Contacts of the helix formed by residues 238 - 267 (chain B) in PDB entry 5HJS
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 LEU 238 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A HIS* 3.6 52.9 - - + +
222A VAL* 4.0 21.1 - - + -
223A GLU* 3.8 32.7 + - + +
236B ASP* 3.1 14.3 + - - +
237B ARG* 1.4 76.8 - - - +
239B MET* 1.4 65.5 + - - +
240B PHE 3.3 1.1 - - - -
241B PRO* 3.3 6.9 - - + +
242B ARG* 3.0 36.1 + - + +
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Residues in contact with MET 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 3.4 43.1 - - + +
229B VAL* 3.9 16.6 - - + -
233B HIS* 3.7 38.6 - - + +
236B ASP* 3.3 35.3 + - - +
238B LEU* 1.4 76.2 - - - +
240B PHE* 1.4 62.4 + - - +
242B ARG* 3.5 24.4 + - - +
243B MET* 3.2 38.9 + - + +
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Residues in contact with PHE 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A HIS* 5.4 1.3 - + - -
240A PHE* 4.6 10.8 - + - -
241A PRO* 4.0 15.5 - - + -
222B VAL* 3.5 40.8 - - + -
225B LEU* 4.2 15.5 - - + -
226B HIS* 3.6 59.7 - + + -
229B VAL* 3.7 19.5 - - + +
237B ARG 4.3 5.4 + - - +
239B MET* 1.4 74.9 - - - +
241B PRO* 1.4 73.2 - - + +
243B MET* 3.2 14.2 + - - +
244B LEU* 3.2 34.5 + - + +
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Residues in contact with PRO 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A VAL* 3.6 25.1 - - + -
226A HIS* 5.5 1.3 - - - +
240A PHE* 3.9 11.7 - - + -
244A LEU* 3.5 28.3 - - + -
237B ARG 3.4 15.0 - - - +
238B LEU* 3.3 20.0 - - + +
240B PHE* 1.4 101.0 - - + +
242B ARG* 1.4 49.2 + - - +
244B LEU* 3.1 8.5 + - + +
245B MET* 2.8 40.9 + - + +
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Residues in contact with ARG 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A GLU* 4.4 16.5 + - - -
219A HIS* 3.5 43.5 - - + +
181B ALA 5.9 0.2 + - - -
184B GLU* 5.2 10.1 + - - +
185B LEU* 3.5 37.5 - - + +
236B ASP* 4.7 5.2 + - - -
238B LEU* 3.0 36.8 + - + +
239B MET* 3.7 23.8 - - - +
241B PRO* 1.4 74.9 - - - +
243B MET* 1.3 61.0 + - - +
245B MET* 3.4 9.4 + - - +
246B LYS* 3.4 26.7 + - - +
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Residues in contact with MET 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU* 4.3 10.3 - - + -
187B LEU* 3.6 30.5 - - + -
191B GLU* 3.5 34.5 - - - +
195B LEU* 3.5 28.8 - - + +
225B LEU* 4.0 18.8 - - + -
229B VAL* 3.7 30.7 - - + -
233B HIS* 4.4 2.0 - - + -
239B MET* 3.2 30.0 + - + +
240B PHE 3.2 5.6 + - - +
242B ARG* 1.3 72.5 - - - +
244B LEU* 1.4 66.5 + - - +
246B LYS* 3.1 17.7 + - - +
247B LEU 4.0 0.5 + - - -
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Residues in contact with LEU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A PRO* 3.6 34.5 - - + +
244A LEU* 4.6 12.8 - - + -
245A MET* 4.1 24.1 - - - +
248A VAL* 4.8 2.6 - - - +
195B LEU* 4.5 3.4 - - + -
198B ILE* 4.3 14.1 - - + -
222B VAL* 4.5 6.3 - - + -
225B LEU* 4.2 18.8 - - + -
240B PHE* 3.2 31.5 + - + +
241B PRO* 3.1 12.4 + - + +
243B MET* 1.4 77.2 - - - +
245B MET* 1.3 58.0 + - - +
246B LYS 3.1 0.2 - - - -
247B LEU* 2.9 35.8 + - + +
248B VAL* 4.1 2.6 + - - +
