Contacts of the helix formed by residues 277 - 301 (chain K) in PDB entry 4BOG
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 TYR 277 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135K PHE* 2.9 30.5 + + - -
136K PRO* 2.5 19.4 - - + +
137K PHE* 2.4 42.7 + + + +
138K ASP* 4.6 0.4 - - - -
210K ILE* 3.5 10.6 - - + +
273K LEU* 4.0 17.5 - - + -
274K ILE* 2.5 65.1 + - + +
276K LYS* 1.3 70.8 - - - +
278K MET* 1.3 58.8 + - - +
280K PHE* 2.7 61.8 + + + +
281K THR* 3.9 1.2 + - - +
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Residues in contact with MET 278 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268K SER* 6.1 3.6 - - - +
273K LEU* 5.4 8.2 - - + +
275K GLY* 2.6 27.0 + - - +
277K TYR* 1.3 71.6 - - - +
279K LEU* 1.3 60.5 + - + +
281K THR* 2.6 41.2 + - + +
282K MET* 2.8 54.3 + - + +
220O PHE* 4.9 17.9 - - + +
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Residues in contact with LEU 279 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275K GLY 3.5 5.4 + - - +
276K LYS* 3.9 14.3 + - - +
277K TYR 3.3 1.0 - - - -
278K MET* 1.3 76.1 - - + +
280K PHE* 1.3 71.5 + - + +
282K MET* 3.0 52.9 + - + +
283K ILE* 3.1 29.6 + - + +
284K PHE* 4.6 1.0 - - - -
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Residues in contact with PHE 280 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137K PHE* 6.6 0.2 - + - -
274K ILE* 6.1 0.4 - - + -
276K LYS* 2.7 22.7 - - + -
277K TYR* 2.7 53.8 + + + +
279K LEU* 1.3 79.0 - - + +
281K THR* 1.3 59.4 + - - +
284K PHE* 2.5 64.8 + + + -
427K ALA* 5.8 9.9 - - + -
428K GLY* 6.5 1.8 - - - -
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Residues in contact with THR 281 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261K VAL* 5.9 2.6 - - - +
264K ILE* 4.8 18.1 - - + +
277K TYR 5.2 0.4 - - - -
278K MET* 2.6 45.1 + - + +
280K PHE* 1.3 79.0 - - - +
282K MET* 1.3 75.8 + - - +
284K PHE* 4.2 7.2 - - - -
285K VAL* 2.6 40.1 + - + +
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Residues in contact with MET 282 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278K MET* 2.8 57.6 + - + +
279K LEU* 3.0 43.0 + - + +
281K THR* 1.3 80.6 - - - +
283K ILE* 1.3 59.5 + - - +
285K VAL* 3.9 4.3 - - - -
286K ILE* 2.8 43.9 + - + +
220O PHE 5.2 5.4 - - - +
223O ILE* 4.7 26.5 - - + -
224O ASN* 5.8 1.1 - - - +
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Residues in contact with ILE 283 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279K LEU* 3.1 26.7 + - + +
282K MET* 1.3 77.5 - - - +
284K PHE* 1.3 63.3 + - + +
286K ILE* 4.3 5.8 - - + -
287K SER* 2.6 40.7 + - - +
290K ILE* 5.8 6.3 - - + -
420K ILE* 6.4 2.7 - - + -
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Residues in contact with PHE 284 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225K PHE* 5.1 6.5 - - - -
279K LEU 4.6 1.3 - - - -
280K PHE* 2.5 56.5 + + + +
281K THR* 3.6 4.7 - - - +
283K ILE* 1.3 88.0 - - + +
285K VAL* 1.3 61.5 + - - +
287K SER* 3.1 11.9 + - - -
288K SER* 3.3 9.7 + - - -
420K ILE* 5.5 7.8 - - + +
423K VAL 5.4 0.4 - - - -
424K SER* 3.0 54.3 - - - -
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Residues in contact with VAL 285 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225K PHE* 5.8 2.5 - - - -
257K LEU* 2.9 41.1 - - + +
260K ILE* 6.2 1.1 - - + -
261K VAL* 5.6 7.4 - - + -
281K THR* 2.6 44.4 + - + +
282K MET* 2.8 8.1 - - - +
284K PHE* 1.3 74.3 - - - +
286K ILE* 1.3 81.5 + - + +
288K SER* 3.0 27.0 - - - -
