Contacts of the helix formed by residues 240 - 266 (chain B) in PDB entry 5U3W
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 GLU 240 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B TYR* 3.4 8.7 - - - -
239B LYS* 1.3 87.4 + - + +
241B ILE* 1.3 67.8 + - + +
242B SER* 3.2 8.7 + - - +
243B VAL* 3.3 25.1 + - + +
244B HIS* 2.9 22.9 + - - +
321B ARG* 2.7 48.9 + - - -
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Residues in contact with ILE 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ILE* 4.0 31.4 - - + -
219B LEU* 3.0 39.3 - - + -
238B TYR* 2.8 26.8 + - + +
240B GLU* 1.3 74.7 - - + +
242B SER* 1.3 69.7 + - - +
244B HIS* 3.4 1.4 + - - +
245B VAL* 2.9 36.6 + - + +
316B PHE* 3.8 25.6 - - + -
320B LEU* 4.4 8.3 - - + -
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Residues in contact with SER 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B GLU* 3.2 15.9 + - - +
241B ILE* 1.3 85.9 - - - +
243B VAL* 1.3 56.9 + - - +
245B VAL* 3.7 2.9 + - - +
246B PHE* 3.1 24.6 + - - +
320B LEU* 3.7 19.5 - - - +
321B ARG* 3.1 30.9 + - - +
324B PHE* 3.8 30.4 - - - +
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Residues in contact with VAL 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B LYS* 5.0 14.1 - - + +
240B GLU* 3.3 33.6 + - + +
242B SER* 1.3 75.2 - - - +
244B HIS* 1.3 66.2 - - - +
246B PHE* 3.2 7.2 + - - +
247B TYR* 2.9 57.8 + - + +
321B ARG* 4.2 2.9 - - - +
324B PHE* 3.8 16.6 - - + -
424B GLU* 4.8 0.2 - - - +
427B THR* 3.7 24.0 - - + +
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Residues in contact with HIS 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU* 4.0 23.3 - - + -
223B GLU* 2.8 30.6 + - + +
232B VAL* 4.1 13.9 - - + -
235B LEU* 3.5 30.6 - - + +
236B PRO 5.2 5.2 + - - -
238B TYR* 3.4 46.4 - + + +
239B LYS 5.9 0.4 - - - +
240B GLU 2.9 7.6 + - - +
241B ILE* 3.6 3.6 - - - +
243B VAL* 1.3 78.1 - - - +
245B VAL* 1.3 61.6 + - + +
247B TYR* 3.2 12.8 + - - +
248B ARG* 3.0 26.2 + - + +
501B 7U1 5.7 0.2 - + - -
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Residues in contact with VAL 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B LEU* 4.5 6.7 - - + -
241B ILE* 2.9 36.2 + - + +
242B SER 3.9 0.7 - - - +
244B HIS* 1.3 69.4 - - - +
246B PHE* 1.3 68.0 + - - +
248B ARG* 3.1 8.9 + - - +
249B CYS* 2.9 29.7 + - - -
316B PHE* 4.4 8.5 - - + -
317B LEU* 4.0 8.1 - - + -
320B LEU* 3.7 29.6 - - + -
328B ILE* 4.7 2.7 - - + -
501B 7U1 3.6 39.3 - - + -
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Residues in contact with PHE 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B SER 3.1 15.4 + - - +
243B VAL 3.3 7.6 - - - +
245B VAL* 1.3 77.1 - - - +
247B TYR* 1.3 63.9 + + - +
249B CYS* 3.1 8.9 + - - +
250B GLN* 2.9 44.9 + - - +
324B PHE* 3.7 24.9 - + + -
327B ILE* 5.0 4.3 - - + -
417B MET* 3.8 30.3 - - + -
420B ILE* 4.4 12.3 - - + -
427B THR* 3.4 34.3 - - + -
429B LEU* 3.8 14.4 - - + -
501B 7U1 3.9 32.3 - - + -
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Residues in contact with TYR 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B LEU* 4.5 17.3 - - + -
236B PRO* 3.5 48.1 - - + +
237B PRO 5.1 4.9 - - - -
239B LYS* 4.5 6.4 - - + -
243B VAL* 2.9 39.3 + - + +
244B HIS* 3.5 12.3 - - - +
246B PHE* 1.3 73.9 - + - +
248B ARG* 1.3 57.6 + - - +
250B GLN* 3.5 19.7 - - - +
251B CME 2.9 36.1 + - - -
426B GLU 4.0 4.0 + - - -
427B THR* 3.6 16.1 - - + -
428B SER* 2.9 48.8 + - - -
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Residues in contact with ARG 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B GLU* 2.9 37.4 + - - -
228B TRP* 3.7 44.7 - - - +
230B GLN* 3.0 41.0 + - - +
232B VAL* 3.8 18.8 - - - +
235B LEU* 3.9 17.2 - - + +
244B HIS* 3.0 26.3 + - + +
245B VAL 3.1 8.5 + - - +
247B TYR* 1.3 75.6 - - - +
249B CYS* 1.3 60.4 + - - +
251B CME 3.4 8.9 + - - +
252B THR* 3.1 27.5 + - - -
501B 7U1 3.8 27.1 - - + -
