Contacts of the helix formed by residues 281 - 306 (chain B) in PDB entry 6I53
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 ILE 281 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B TYR* 3.0 31.1 + - + +
144B PRO* 3.8 15.7 - - + -
221B PHE* 4.3 12.8 - - + -
225B THR* 3.4 30.1 - - + +
226B TYR* 4.1 12.1 - - + +
268B LEU* 3.8 35.0 - - + -
279B LYS* 4.1 13.5 - - - -
280B ALA* 1.3 75.1 - - - +
282B ASP* 1.3 63.8 + - - +
283B MET 3.3 0.7 - - - -
284B TYR* 3.4 3.7 + - + +
285B LEU* 3.1 34.3 + - + +
442B TYR* 4.1 3.1 - - - -
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Residues in contact with ASP 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ILE* 4.3 18.0 - - + +
229A GLN* 4.4 6.2 + - - -
265B ASN* 4.2 15.2 + - - +
268B LEU* 4.6 6.8 - - - +
277B TYR 4.8 2.4 - - - +
278B VAL* 3.8 14.6 - - + +
279B LYS* 3.0 46.6 + - - +
281B ILE* 1.3 82.4 - - - +
283B MET* 1.3 57.3 + - - +
284B TYR 3.2 2.0 - - - -
285B LEU* 4.3 5.3 - - - +
286B MET* 3.3 42.6 - - - +
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Residues in contact with MET 283 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B VAL* 3.7 20.6 - - + +
279B LYS 2.9 19.2 + - - +
280B ALA* 3.9 9.6 - - - +
281B ILE 3.3 0.4 - - - -
282B ASP* 1.3 77.1 - - - +
284B TYR* 1.3 58.5 + - - +
286B MET* 5.2 0.4 - - - -
287B GLY* 3.7 7.8 + - - +
438B PHE* 3.6 21.2 - - + -
442B TYR* 4.4 9.7 - - + -
446B TYR* 3.7 24.9 - - + +
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Residues in contact with TYR 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B THR 5.9 0.2 - - - -
226B TYR* 3.5 34.3 - + + -
229B SER* 4.1 16.6 - - - -
230B ILE* 3.3 27.7 - - - +
281B ILE* 3.4 8.8 + - + +
282B ASP 3.2 0.4 - - - -
283B MET* 1.3 78.9 - - - +
285B LEU* 1.3 69.2 + - + +
286B MET 3.3 1.1 - - - -
287B GLY 3.6 0.9 - - - +
288B CYS* 2.8 52.8 + - - -
435B PHE* 4.1 1.7 - - - -
438B PHE* 3.8 16.8 - + - -
439B ASN* 3.2 28.0 + - - -
442B TYR* 3.8 40.6 - + + +
443B TRP* 4.5 4.2 + - - -
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Residues in contact with LEU 285 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B THR* 4.5 10.3 - - - +
229B SER* 4.0 24.9 - - - +
261B MET* 3.7 16.8 - - + +
264B ILE* 3.9 30.3 - - + -
265B ASN* 4.5 26.0 - - + +
268B LEU* 3.8 29.4 - - + -
281B ILE* 3.1 20.5 + - + +
282B ASP* 4.8 5.2 - - - +
284B TYR* 1.3 79.5 - - + +
286B MET* 1.3 62.7 + - + +
289B PHE* 3.1 26.3 + - - +
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Residues in contact with MET 286 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ILE* 3.9 28.9 - - + +
232A LEU* 3.8 23.3 - - + -
609A POV 3.8 37.7 - - + -
265B ASN* 5.1 11.2 - - - +
278B VAL* 4.8 7.9 - - + -
282B ASP* 3.3 28.1 + - + +
283B MET* 5.1 0.9 - - - -
285B LEU* 1.3 79.3 - - + +
287B GLY* 1.3 60.6 + - - +
289B PHE* 3.5 8.8 + - - +
290B VAL* 3.3 25.6 + - - +