289K ILE* 3.2 12.1 + - + +
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Residues in contact with ILE 286 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282K MET* 2.8 47.3 + - + +
283K ILE* 3.4 5.2 - - + +
285K VAL* 1.3 91.4 - - + +
287K SER* 1.3 53.3 + - - +
289K ILE* 2.6 28.6 - - + +
290K ILE* 2.6 47.5 + - + +
223O ILE* 5.0 7.4 - - + +
227O ALA* 4.1 28.7 - - + -
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Residues in contact with SER 287 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283K ILE* 2.6 27.1 + - - -
284K PHE* 3.1 6.5 + - - -
286K ILE* 1.3 68.7 - - - +
288K SER* 1.3 56.0 + - - +
289K ILE 2.7 5.2 - - - -
290K ILE* 3.7 13.7 - - - -
291K VAL* 2.6 59.5 + - - +
416K LEU* 5.1 1.6 - - - +
420K ILE* 4.0 27.1 - - - +
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Residues in contact with SER 288 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225K PHE* 3.8 39.6 - - - -
229K THR* 4.8 4.5 + - - +
253K LEU* 4.4 14.0 - - - +
254K THR* 5.1 0.7 + - - -
257K LEU* 4.6 9.5 - - - +
284K PHE 3.3 3.4 + - - -
285K VAL* 3.0 19.7 + - - -
287K SER* 1.3 77.4 - - - +
289K ILE* 1.3 55.4 - - - +
291K VAL* 4.3 3.1 - - - +
292K THR* 2.4 40.9 + - - +
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Residues in contact with ILE 289 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254K THR* 3.2 29.4 - - + +
257K LEU* 5.7 3.8 - - + -
285K VAL* 3.4 15.3 - - + +
286K ILE* 2.6 32.8 - - + +
288K SER* 1.3 80.9 - - - +
290K ILE* 1.3 66.6 + - + +
292K THR* 2.3 23.7 + - + +
293K VAL* 3.2 14.8 + - + +
227O ALA 5.2 2.0 - - - +
231O LEU* 3.9 45.5 - - + +
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Residues in contact with ILE 290 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283K ILE* 5.8 6.7 - - + -
286K ILE* 2.6 39.7 + - + +
287K SER* 3.7 12.6 - - - -
289K ILE* 1.3 76.0 - - + +
291K VAL* 1.3 59.9 + - + +
293K VAL* 2.9 29.5 - - + +
294K VAL* 3.1 10.4 + - - +
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Residues in contact with VAL 291 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229K THR* 4.9 7.4 - - + -
233K PHE* 4.4 9.4 - - + -
287K SER* 2.6 48.6 + - - +
288K SER* 4.3 3.1 - - - +
290K ILE* 1.3 69.5 - - + +
292K THR* 1.3 54.5 + - - +
294K VAL* 2.9 8.1 - - + +
295K VAL* 2.4 66.8 + - + +
413K VAL* 3.9 23.6 - - + -
416K LEU* 4.4 18.4 - - + -
417K ILE* 6.2 0.2 - - + -
420K ILE* 5.6 1.6 - - + -
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Residues in contact with THR 292 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229K THR* 5.2 11.8 - - + +
232K VAL* 5.8 0.2 - - - -
250K LEU* 3.1 31.9 - - + -
253K LEU* 5.4 7.0 - - + -
254K THR* 5.8 2.5 - - - +
288K SER* 2.4 29.9 + - - +
289K ILE* 2.3 34.8 + - + +
291K VAL* 1.3 76.3 - - - +
293K VAL* 1.3 59.9 + - - -
295K VAL* 4.1 1.6 - - - -
296K ILE* 2.4 48.2 + - + +
231O LEU* 5.7 1.6 - - - +
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Residues in contact with VAL 293 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289K ILE* 3.5 11.4 - - + +
290K ILE* 2.9 27.6 - - + +
292K THR* 1.3 78.5 + - - +
294K VAL* 1.3 56.5 + - + +
296K ILE* 4.2 3.8 - - - -
297K ASN* 2.6 40.8 + - - +
231O LEU* 4.8 6.1 - - + +
234O SER* 3.1 32.5 - - - +
235O LEU 4.7 0.4 - - - +
238O LEU* 3.5 30.5 - - + +
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Residues in contact with VAL 294 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290K ILE 3.1 9.4 + - - +
