Contacts of the helix formed by residues 281 - 307 (chain B) in PDB entry 2BG9
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).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B VAL* 6.3 0.7 - - + -
279B ILE 4.5 4.5 - - - +
280B ILE* 1.3 85.4 - - + +
282B SER* 1.3 53.9 + - - +
283B TYR* 3.3 2.0 - - - -
284B LEU* 2.4 54.4 + - + +
285B MET* 2.5 55.9 + - + +
288B MET* 5.5 3.1 - - + -
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Residues in contact with SER 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B PRO* 6.4 0.4 - - - -
137B PHE* 5.4 0.6 - - - -
280B ILE* 3.3 17.2 - - - +
281B ILE* 1.3 77.1 - - - +
283B TYR* 1.3 87.0 + - - -
285B MET* 3.1 28.8 + - - +
286B PHE* 2.6 31.5 + - - -
460B HIS* 3.3 33.0 + - - -
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Residues in contact with TYR 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B PHE* 4.1 42.3 + + + -
136B PRO* 5.7 1.1 - - + -
137B PHE* 2.7 46.0 - + - -
221B ILE* 4.9 26.2 - - + -
280B ILE* 5.1 5.6 - - + -
281B ILE 2.7 2.6 + - - +
282B SER* 1.3 95.5 + - - +
284B LEU* 1.3 55.2 + - - +
286B PHE* 3.3 15.1 - + + -
287B ILE* 2.7 42.0 + - + +
457B ASP* 4.7 9.9 - - - -
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Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B VAL* 3.7 34.3 - - + +
271B PRO* 6.3 0.4 - - + -
274B SER* 5.5 8.7 - - - +
281B ILE* 2.4 32.0 + - + +
283B TYR* 1.3 72.9 - - + +
285B MET* 1.3 52.0 + - - +
287B ILE* 3.2 27.1 - - + -
288B MET* 2.5 56.8 + - + +
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Residues in contact with MET 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ILE* 6.5 0.2 - - - -
281B ILE* 2.5 42.8 + - + +
282B SER* 3.2 27.1 - - - +
284B LEU* 1.3 73.2 - - - +
286B PHE* 1.3 63.4 + - + +
288B MET* 2.9 11.8 - - - +
289B ILE* 2.9 23.6 - - + +
456B LEU* 6.0 3.6 - - + -
460B HIS* 5.2 7.9 - - + +
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Residues in contact with PHE 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B SER* 2.6 37.7 - - - -
283B TYR* 3.3 13.5 - + + -
285B MET* 1.3 79.3 - - + +
287B ILE* 1.3 83.7 + - + +
288B MET 2.9 5.6 - - - -
289B ILE* 2.7 15.5 + - + +
290B LEU* 2.4 49.9 + - + +
453B SER* 3.3 15.7 - - - -
456B LEU* 4.4 12.3 - - + -
457B ASP* 2.7 42.0 - - - -
460B HIS* 3.7 20.9 - + - -
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Residues in contact with ILE 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B THR* 6.0 6.3 - - + -
228B CYS* 5.1 14.2 - - - -
270B VAL* 6.0 4.5 - - + -
283B TYR* 2.7 36.4 + - + +
284B LEU* 3.2 33.4 - - + -
286B PHE* 1.3 94.7 - - + +
288B MET* 1.3 57.9 + - - +
290B LEU* 3.1 16.3 - - + +
291B VAL* 2.4 42.9 + - + +
457B ASP* 5.3 0.4 - - - +
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Residues in contact with MET 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A VAL* 5.2 14.4 - - + -
217A ASN* 5.5 12.6 - - + +
220A ILE* 5.8 3.4 - - + -
281B ILE* 6.0 2.9 - - + -
284B LEU* 2.5 35.6 + - + +
285B MET* 2.9 13.9 - - - +
287B ILE* 1.3 79.3 - - + +
289B ILE* 1.3 61.2 + - + +
291B VAL* 2.6 37.7 - - + +
292B ALA* 2.9 10.0 + - + +
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Residues in contact with ILE 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B MET* 2.9 21.5 - - + +
286B PHE* 3.0 16.8 - - + +
288B MET* 1.3 83.8 - - + +
290B LEU* 1.3 50.2 + - + +
291B VAL 3.0 1.3 - - - -
292B ALA* 3.1 6.1 + - + +
293B PHE* 2.6 85.6 + - + -
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Residues in contact with LEU 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B CYS* 5.2 14.8 - - + -