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Residues in contact with GLY 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B MET 3.7 6.2 + - - -
284B TYR 3.3 7.9 + - - -
285B LEU 3.2 0.6 - - - -
286B MET* 1.3 78.2 - - - +
288B CYS* 1.3 61.3 + - - +
290B VAL* 3.2 16.0 + - - +
291B PHE* 3.2 21.9 - - - -
438B PHE* 3.7 25.1 - - - -
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Residues in contact with CYS 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B SER* 3.5 28.0 - - - +
233B THR* 3.8 8.8 + - - +
261B MET* 3.7 8.7 - - + -
284B TYR* 2.8 47.0 + - - +
287B GLY* 1.3 69.9 - - - +
289B PHE* 1.3 63.1 + - - +
290B VAL 3.3 0.2 - - - -
291B PHE* 3.6 10.4 + - - +
292B VAL* 3.3 26.5 + - - +
435B PHE* 3.6 27.1 - - - -
438B PHE* 4.4 1.3 - - - -
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Residues in contact with PHE 289 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A PRO* 6.5 0.4 - - + -
236A MET* 3.8 45.3 - - + -
240A LEU* 5.1 5.6 - - + -
258B VAL* 4.0 40.4 - - + -
261B MET* 3.9 28.0 - - + +
262B THR* 4.3 7.0 - - - -
285B LEU 3.1 19.1 + - - +
286B MET* 3.6 12.3 - - - +
287B GLY 3.2 0.4 - - - -
288B CYS* 1.3 77.0 - - - +
290B VAL* 1.3 61.4 + - + +
292B VAL* 3.3 5.2 + - + +
293B PHE* 2.8 34.8 + + + +
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Residues in contact with VAL 290 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A MET* 6.0 4.0 - - + -
609A POV 5.3 8.3 - - - -
286B MET 3.3 17.0 - - - +
287B GLY* 3.2 9.7 + - - +
289B PHE* 1.3 80.3 - - + +
291B PHE* 1.3 58.3 + - + +
293B PHE* 4.2 9.0 - - + -
294B LEU* 2.6 58.3 + - + +
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Residues in contact with PHE 291 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B THR* 4.0 15.0 - - + -
236B SER* 4.3 3.4 + - - -
237B TRP* 4.5 8.9 + + - +
287B GLY 3.2 26.2 - - - -
288B CYS* 3.6 7.1 + - - +
290B VAL* 1.3 79.2 - - + +
292B VAL* 1.3 60.0 + - - +
294B LEU* 4.2 9.7 - - + +
295B ALA* 3.3 22.3 + - - +
431B PHE* 5.0 20.4 - + - -
434B THR* 3.6 30.7 - - + -
435B PHE* 3.6 48.0 - + + -
438B PHE* 3.7 28.5 - + + -
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Residues in contact with VAL 292 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B THR* 4.1 13.2 - - + +
236B SER* 4.1 15.8 - - - +
254B GLY* 4.6 3.6 - - - +
257B THR* 3.7 42.0 - - + +
258B VAL* 3.7 25.3 - - + +
261B MET* 3.9 13.0 - - + -
288B CYS 3.3 14.5 + - - +
289B PHE* 3.3 10.7 + - + +
290B VAL 3.2 0.2 - - - -
291B PHE* 1.3 76.8 - - - +
293B PHE* 1.3 62.2 + - - +
295B ALA* 3.2 12.0 + - - +
296B LEU* 3.3 13.3 + - - +
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Residues in contact with PHE 293 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A MET* 3.6 32.5 - - + -
239A ILE* 3.6 29.4 - - + -
240A LEU* 3.6 41.3 - - + -
243A VAL* 5.1 0.4 - - + -
258B VAL* 4.8 5.4 - - + -
289B PHE* 2.8 33.2 + + + +
290B VAL* 3.1 9.8 + - + +
292B VAL* 1.3 75.2 - - - +
294B LEU* 1.3 64.6 + - + +