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Residues in contact with CYS 249 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B VAL* 2.9 31.1 + - - -
246B PHE* 3.4 9.2 - - - +
248B ARG* 1.3 73.6 - - - +
250B GLN* 1.3 57.1 + - - +
252B THR* 3.3 2.8 + - - -
253B THR* 2.9 33.3 + - - -
328B ILE* 4.8 9.6 - - - -
501B 7U1 3.5 77.7 - - + +
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Residues in contact with GLN 250 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B PHE* 2.9 26.2 + - + +
247B TYR* 3.5 22.4 - - - +
248B ARG 3.3 0.2 - - - -
249B CYS* 1.3 73.1 - - - +
251B CME 1.3 76.7 + - - +
253B THR* 3.3 1.4 + - - -
254B VAL* 3.1 29.3 + - - +
417B MET* 5.6 0.9 - - - +
428B SER* 3.0 22.8 + - - -
429B LEU* 3.5 7.6 - - - +
430B HIS* 2.8 38.5 + - + +
433B LEU* 3.5 19.3 - - + +
501B 7U1 3.8 16.6 - - + +
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Residues in contact with CME 251 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LYS* 5.0 6.1 + - - -
230B GLN* 3.6 41.0 + - + -
234B GLY 5.6 2.7 - - - -
235B LEU* 3.2 34.1 - - + -
236B PRO* 6.2 2.7 - - - -
247B TYR* 2.9 16.7 + - - +
248B ARG* 3.6 7.9 - - - +
250B GLN* 1.3 91.6 + - - +
252B THR* 1.3 61.5 + - - +
254B VAL* 3.4 19.6 + - + +
255B GLU* 3.0 26.5 + - - +
430B HIS* 3.5 30.0 + - + +
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Residues in contact with THR 252 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ARG* 3.1 17.5 + - - -
249B CYS 3.8 4.0 - - - -
250B GLN 3.3 0.2 - - - -
251B CME 1.3 71.6 + - - +
253B THR* 1.3 59.5 + - - +
255B GLU* 3.4 6.5 + - + +
256B THR* 2.8 40.0 + - - +
501B 7U1 3.4 44.8 - - + +
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Residues in contact with THR 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B CYS 2.9 20.0 + - - -
250B GLN 3.5 6.1 - - - -
251B CME 3.3 0.2 - - - -
252B THR* 1.3 76.9 - - - +
254B VAL* 1.3 58.5 + - - +
256B THR* 3.1 6.5 + - - -
257B VAL* 2.9 32.3 + - + +
287B HIS* 4.1 8.5 - - + +
290B ILE* 3.9 14.8 - - + +
291B PHE* 6.1 0.2 - - - -
433B LEU* 3.6 26.7 - - + -
501B 7U1 3.6 50.1 + - - +
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Residues in contact with VAL 254 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A PHE* 3.8 25.1 - - + -
250B GLN 3.1 16.7 + - - +
251B CME 3.9 15.9 - - + +
253B THR* 1.3 74.8 - - - +
255B GLU* 1.3 63.2 + - - +
257B VAL* 3.3 10.6 + - - +
258B ARG* 3.2 23.3 + - + +
430B HIS* 3.7 45.1 - - + +
432B LEU* 4.2 5.8 - - + -
433B LEU* 4.0 19.3 - - + -
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Residues in contact with GLU 255 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B LYS* 3.3 42.8 + - + +
251B CME 3.0 20.8 + - - +
252B THR* 3.8 7.6 - - + +
254B VAL* 1.3 77.6 - - - +
256B THR* 1.3 61.6 + - - +
258B ARG* 3.2 34.6 + - - +
259B GLU* 3.3 33.1 + - - +
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Residues in contact with THR 256 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B PHE* 4.9 0.9 - - + -
252B THR* 2.8 27.1 + - - +
253B THR* 3.1 5.1 + - - -
255B GLU* 1.3 74.9 - - - +
257B VAL* 1.3 60.3 + - - +
259B GLU* 3.1 18.8 + - - +
260B LEU* 2.9 28.1 + - + +
290B ILE* 3.6 28.4 - - + +
293B MET* 3.6 23.6 - - + -
501B 7U1 5.1 2.8 - - - -
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Residues in contact with VAL 257 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A PHE* 4.8 0.9 - - + -
501A B7G 3.9 35.0 - - + -
253B THR* 2.9 24.8 + - + +
254B VAL* 3.5 11.0 - - - +
256B THR* 1.3 76.0 - - - +
258B ARG* 1.3 57.0 + - - +
260B LEU* 3.5 7.6 + - - +
261B THR* 2.9 33.9 + - - +
286B VAL* 4.0 23.5 - - + +
287B HIS* 6.0 0.2 - - + -
290B ILE* 3.9 17.0 - - + +
432B LEU* 4.0 14.6 - - + -
433B LEU* 5.1 1.3 - - + -
436B ILE* 4.7 8.3 - - + -
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Residues in contact with ARG 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A SER* 4.1 22.6 + - - +