286B PHE* 2.4 38.5 + - + +
287B ILE* 3.1 33.4 - - + +
289B ILE* 1.3 72.9 - - + +
291B VAL* 1.3 62.3 + - - +
293B PHE* 3.3 10.8 - - + +
294B SER* 3.0 25.8 + - - -
449B ILE* 3.9 22.9 - - + +
450B GLY* 4.8 4.7 - - - -
453B SER* 2.8 32.1 - - - +
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Residues in contact with VAL 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B LEU* 3.3 36.8 - - + +
287B ILE* 2.4 31.5 + - + +
288B MET* 2.6 29.6 - - + +
290B LEU* 1.3 72.5 - - - +
292B ALA* 1.3 79.6 + - + +
293B PHE 2.9 1.8 + - - -
294B SER* 3.1 2.6 + - - -
295B VAL* 2.7 46.0 + - + +
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B MET* 2.9 10.5 + - + +
289B ILE* 3.4 12.8 - - + +
291B VAL* 1.3 84.0 - - + +
293B PHE* 1.3 63.9 + - + +
295B VAL* 3.4 8.7 - - - +
296B ILE* 2.9 39.8 + - + +
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Residues in contact with PHE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ILE* 2.6 55.9 + - + +
290B LEU* 3.3 13.7 - - + +
291B VAL 2.9 1.2 - - - -
292B ALA* 1.3 79.1 - - + +
294B SER* 1.3 52.7 + - - +
296B ILE* 4.2 2.1 - - + +
297B LEU* 2.7 40.8 + - - +
445B THR* 5.8 1.3 - - + -
449B ILE* 3.5 55.2 - - + -
452B PHE* 6.1 0.2 - + - -
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Residues in contact with SER 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B CYS 5.3 1.6 + - - -
231B ILE* 5.4 4.4 - - - +
232B SER* 4.8 9.9 + - - -
235B ALA* 4.8 11.6 - - - +
239B PHE* 5.5 4.3 - - - -
259B LEU* 5.2 8.1 - - - +
263B LEU* 5.0 15.7 - - - -
290B LEU 3.0 17.4 + - - -
291B VAL* 3.9 2.5 - - - -
293B PHE* 1.3 71.4 - - - +
295B VAL* 1.3 59.9 + - - +
297B LEU* 4.3 6.1 - - - -
298B SER* 2.8 32.6 + - - -
449B ILE* 5.3 0.8 - - - +
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Residues in contact with VAL 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LEU* 5.9 7.9 - - + -
259B LEU* 6.4 0.7 - - - -
260B THR* 6.0 8.7 - - + +
263B LEU* 5.4 13.2 - - + -
291B VAL* 2.7 42.8 + - + +
292B ALA* 3.4 9.9 - - - +
294B SER* 1.3 72.6 - - - +
296B ILE* 1.3 68.3 + - + +
298B SER* 2.6 21.7 + - - -
299B VAL* 2.9 22.7 + - + +
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Residues in contact with ILE 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A PHE* 5.8 6.1 - - + -
292B ALA* 2.9 23.3 + - + +
293B PHE* 4.2 2.0 - - + +
295B VAL* 1.3 78.6 - - + +
297B LEU* 1.3 58.5 + - - +
298B SER 3.2 1.8 - - - -
299B VAL* 3.5 13.5 - - + -
300B VAL* 2.6 42.4 + - + +
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Residues in contact with LEU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B PHE* 4.9 11.4 - - + -
293B PHE 2.7 25.0 + - - +
294B SER* 4.1 4.3 - - - +
296B ILE* 1.3 75.5 - - - +
298B SER* 1.3 58.5 + - - +
300B VAL* 3.7 9.0 - - + +
301B VAL* 2.8 56.0 + - + +
441B TYR* 4.7 9.2 - - + +
442B ILE* 3.9 21.8 - - + -
445B THR* 3.1 44.4 - - + +
446B MET* 5.0 4.9 - - + +
449B ILE* 5.3 2.7 - - + -
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Residues in contact with SER 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B PHE* 4.4 13.4 - - - -
256B LEU* 2.8 49.2 - - - +
259B LEU* 4.9 6.7 - - - +
260B THR* 5.2 3.8 + - - -
294B SER 2.8 16.0 + - - -
295B VAL* 2.6 23.4 + - - -
297B LEU* 1.3 74.3 - - - +
299B VAL* 1.3 57.9 + - - +
301B VAL* 2.6 29.6 - - - +
302B LEU 3.1 3.3 + - - -
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Residues in contact with VAL 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LEU* 5.5 10.8 - - + -
227A PHE* 4.2 26.7 - - + -
228A LEU* 4.9 10.8 - - + -
231A LEU* 4.5 13.3 - - + +
256B LEU* 5.0 2.0 - - + -
260B THR* 5.6 5.2 - - - +