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Residues in contact with MET 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ILE* 3.6 16.8 - - + -
202A SER* 5.8 0.2 - - - +
218A GLN* 3.5 36.3 - - - +
219A HIS* 6.4 1.8 - - + +
222A VAL* 5.1 6.3 - - + -
244A LEU* 4.1 26.5 - - + +
247A LEU* 3.8 20.2 - - + -
241B PRO* 2.8 23.1 + - + +
242B ARG* 3.7 9.2 - - - +
243B MET 3.3 0.4 - - - -
244B LEU* 1.3 72.1 - - - +
246B LYS* 1.4 66.6 + - - +
247B LEU 3.1 0.4 - - - -
248B VAL* 3.2 39.2 + - + +
249B SER* 3.7 6.9 + - - -
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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
----------------------------------------------------------
215A GLU* 4.4 14.6 + - - -
136B LEU* 5.7 1.8 - - + -
178B PHE* 3.9 16.9 - - + -
181B ALA* 4.0 37.2 - - - +
182B MET* 3.6 29.2 - - + -
185B LEU* 3.8 17.9 - - + +
195B LEU* 5.0 4.3 - - + -
242B ARG* 3.4 16.2 + - - +
243B MET* 3.1 11.1 + - - +
244B LEU 3.1 1.8 - - - -
245B MET* 1.4 79.5 - - - +
247B LEU* 1.4 55.8 - - - +
249B SER* 3.3 15.2 + - - +
250B LEU* 3.1 30.4 + - - +
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Residues in contact with LEU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A MET* 3.8 16.4 - - + -
248A VAL* 3.5 26.0 - - + +
132B GLU* 4.9 4.0 - - - +
136B LEU* 5.0 1.1 - - + -
195B LEU* 3.9 40.6 - - + +
198B ILE* 3.5 31.6 - - + +
199B SER* 4.0 14.8 - - - +
244B LEU* 2.9 18.2 + - + +
246B LYS* 1.4 75.1 - - - +
248B VAL* 1.4 62.0 + - - +
250B LEU* 3.7 25.9 + - + +
251B ARG* 3.5 14.0 + - - +
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Residues in contact with VAL 248 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A LEU 4.8 0.7 - - - +
247A LEU* 3.7 21.8 - - + +
248A VAL* 3.7 31.2 - - + +
251A ARG* 3.4 52.6 - - + +
244B LEU 4.6 0.4 - - - +
245B MET* 3.3 37.9 - - + +
247B LEU* 1.4 75.4 - - - +
249B SER* 1.4 62.6 + - - +
251B ARG* 3.1 20.4 + - - +
252B THR 3.5 1.4 + - - -
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Residues in contact with SER 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ASP* 2.9 33.8 + - - +
251A ARG* 4.3 1.8 - - - +
178B PHE* 4.1 18.8 - - - -
245B MET 3.7 8.2 + - - -
246B LYS* 3.3 19.7 + - - +
248B VAL* 1.4 78.5 - - - +
250B LEU* 1.4 60.7 - - - -
252B THR* 3.2 7.4 + - - -
253B LEU* 3.1 26.0 + - - +
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B GLU* 3.4 50.7 - - + +
135B LEU* 4.0 11.0 - - + -
136B LEU* 3.6 35.2 - - + -
178B PHE* 3.7 26.7 - - + -
199B SER* 5.0 0.7 - - - +
246B LYS 3.1 16.1 + - - +
247B LEU* 3.7 28.5 - - + +
248B VAL 3.3 0.4 - - - -
249B SER* 1.4 70.8 - - - +
251B ARG* 1.3 60.6 + - - +
253B LEU* 3.3 9.5 + - + +
254B SER* 3.0 28.1 + - - -
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Residues in contact with ARG 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A VAL* 3.5 44.4 + - + +
251A ARG* 3.7 16.2 - - + +
252A THR* 3.1 30.7 + - - +
255A SER* 5.8 0.5 - - - -
132B GLU* 3.3 17.8 + - - +
202B SER* 3.5 15.6 + - - -
204B ASP* 2.8 45.8 + - - -
205B ARG* 2.9 28.7 - - - +
247B LEU 3.5 3.1 + - - +
248B VAL 3.1 10.3 + - - +
250B LEU* 1.3 77.7 - - - +
252B THR* 1.3 61.4 + - - +
254B SER* 3.5 5.7 + - - -
