Contacts of the helix formed by residues 277 - 301 (chain N) 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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135N PHE* 3.8 23.6 - + - -
136N PRO* 3.3 27.7 - - + +
137N PHE* 3.3 38.4 - + - -
138N ASP* 4.7 0.9 + - - -
210N ILE* 4.1 1.1 - - + +
273N LEU* 4.5 11.7 - - + -
274N ILE* 2.9 48.8 + - + +
275N GLY 2.4 6.9 + - - -
276N LYS* 1.3 70.2 - - - +
278N MET* 1.3 53.3 + - - +
279N LEU 2.9 4.9 - - - -
280N PHE* 2.7 63.8 + + - +
281N THR* 4.0 0.5 + - - -
431N ILE* 4.8 10.9 - - + +
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Residues in contact with MET 278 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231M ASN* 4.9 4.9 - - - +
261N VAL* 5.0 10.3 - - + -
264N ILE* 3.6 39.3 - - + -
268N SER* 6.2 0.9 - - - +
273N LEU* 5.5 9.0 - - + +
275N GLY* 2.9 14.3 + - - +
277N TYR* 1.3 75.3 - - - +
279N LEU* 1.3 51.2 + - + +
281N THR* 2.6 50.7 + - - -
282N MET* 2.8 64.0 + - + +
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Residues in contact with LEU 279 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275N GLY 3.7 9.6 - - - +
276N LYS* 3.2 36.1 - - + +
278N MET* 1.3 77.8 - - + +
280N PHE* 1.3 68.4 + - + +
282N MET* 3.2 24.8 - - + +
283N ILE* 3.5 14.3 + - - +
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Residues in contact with PHE 280 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276N LYS* 2.6 27.6 - - + -
277N TYR* 2.7 49.2 + + - +
279N LEU* 1.3 76.9 - - + +
281N THR* 1.3 58.7 + - - +
284N PHE* 2.6 64.0 + + + -
424N SER 5.8 1.3 - - - -
427N ALA* 5.6 7.6 - - + -
428N GLY* 5.4 12.6 - - - -
431N ILE* 4.0 24.7 - - + -
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Residues in contact with THR 281 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218N VAL* 4.0 27.8 - - + -
222N CYS* 6.2 3.4 - - - -
260N ILE* 6.5 0.4 - - + -
261N VAL* 6.3 0.4 - - - -
264N ILE* 5.5 6.5 - - + -
277N TYR 4.3 0.5 + - - -
278N MET* 2.6 46.1 + - - -
280N PHE* 1.3 75.4 - - - +
282N MET* 1.3 68.5 + - - +
284N PHE* 4.0 10.5 - - + -
285N VAL* 2.7 31.3 + - + +
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Residues in contact with MET 282 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231M ASN* 3.9 26.5 - - - +
234M THR* 5.3 11.0 - - + -
261N VAL* 5.5 6.7 - - + -
278N MET* 2.8 35.4 + - + +
279N LEU* 3.2 23.6 - - + +
280N PHE 3.2 0.2 - - - -
281N THR* 1.3 79.3 - - - +
283N ILE* 1.3 54.2 + - + +
285N VAL* 3.9 6.6 - - + +
286N ILE* 2.7 67.4 + - + +
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Residues in contact with ILE 283 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279N LEU 3.6 14.1 - - - +
280N PHE* 3.9 2.9 - - - +
282N MET* 1.3 80.0 - - + +
284N PHE* 1.3 70.9 + - + +
286N ILE* 3.1 17.4 - - + +
287N SER* 2.5 37.8 + - - -
290N ILE* 4.8 1.2 - - - +
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Residues in contact with PHE 284 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222N CYS* 6.0 8.7 - - - -
225N PHE* 5.9 0.8 - - + -
280N PHE* 2.6 58.2 + + + +