295B VAL* 2.9 29.4 + - + +
296B ILE* 3.1 15.8 + - + +
298B SER* 1.3 81.4 + - - +
300B VAL* 1.3 61.3 + - - +
302B LEU* 2.8 16.4 - - + +
303B ASN* 2.8 22.3 + - - +
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Residues in contact with VAL 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A PHE* 5.6 6.3 - - + -
296B ILE* 2.6 32.0 + - + +
297B LEU* 3.7 13.9 - - + +
299B VAL* 1.3 71.1 - - - +
301B VAL* 1.3 61.4 + - + +
302B LEU 2.9 1.6 - - - -
303B ASN* 2.7 17.7 + - + +
304B LEU* 2.4 32.2 + - - +
441B TYR* 5.5 8.3 - - + -
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Residues in contact with VAL 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B VAL* 5.2 1.3 - - + -
239B PHE* 4.3 18.8 - - + -
256B LEU* 4.8 0.9 - - + -
297B LEU* 2.8 42.5 + - + +
298B SER* 2.6 37.2 - - - +
300B VAL* 1.3 79.8 - - + +
302B LEU* 1.3 51.8 + - - +
304B LEU* 2.8 19.5 + - + +
305B HIS* 2.5 51.3 + - + +
442B ILE* 3.8 17.9 - - + -
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Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A LEU* 4.2 21.5 - - + -
231A LEU* 4.9 9.2 - - + -
235A LEU* 5.8 1.9 - - + +
242A LYS* 4.3 4.9 + - - +
252B SER* 4.9 1.1 - - - +
253B ILE* 3.2 51.4 - - + +
256B LEU* 3.3 29.8 - - + -
298B SER 3.2 6.3 - - - +
299B VAL* 2.8 19.5 - - + +
301B VAL* 1.3 83.2 - - - +
303B ASN* 1.3 55.2 + - - +
305B HIS* 3.1 21.7 + - + +
306B HIS* 2.8 24.8 + - - +
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Residues in contact with ASN 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A PHE* 2.8 36.6 - - + -
231A LEU* 3.6 16.4 - - + +
299B VAL 2.8 11.5 + - - +
300B VAL* 2.7 21.8 + - + +
302B LEU* 1.3 75.8 - - - +
304B LEU* 1.3 65.1 + - - +
305B HIS 3.1 0.2 - - - -
306B HIS* 3.9 14.0 - - - +
307B ARG* 3.0 25.1 + - - +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PRO* 6.1 3.1 - - + -
300B VAL 2.4 18.3 + - - +
301B VAL* 2.9 32.5 - - + +
303B ASN* 1.3 71.8 - - - +
305B HIS* 1.3 77.8 + - + +
307B ARG* 3.8 28.9 + - - +
434B VAL* 3.8 32.1 - - + -
435B ALA* 4.4 19.3 - - + +
438B LEU* 4.2 21.8 - - + -
442B ILE* 5.1 2.9 - - + -
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Residues in contact with HIS 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LYS* 4.3 2.5 - - - +
238B VAL* 4.1 23.2 + - + +
239B PHE* 6.0 0.2 - - - -
242B PRO* 4.3 15.6 - - + +
248B LYS* 3.9 23.0 - - + +
249B MET* 5.7 1.0 - - - -
252B SER* 4.3 11.4 - - - +
301B VAL* 2.5 42.5 + - + +
302B LEU* 3.1 25.8 - - + +
304B LEU* 1.3 88.2 - - + +
306B HIS* 1.3 50.9 + - - +
308B SER* 4.3 4.9 + - - -
311B THR* 4.6 1.9 - - - +
312B HIS* 2.6 49.0 + + + +
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Residues in contact with HIS 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU* 5.5 6.7 - - + -
234A TYR* 3.1 3.2 + - + -
235A LEU* 2.6 63.0 + - + -
238A ASP* 3.0 44.9 + - + +
239A SER* 3.5 4.7 - - - -
242A LYS* 4.1 4.7 - - - +
302B LEU 2.8 15.0 + - - +
303B ASN* 3.3 16.1 + - - +
305B HIS* 1.3 72.6 - - - +
307B ARG* 1.3 55.3 + - - +
308B SER 2.4 22.0 + - - +
312B HIS 2.4 23.8 - - - -
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Residues in contact with ARG 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A ASP* 5.9 2.9 - - - -
303B ASN* 3.0 17.2 + - - +
304B LEU* 3.8 22.5 + - - +
305B HIS 3.5 2.0 - - - -
306B HIS* 1.3 77.2 - - - +
308B SER* 1.3 76.8 + - - +
309B PRO* 3.7 7.8 - - - +
429B GLN 3.4 21.2 + - - -
430B TYR* 4.1 9.3 - - - +
431B VAL* 4.9 2.8 - - - +
432B ALA 5.7 1.6 - - - +
434B VAL* 2.9 39.8 - - - +
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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