255B SER* 3.4 18.5 + - - -
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Residues in contact with THR 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ASP* 5.2 3.8 - - - +
206A PRO* 6.6 0.4 - - + -
251A ARG* 2.7 44.4 + - - +
248B VAL 3.5 1.0 + - - -
249B SER* 3.2 10.3 + - - -
251B ARG* 1.3 76.8 - - - +
253B LEU* 1.3 59.6 + - + +
255B SER* 3.1 10.7 + - - -
256B VAL* 3.0 37.6 + - + +
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 3.7 28.4 - - + +
171B PHE* 4.0 9.1 - - + -
174B PRO* 3.7 40.8 - - + +
175B ILE* 4.0 8.1 - - + +
178B PHE* 3.5 45.1 - - + -
249B SER* 3.1 14.0 + - - +
250B LEU* 3.3 13.4 + - + +
252B THR* 1.3 74.4 - - + +
254B SER* 1.3 60.2 + - - +
256B VAL* 3.3 7.1 + - + +
257B HIS* 2.8 29.3 + - - +
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Residues in contact with SER 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B THR* 4.6 8.5 + - - +
131B ILE* 3.6 29.5 - - - +
132B GLU* 4.1 14.9 + - - -
135B LEU* 5.1 0.6 - - - +
250B LEU 3.0 16.6 + - - -
251B ARG* 3.6 9.0 - - - -
252B THR 3.2 0.4 - - - -
253B LEU* 1.3 76.0 - - - +
255B SER* 1.3 56.7 + - - +
257B HIS* 3.4 6.2 + - - +
258B SER* 3.0 25.3 + - - -
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Residues in contact with SER 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A SER* 2.7 35.2 + - - -
251B ARG 3.4 9.0 + - - -
252B THR* 3.1 13.6 + - - -
254B SER* 1.3 76.3 - - - +
256B VAL* 1.3 63.2 + - - +
257B HIS 3.2 0.2 - - - -
258B SER* 2.8 25.9 + - - -
259B GLU* 3.2 22.3 + - - -
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Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B GLN* 5.1 1.0 - - - +
170B GLU* 3.2 28.7 - - + +
171B PHE* 3.6 20.4 - - + +
174B PRO* 4.5 14.4 - - + -
252B THR* 3.0 29.6 + - + +
253B LEU* 3.6 10.8 - - + +
255B SER* 1.3 74.9 - - - +
257B HIS* 1.3 62.3 + - - +
259B GLU* 3.3 19.6 + - - +
260B GLN* 3.1 20.4 + - - +
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Residues in contact with HIS 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ILE* 3.5 27.1 - - + +
171B PHE* 3.6 33.9 - + + -
253B LEU 2.8 17.9 + - - +
254B SER 3.4 6.9 + - - +
255B SER 3.2 0.2 - - - -
256B VAL* 1.3 74.7 - - - +
258B SER* 1.3 67.6 + - - +
260B GLN* 3.0 7.1 + - + +
261B VAL* 3.0 38.9 + - + +
279B TRP* 3.3 45.1 + + + -
301B 668 3.0 25.7 + - - -
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Residues in contact with SER 258 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A SER* 5.6 0.2 + - - -
259A GLU* 5.6 1.6 + - - -
254B SER 3.0 14.6 + - - -
255B SER* 2.8 20.5 + - - -
257B HIS* 1.3 80.4 + - - +
259B GLU* 1.4 61.1 + - - +
261B VAL* 3.4 9.0 + - - +
262B PHE* 3.1 22.3 + - - +
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Residues in contact with GLU 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A SER* 6.0 1.7 - - - -
168B GLN* 4.2 7.7 - - - +
255B SER* 3.2 24.0 + - - +
256B VAL* 3.5 21.4 - - + +
257B HIS 3.2 0.4 - - - -
258B SER* 1.4 81.2 + - - +
260B GLN* 1.4 58.4 + - - +
262B PHE* 3.4 10.4 + - - +
263B ALA* 3.0 27.0 + - - +
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Residues in contact with GLN 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B GLY 4.2 3.4 + - - -