274A PHE* 3.4 46.2 - - + +
254B VAL* 3.2 15.2 + - - +
255B GLU* 3.3 31.6 - - - +
256B THR 3.1 0.8 - - - -
257B VAL* 1.3 76.6 - - - +
259B GLU* 1.3 61.5 + - + +
261B THR* 3.4 7.5 + - - -
262B GLU* 3.3 28.0 + - - +
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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
----------------------------------------------------------
189B ASN* 3.5 25.1 - - - +
190B PHE* 3.3 30.1 - - + +
191B ASN* 3.4 24.3 + - - +
255B GLU* 3.3 34.5 + - - +
256B THR* 3.1 19.3 + - - +
258B ARG* 1.3 75.9 - - + +
260B LEU* 1.3 58.4 + - - +
262B GLU* 3.1 7.7 + - - +
263B PHE* 2.8 28.6 + - - +
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Residues in contact with LEU 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B PHE* 3.8 15.0 - - + -
256B THR 2.9 20.6 + - - +
257B VAL 3.8 4.3 - - - +
258B ARG 3.3 0.2 - - - -
259B GLU* 1.3 74.9 - - - +
261B THR* 1.3 59.0 + - - +
263B PHE* 3.7 7.3 - - + +
264B ALA* 2.9 32.2 + - - +
282B LEU* 4.2 4.2 - - + +
286B VAL* 3.9 23.8 - - + +
289B ALA* 3.8 18.2 - - + -
290B ILE* 3.9 17.3 - - + -
293B MET* 3.7 22.7 - - + -
352B ILE* 3.7 29.8 - - + -
356B ILE* 4.7 7.0 - - + +
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Residues in contact with THR 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A PHE* 5.7 0.2 - - - -
275A LEU* 4.1 22.9 - - + +
501A B7G 3.7 22.2 - - + +
257B VAL* 2.9 22.8 + - - +
258B ARG* 3.7 7.3 - - - -
259B GLU 3.2 0.4 - - - -
260B LEU* 1.3 75.3 - - - +
262B GLU* 1.3 71.8 + - - +
264B ALA* 3.3 1.6 + - - +
265B LYS* 3.0 41.7 + - - +
282B LEU* 3.8 24.5 - - + +
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Residues in contact with GLU 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A SER 5.2 4.9 - - - +
189B ASN* 3.2 22.4 - - - +
258B ARG 3.5 12.8 - - - +
259B GLU* 3.1 6.9 + - - +
261B THR* 1.3 87.8 - - - +
263B PHE* 1.3 61.4 + - - +
265B LYS* 3.5 17.6 + - - +
266B SER* 2.9 28.1 + - - -
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Residues in contact with PHE 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B ILE* 3.7 19.3 - - + -
185B ALA* 3.8 7.6 - - + -
186B TYR* 3.6 43.1 - + + -
189B ASN* 3.8 12.0 - - + +
190B PHE* 3.9 22.0 - + + -
259B GLU 2.8 17.0 + - - +
260B LEU* 3.7 7.9 - - + +
262B GLU* 1.3 77.2 - - - +
264B ALA* 1.3 67.8 + - + +
266B SER* 3.0 17.2 + - - -
267B ILE* 3.6 14.9 + - + +
349B ALA* 3.5 24.0 - - - -
352B ILE* 3.9 24.7 - - + -
353B ALA* 4.0 16.4 - - + -
356B ILE* 5.5 3.8 - - + -
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Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LEU 2.9 18.4 + - - +
261B THR 3.7 3.4 - - - +
263B PHE* 1.3 80.4 - - + +
265B LYS* 1.3 58.4 + - - +
267B ILE* 2.9 29.4 + - - +
270B PHE* 3.2 52.2 - - + +
282B LEU* 4.3 10.1 - - + -
356B ILE* 4.4 9.0 - - + -
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Residues in contact with LYS 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A LYS* 3.9 27.3 - - - +
275A LEU* 3.6 28.6 - - - +
278A GLN* 5.1 2.7 + - - +
261B THR* 3.0 31.0 + - + +
262B GLU* 3.8 21.3 - - - +
264B ALA* 1.3 77.7 - - - +
266B SER* 1.3 57.3 + - - +
267B ILE 3.1 7.4 + - - +
268B PRO* 4.9 1.0 - - - +
270B PHE* 3.9 11.2 - - + -
271B SER* 2.6 29.3 + - - +
275B LEU* 3.9 1.2 - - - +
278B GLN* 2.9 26.5 + - - +
----------------------------------------------------------
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Residues in contact with SER 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B HIS* 3.1 26.5 + - - -
185B ALA* 3.6 23.5 - - - +
188B LYS* 5.7 5.0 + - - +
189B ASN* 3.5 11.6 + - - -
262B GLU 2.9 16.3 + - - -
263B PHE 3.0 16.3 + - - -
265B LYS* 1.3 75.4 - - - +
267B ILE* 1.3 58.6 + - - +
268B PRO* 3.9 1.3 - - - -
----------------------------------------------------------
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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