296B LEU* 3.5 4.0 + - - +
297B LEU* 3.1 58.8 + - + +
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Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B VAL* 2.6 42.7 + - + +
291B PHE* 4.5 8.3 - - + +
293B PHE* 1.3 74.4 - - + +
295B ALA* 1.3 60.0 + - - +
296B LEU 3.2 0.4 - - - -
297B LEU* 3.8 26.2 - - + +
298B GLU* 3.1 26.0 + - - +
431B PHE* 4.1 24.8 - - + -
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B SER* 3.9 28.7 - - - +
237B TRP* 4.6 1.8 - - + -
239B SER* 4.1 12.6 + - - -
240B PHE* 4.0 17.5 - - + -
250B ARG 5.7 0.5 - - - +
254B GLY* 5.8 2.6 - - - -
291B PHE 3.3 19.2 + - - +
292B VAL 3.2 8.0 + - - +
294B LEU* 1.3 76.7 - - - +
296B LEU* 1.3 57.3 + - - +
298B GLU* 3.8 11.6 - - - +
299B TYR* 4.0 6.8 + - - +
431B PHE* 4.1 9.2 - - + -
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A LEU* 3.7 28.7 - - + -
243A VAL* 4.8 4.4 - - + +
258A PHE* 4.1 21.0 - - + -
250B ARG 4.2 9.6 - - - +
251B VAL* 4.2 13.7 - - + +
254B GLY* 3.5 42.2 - - - +
255B ILE* 3.7 14.8 - - + -
258B VAL* 4.7 2.9 - - + -
292B VAL 3.3 12.8 + - - +
293B PHE* 4.0 5.4 - - - +
294B LEU 3.2 0.4 - - - -
295B ALA* 1.3 77.8 - - - +
297B LEU* 1.3 63.5 + - - +
298B GLU 3.1 1.5 + - - -
299B TYR* 3.5 7.4 + - + +
300B ALA* 3.5 18.4 + - - +
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Residues in contact with LEU 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ILE* 5.7 1.3 - - + -
243A VAL* 3.8 31.6 - - + -
293B PHE* 3.1 46.7 + - + +
294B LEU* 3.8 25.8 - - + +
296B LEU* 1.3 74.2 - - - +
298B GLU* 1.3 59.1 + - - +
299B TYR 3.4 0.2 - - - -
300B ALA* 3.8 5.2 - - + +
301B PHE* 3.0 28.1 + - - +
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B SER* 5.5 0.3 + - - -
240B PHE* 3.2 29.0 - - + -
250B ARG* 3.0 23.0 + - - -
294B LEU 3.1 17.9 + - - +
295B ALA* 3.8 9.2 - - - +
296B LEU 3.1 0.4 - - - -
297B LEU* 1.3 76.5 - - - +
299B TYR* 1.3 58.1 + - - +
301B PHE* 3.3 8.2 + - + +
302B VAL* 2.9 27.1 + - - +
423B ILE* 3.3 25.5 - - + +
424B ASP* 3.2 16.7 - - - +
426B TRP* 6.1 1.1 - - + -
427B SER* 3.7 14.1 + - - +
431B PHE* 4.8 6.1 - - + -
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Residues in contact with TYR 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LEU* 4.7 3.4 - - + -
254A ALA* 6.0 0.2 - - + -
258A PHE* 6.0 0.9 - + - -
239B SER* 5.8 1.6 - - - +
244B TYR* 3.3 21.1 + - + -
246B ALA 4.4 1.1 - - - -
247B SER* 3.2 34.9 + - - -
250B ARG* 3.4 59.5 - - + +
251B VAL* 3.8 31.6 - - + -
295B ALA 4.0 6.3 + - - +
296B LEU* 3.5 12.2 + - + +
297B LEU 3.4 0.2 - - - -
298B GLU* 1.3 82.9 + - - +
300B ALA* 1.3 54.5 + - + +
302B VAL* 2.9 7.3 + - + +
303B ASN* 2.5 67.6 + - + +
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Residues in contact with ALA 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A VAL* 3.7 31.0 - - + +
246A TRP* 4.0 12.5 - - + +
247A LEU* 3.8 22.4 - - + -
258A PHE* 5.8 1.1 - - + -
296B LEU 3.5 7.9 + - - +
297B LEU* 4.0 9.9 - - + +