167B LEU* 3.4 5.8 - - - -
168B GLN* 2.9 53.2 + - - +
171B PHE* 3.6 27.6 - - + +
256B VAL 3.1 10.5 + - - +
257B HIS* 3.0 10.9 + - + +
259B GLU* 1.4 74.3 - - - +
261B VAL* 1.3 63.3 + - - +
263B ALA* 3.4 5.6 + - - +
264B LEU* 3.1 34.4 + - - +
267B GLN* 5.4 1.2 - - - +
301B 668 3.1 31.6 - - - -
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Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B HIS* 3.0 46.4 + - + +
258B SER* 3.8 9.4 - - - +
259B GLU 3.4 0.4 - - - -
260B GLN* 1.3 72.4 - - - +
262B PHE* 1.3 65.1 + - - +
264B LEU* 3.2 19.5 + - - +
265B ARG* 3.4 13.2 + - + +
271B LEU* 4.2 13.5 - - + -
279B TRP* 3.9 30.1 - - + +
280B ASP* 3.3 25.0 - - - +
281B VAL* 6.1 2.7 - - + -
301B 668 5.0 4.3 - - - +
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Residues in contact with PHE 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A PHE* 6.6 0.2 - + - -
258B SER 3.1 14.2 + - - +
259B GLU* 3.5 11.9 - - - +
261B VAL* 1.3 76.5 - - - +
263B ALA* 1.4 57.9 + - + +
265B ARG* 3.0 35.8 + - + +
266B LEU* 3.4 41.7 + - + +
281B VAL* 6.4 1.6 - - + -
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Residues in contact with ALA 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B GLN* 3.5 29.8 - - - +
259B GLU 3.0 13.7 + - - +
260B GLN* 3.4 11.8 + - - +
262B PHE* 1.4 74.3 - - + +
264B LEU* 1.3 60.6 + - - +
266B LEU* 3.4 19.4 + - + +
267B GLN* 3.2 34.1 + - - +
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Residues in contact with LEU 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PHE* 4.1 16.2 - - + -
166B GLY 4.2 3.6 - - - +
260B GLN* 3.1 28.6 + - - +
261B VAL* 3.4 9.9 - - - +
262B PHE 3.2 0.4 - - - -
263B ALA* 1.3 73.9 - - - +
265B ARG* 1.3 63.5 + - - +
267B GLN* 3.6 23.7 + - - +
268B ASP* 3.2 3.3 + - - -
269B LYS* 3.0 51.2 + - + +
271B LEU* 3.9 25.6 - - + -
301B 668 3.1 38.8 - - - +
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Residues in contact with ARG 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B VAL* 3.4 8.7 + - + +
262B PHE* 3.0 24.8 + - + +
264B LEU* 1.3 77.2 - - - +
266B LEU* 1.4 62.5 + - + +
268B ASP* 3.1 19.7 + - - +
269B LYS 5.1 0.9 - - - -
276B SER* 5.3 0.6 + - - -
280B ASP* 3.9 32.8 + - - +
281B VAL* 2.8 38.6 + - - +
282B HIS* 4.6 7.7 + - - -
----------------------------------------------------------
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Residues in contact with LEU 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B PHE* 3.4 44.6 + - + +
263B ALA* 3.7 21.3 - - + +
264B LEU 3.4 0.2 - - - -
265B ARG* 1.4 77.4 - - + +
267B GLN* 1.3 56.0 + - + +
268B ASP* 3.3 3.5 + - - +
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Residues in contact with GLN 267 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B GLY* 4.2 9.9 + - - -
168B GLN* 5.6 1.0 + - - -
260B GLN* 5.4 1.4 - - - +
263B ALA* 3.2 27.8 - - - +
264B LEU* 3.7 21.8 - - - +
266B LEU* 1.3 75.4 - - + +
268B ASP* 1.4 66.6 + - - +
269B LYS* 3.1 42.1 + - + +
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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