 + - + +
215B LEU* 5.7 0.9 - - + -
216B LYS* 3.5 23.5 + - - +
217B PHE 4.3 1.6 + - - -
218B GLU* 3.6 32.6 + - - +
239B ALA 3.0 11.4 + - - +
240B LEU* 3.2 15.5 - - + +
242B SER* 1.3 78.8 + - - +
244B VAL* 1.3 69.8 + - + +
246B LYS* 2.8 20.8 + - - +
247B GLY 3.2 3.1 + - - -
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Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 4.8 9.6 - - + -
164B ILE* 3.6 42.0 - - + -
165B CYS* 5.3 2.9 - - - -
168B MET* 4.0 24.0 - - + -
240B LEU 3.0 14.2 + - - +
241B GLY* 3.6 7.4 - - - +
243B GLN* 1.3 77.7 - - - +
245B CYS* 1.3 57.0 + - - +
247B GLY* 2.8 24.4 + - - -
248B ILE* 3.0 32.6 + - + +
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Residues in contact with CYS 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ALA* 3.8 22.0 - - - -
29B ILE* 4.2 12.8 - - - -
159B LEU* 5.0 3.8 - - - -
161B LEU* 4.0 8.9 - - + +
241B GLY 2.6 24.6 + - - +
242B SER* 3.6 8.3 - - - +
244B VAL* 1.3 74.0 - - - +
246B LYS* 1.3 61.7 + - - +
248B ILE* 3.5 8.5 + - - +
249B ARG* 3.2 23.7 + - - +
262B CYS* 3.4 32.3 - - - -
264B LEU* 4.2 3.6 - - + -
283B GLN* 4.2 4.5 - - - +
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Residues in contact with LYS 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B GLU* 3.3 39.4 + - + +
219B GLY* 5.3 4.2 - - - -
242B SER 2.8 12.2 + - - +
243B GLN* 2.8 15.0 + - - +
245B CYS* 1.3 69.4 - - - +
247B GLY* 1.3 70.7 + - - +
249B ARG* 3.3 34.7 + - - +
250B ASP* 3.0 40.3 + - - +
281B ASP* 6.2 0.6 - - - -
282B ALA* 5.6 1.8 - - - +
283B GLN* 3.6 13.3 + - - +
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Residues in contact with GLY 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B GLN 3.2 4.0 + - - -
244B VAL* 2.8 10.4 + - - -
246B LYS* 1.3 78.1 - - - +
248B ILE* 1.3 64.5 + - - +
250B ASP* 2.8 21.4 + - - +
251B SER* 3.1 13.9 + - - -
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Residues in contact with ILE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE* 4.7 2.7 - - + -
141B ILE* 4.9 2.8 - - + +
142B PHE* 3.3 40.8 - - + -
145B ALA* 3.4 34.5 - - + +
146B CYS* 6.0 0.7 - - + -
159B LEU* 4.6 15.5 - - + -
161B LEU* 6.2 1.1 - - + -
244B VAL* 3.0 47.5 + - + +
245B CYS* 3.7 8.1 - - - +
247B GLY* 1.3 71.7 - - - +
249B ARG* 1.3 66.0 + - - +
251B SER* 3.0 20.4 + - - -
252B ILE* 3.2 13.3 + - + +
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Residues in contact with ARG 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE* 4.0 19.3 - - + -
245B CYS 3.2 13.1 + - - +
246B LYS* 3.5 33.3 - - - +
247B GLY 3.2 0.2 + - - -
248B ILE* 1.3 80.2 - - + +
250B ASP* 1.3 60.4 + - - +
252B ILE* 3.6 12.7 - - + +
253B LYS* 3.3 20.1 + - - +
258B TYR 4.7 1.6 - - - +
260B THR* 3.1 45.8 + - - +
262B CYS* 3.3 29.5 - - - +
281B ASP* 3.6 19.2 + - - -
282B ALA 3.6 19.1 + - - +
283B GLN* 2.8 25.2 + - - +
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Residues in contact with ASP 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B LYS* 3.0 39.0 + - - +
247B GLY* 2.8 19.4 + - - +
249B ARG* 1.3 72.9 - - - +
251B SER* 1.3 64.9 + - - +
253B LYS* 3.2 15.1 + - - +
254B ASP* 2.9 33.9 + - - +
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Residues in contact with SER 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 6.4 0.9 - - - -
141B ILE* 4.1 16.2 - - - -
247B GLY 3.1 11.9 + - - -
248B ILE* 3.0 11.3 + - - -
250B ASP* 1.3 75.8 - - - +
252B ILE* 1.3 58.1 + - - +
254B ASP* 2.9 5.6 + - - +
255B ILE* 2.7 46.9 + - - +
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Residues in contact with ILE 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B MET* 4.8 2.0 - - - -
138B ALA* 3.8 16.8 - - + +
141B ILE* 3.6 36.1 - - + -
142B PHE* 3.6 38.6 - - + -
248B ILE 3.4 14.1 - - - +
249B ARG* 3.6 13.2 - - + +
251B SER* 1.3 77.2 - - - +
253B LYS* 1.3 56.3 + - - +
256B LEU* 2.8 33.7 + - + -
257B GLY 2.9 5.4 + - - -
258B TYR* 4.0 25.1 - - + +
260B THR* 4.7 11.0 - - + -
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Residues in contact with LYS 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B LYS* 4.6 10.3 - - - +
249B ARG 3.3 10.0 + - - +
250B ASP* 3.2 19.9 + - - +
251B SER 3.1 0.8 - - - -
252B ILE* 1.3 81.0 - - - +
254B ASP* 1.3 62.4 + - - +
257B GLY* 2.7 26.7 + - - -
258B TYR 3.7 19.3 - - - +
259B THR* 3.7 24.6 - - + +
281B ASP* 4.6 17.5 - - - +
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Residues in contact with ASP 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ASP* 2.9 22.6 + - - +
251B SER* 2.9 5.9 + - - +
253B LYS* 1.3 85.4 - - - +
255B ILE* 1.3 73.3 + - + +
256B LEU 4.8 0.2 - - - -
257B GLY* 4.4 1.4 + - - -
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Residues in contact with ILE 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 6.0 7.6 - - + -
173A ASN* 5.6 7.9 - - - +
195A ILE* 4.5 17.5 - - + -
141B ILE* 3.7 25.6 - - + -
251B SER* 2.7 33.3 + - - +
254B ASP* 1.3 80.5 - - + +
256B LEU* 1.3 69.0 + - + +
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Residues in contact with LEU 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ILE* 4.0 10.1 - - + -
41B MET* 3.9 14.9 - - - +
134B GLU* 4.4 2.5 - - - +
137B LYS* 3.7 27.4 - - + +
138B ALA* 3.5 37.9 - - + +
141B ILE* 3.6 14.1 - - + -
252B ILE* 2.8 13.6 + - + +
254B ASP 4.8 0.2 - - - -
255B ILE* 1.3 92.4 - - + +
257B GLY* 1.3 63.2 + - - +
258B TYR* 3.7 40.4 - - + -
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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