281N THR* 3.8 9.2 - - + +
283N ILE* 1.3 87.6 - - + +
285N VAL* 1.3 60.2 + - + +
287N SER* 2.6 27.4 + - - -
288N SER* 3.3 5.0 + - - -
420N ILE* 4.6 12.7 - - + +
423N VAL* 5.3 5.8 - - + -
424N SER* 2.9 51.8 - - - +
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Residues in contact with VAL 285 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222N CYS* 5.3 0.7 - - - -
225N PHE* 3.1 42.8 - - + -
257N LEU* 4.2 29.1 - - + +
261N VAL* 5.6 8.7 - - + -
281N THR* 2.7 26.2 + - + +
282N MET* 4.0 8.5 - - + +
284N PHE* 1.3 72.6 - - + +
286N ILE* 1.3 70.1 + - + +
287N SER 2.6 5.4 - - - -
288N SER* 2.8 18.4 + - - +
289N ILE* 3.0 13.7 + - + +
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Residues in contact with ILE 286 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234M THR* 5.7 6.3 - - + -
238M LEU* 4.0 30.3 - - + -
282N MET* 2.7 75.9 + - + +
283N ILE* 3.1 19.1 - - + +
285N VAL* 1.3 75.3 - - + +
287N SER* 1.3 52.7 + - - +
289N ILE* 3.0 7.5 + - + -
290N ILE* 2.4 56.6 + - + +
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Residues in contact with SER 287 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283N ILE 2.5 12.3 + - - -
284N PHE* 2.6 18.2 - - - -
285N VAL 2.6 0.8 - - - -
286N ILE* 1.3 76.5 - - - +
288N SER* 1.3 55.3 + - - -
290N ILE* 2.9 23.3 - - - +
291N VAL* 2.7 47.7 + - - +
417N ILE* 5.7 0.3 - - - +
420N ILE* 3.1 29.2 - - - +
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Residues in contact with SER 288 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225N PHE* 5.2 10.2 - - - -
229N THR* 3.1 31.2 - - - +
253N LEU* 4.8 7.9 - - - +
257N LEU* 5.4 7.3 - - - +
284N PHE 3.3 3.9 + - - -
285N VAL* 2.8 22.8 + - - -
287N SER* 1.3 74.7 - - - +
289N ILE* 1.3 57.6 + - - +
291N VAL* 3.9 5.1 - - - +
292N THR* 2.7 31.1 + - - -
417N ILE* 6.0 5.4 - - - -
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Residues in contact with ILE 289 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238M LEU* 3.6 36.3 - - + -
241M PHE* 4.6 4.3 - - + -
253N LEU* 5.7 4.3 - - + -
254N THR* 4.7 8.3 - - - +
257N LEU* 4.8 17.3 - - + -
258N LEU* 4.6 20.2 - - + -
285N VAL* 3.0 11.3 + - + +
286N ILE* 3.4 13.5 - - + +
287N SER 3.0 0.4 - - - -
288N SER* 1.3 75.8 - - - +
290N ILE* 1.3 58.1 + - + +
291N VAL 3.0 0.3 + - - -
292N THR* 3.0 10.8 + - + +
293N VAL* 2.5 51.6 + - + +
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Residues in contact with ILE 290 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283N ILE 4.8 1.3 - - - +
286N ILE* 2.4 51.8 + - + +
287N SER* 2.7 52.0 - - - +
289N ILE* 1.3 66.6 - - + +
291N VAL* 1.3 66.4 + - + +
293N VAL* 2.8 29.9 - - - +
294N VAL* 3.0 13.7 + - - +
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Residues in contact with VAL 291 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233N PHE* 3.7 8.3 - - + -
287N SER* 2.7 41.8 + - - +
288N SER* 3.9 4.3 - - - +
290N ILE* 1.3 79.6 - - + +
292N THR* 1.3 57.0 + - - +
293N VAL 2.9 1.2 + - - -
294N VAL* 3.0 3.6 + - - -
295N VAL* 2.4 67.6 + - + +