298B GLU 3.4 0.4 - - - -
299B TYR* 1.3 78.6 - - + +
301B PHE* 1.3 56.7 + - - +
303B ASN 3.9 0.9 - - - -
304B TYR* 3.3 25.8 + - - +
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Residues in contact with PHE 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B LEU 3.0 17.3 + - - +
298B GLU* 3.5 7.9 - - + +
299B TYR 3.1 0.2 - - - -
300B ALA* 1.3 77.4 - - - +
302B VAL* 1.3 61.8 + - - +
304B TYR* 3.8 11.4 + + - +
305B ILE* 3.3 50.0 + - + +
309B ARG* 6.3 1.1 - - - -
417B LEU* 3.6 31.6 - - + -
423B ILE* 3.7 22.2 - - + -
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Residues in contact with VAL 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B TYR* 3.9 19.1 - - + -
250B ARG* 4.0 7.6 - - - +
298B GLU* 2.9 38.0 + - - +
299B TYR* 2.9 12.8 + - + +
301B PHE* 1.3 77.1 - - - +
303B ASN* 1.3 61.5 + - - +
304B TYR 3.1 2.2 + - - -
305B ILE* 3.3 4.2 + - - +
306B PHE* 3.3 23.4 + - - +
420B VAL* 3.7 31.3 - - + +
423B ILE* 4.2 20.2 - - + -
424B ASP* 4.0 8.7 - - - +
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Residues in contact with ASN 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TRP 4.2 5.3 - - - +
247A LEU* 3.4 36.0 - - + +
248A ASN* 3.6 21.3 + - - +
251A SER* 4.6 2.0 + - - -
244B TYR 5.5 0.2 - - - +
247B SER* 4.4 4.5 + - - -
299B TYR* 2.5 51.5 + - + +
300B ALA 4.1 0.7 - - - -
302B VAL* 1.3 73.1 - - - +
304B TYR* 1.3 57.2 + - - +
306B PHE* 4.5 0.9 - - - -
307B PHE* 3.1 44.9 - - - +
----------------------------------------------------------
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Residues in contact with TYR 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TRP* 3.6 42.3 - + + +
397A ARG* 3.3 31.2 + - - -
300B ALA 3.3 18.9 + - - +
301B PHE* 4.1 13.0 - + - +
302B VAL 3.1 0.8 - - - -
303B ASN* 1.3 78.3 - - - +
305B ILE* 1.3 65.8 + - + +
308B GLY* 2.8 35.3 + - - +
309B ARG* 3.1 57.4 + - + +
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Residues in contact with ILE 305 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PHE* 3.3 49.3 + - + +
302B VAL* 3.3 5.3 + - - +
304B TYR* 1.3 80.7 - - + +
306B PHE* 1.3 59.5 + - - +
309B ARG* 3.4 28.1 - - + +
310B GLY* 3.1 25.6 + - - -
417B LEU* 5.0 1.3 - - + -
418B THR* 4.3 29.8 - - + +
419B ASP 4.4 6.5 - - - +
420B VAL* 4.7 10.8 - - + -
423B ILE* 3.7 15.3 - - + -
----------------------------------------------------------
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Residues in contact with PHE 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A TRP* 3.2 47.4 - + - -
318A ASP 3.6 22.9 - - - -
319A GLY* 4.4 9.0 - - - -
244B TYR* 3.4 43.5 - + + -
245B ASP* 4.3 5.8 - - - -
302B VAL 3.3 12.3 + - - +
303B ASN* 5.3 0.2 - - - -
305B ILE* 1.3 79.1 - - - +
307B PHE* 1.3 86.1 + + + +
310B GLY* 4.3 2.2 - - - -
420B VAL* 3.6 27.8 - - + -
----------------------------------------------------------
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il