291K VAL* 2.9 18.2 + - + +
292K THR 2.7 4.6 + - - -
293K VAL* 1.3 81.1 - - + +
295K VAL* 1.3 83.8 + - + +
297K ASN* 3.7 10.9 - - - +
298K THR* 2.5 51.2 + - - +
409K ILE* 6.0 4.7 - - + -
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Residues in contact with VAL 295 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232K VAL* 3.6 37.0 - - + +
233K PHE* 4.7 16.4 - - + -
236K PRO* 6.1 0.2 - - + -
291K VAL* 2.4 63.6 + - + +
292K THR 2.7 1.5 + - - +
294K VAL* 1.3 79.4 - - + +
296K ILE* 1.3 54.2 + - + +
298K THR* 3.3 7.7 - - - +
299K HIS* 2.4 39.6 + - + +
409K ILE* 5.4 16.3 - - + +
413K VAL* 4.9 5.6 - - + -
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Residues in contact with ILE 296 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232K VAL* 4.4 5.6 - - + -
243K MET 5.8 1.6 - - - +
246K SER* 5.8 0.2 - - - -
250K LEU* 3.1 49.8 - - + -
292K THR* 2.4 69.4 + - + +
293K VAL* 3.7 4.0 - - - +
295K VAL* 1.3 74.4 - - + +
297K ASN* 1.3 58.5 + - - +
298K THR 3.1 1.1 - - - -
299K HIS* 3.0 29.8 - - + +
300K HIS* 2.8 45.5 + - + +
238O LEU* 5.4 9.0 - - + -
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Residues in contact with ASN 297 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293K VAL 2.6 23.7 + - - +
294K VAL* 3.7 12.1 + - - +
296K ILE* 1.3 77.0 - - - +
298K THR* 1.3 54.3 + - - +
300K HIS* 3.0 12.0 - - - +
301K ARG* 2.4 30.9 + - - +
238O LEU* 4.5 17.2 - - + +
242O LEU* 5.9 1.6 - - + -
245O GLN* 2.7 38.1 + - - +
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Residues in contact with THR 298 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294K VAL* 2.5 33.6 + - - +
295K VAL* 3.5 4.7 - - - +
297K ASN* 1.3 73.5 + - - +
299K HIS* 1.3 69.1 + - - +
300K HIS 2.8 1.8 - - - -
301K ARG* 2.7 65.2 + - - +
405K VAL* 5.8 0.9 - - + -
409K ILE* 4.2 27.4 - - + -
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Residues in contact with HIS 299 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232K VAL* 3.4 29.0 + - + +
235K LEU* 5.3 2.4 - - + +
236K PRO* 3.5 30.6 - - + +
243K MET* 4.2 35.3 + - + +
246K SER* 4.7 10.4 - - - -
295K VAL* 2.4 32.4 + - + +
296K ILE* 3.0 36.3 - - + +
298K THR* 1.3 69.4 - - - +
300K HIS* 1.3 55.1 - + + +
301K ARG* 4.5 4.6 + - - +
306K HIS* 2.1 35.7 + + - +
406K ILE* 6.0 2.5 - - - -
409K ILE* 6.1 2.0 - - - -
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Residues in contact with HIS 300 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243K MET* 5.1 12.8 + - + +
244K THR 5.6 0.2 + - - -
247K ILE* 5.3 5.1 - - + +
250K LEU* 6.2 1.1 - - + -
296K ILE* 2.8 29.2 + - + +
297K ASN* 3.0 15.0 - - - +
299K HIS* 1.3 78.0 + - + +
301K ARG* 1.3 47.4 + - - -
302K SER 2.5 20.0 + - - -
306K HIS* 2.5 30.9 - - + +
238O LEU* 5.6 6.6 - - + +
242O LEU* 3.4 40.6 - - + +
245O GLN* 3.3 25.2 - - + +
246O ALA 4.9 1.3 - - - +
250O LYS* 4.5 14.2 - - - -
253O LEU* 3.8 23.1 - - + +
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Residues in contact with ARG 301 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297K ASN* 2.4 19.9 + - - +
298K THR* 2.7 59.8 + - - +
299K HIS 4.5 4.0 + - - +
300K HIS* 1.3 60.2 - - - +
302K SER* 1.3 65.7 + - - +
303K PRO* 4.1 4.5 - - - +
400K LYS 5.3 0.4 + - - -
401K TYR* 6.1 0.8 - - - +
402K VAL* 4.6 16.6 + - - +
405K VAL* 3.3 27.5 - - - +
406K ILE* 3.0 38.1 - - - +
245O GLN* 4.0 20.9 - - - +
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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