413N VAL* 3.4 34.8 - - + -
417N ILE* 5.1 5.4 - - + -
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Residues in contact with THR 292 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241M PHE* 6.1 0.9 - - + -
229N THR* 6.5 0.9 - - - -
232N VAL* 4.9 2.7 - - - +
250N LEU* 2.5 39.5 - - + +
253N LEU* 5.2 2.5 - - + -
288N SER* 2.7 20.7 + - - +
289N ILE* 3.2 20.9 - - + +
291N VAL* 1.3 72.6 - - - +
293N VAL* 1.3 69.2 - - + +
295N VAL* 3.0 13.2 - - - +
296N ILE* 2.7 52.0 + - + +
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Residues in contact with VAL 293 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241M PHE* 2.9 46.9 - - + -
245M LEU* 4.8 2.9 - - + -
289N ILE* 2.5 38.9 + - + +
290N ILE* 2.8 15.9 - - - +
292N THR* 1.3 78.4 - - + +
294N VAL* 1.3 60.8 + - + +
297N ASN* 2.4 54.2 + - - +
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Residues in contact with VAL 294 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290N ILE 3.0 9.7 + - - +
291N VAL* 3.8 5.8 - - - +
293N VAL* 1.3 86.2 - - + +
295N VAL* 1.3 59.5 + - + +
297N ASN* 4.1 3.4 - - - -
298N THR* 2.3 60.8 + - + +
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Residues in contact with VAL 295 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232N VAL* 4.0 23.6 - - + -
233N PHE* 3.9 12.3 - - + -
291N VAL* 2.4 65.9 + - + +
292N THR* 3.0 17.0 - - - +
294N VAL* 1.3 73.0 - - + +
296N ILE* 1.3 62.5 + - + +
298N THR* 3.1 6.4 - - - -
299N HIS* 2.2 35.5 + - - +
409N ILE* 4.4 20.9 - - + +
413N VAL* 4.2 8.1 - - + -
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Residues in contact with ILE 296 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232N VAL* 4.4 9.2 - - + -
246N SER* 3.5 17.0 - - - +
247N ILE* 4.4 14.6 - - + -
250N LEU* 3.0 30.3 - - + -
292N THR* 2.7 49.4 + - + +
293N VAL 4.7 0.2 - - - +
295N VAL* 1.3 77.4 - - - +
297N ASN* 1.3 61.6 + - - +
299N HIS* 2.9 30.4 - - + +
300N HIS* 2.4 50.1 + - + +
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Residues in contact with ASN 297 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241M PHE* 5.1 0.6 - - - -
245M LEU* 3.0 45.6 - - - +
249M LEU* 4.3 15.8 - - - +
252M GLU* 5.1 1.7 - - - +
292N THR 4.3 0.8 + - - -
293N VAL* 2.4 41.0 + - - +
294N VAL* 3.4 4.3 - - - +
296N ILE* 1.3 78.5 - - - +
298N THR* 1.3 51.8 + - - +
300N HIS* 3.1 6.5 + - - +
301N ARG* 2.7 31.9 + - - +
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Residues in contact with THR 298 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294N VAL* 2.3 59.8 + - + +
295N VAL* 3.4 7.4 - - - +
297N ASN* 1.3 67.8 - - - +
299N HIS* 1.3 61.6 + - - -
301N ARG* 2.6 74.5 + - + +
405N VAL* 5.7 2.0 - - + -
409N ILE* 5.0 13.0 - - + -
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Residues in contact with HIS 299 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232N VAL* 3.6 9.9 + - - +
235N LEU* 5.4 0.2 - - + -
236N PRO* 2.8 56.2 - - + +
240N GLY* 5.0 0.4 - - - -
243N MET* 4.4 19.3 - - + +
246N SER* 3.9 18.1 + - - -
295N VAL 2.2 30.0 + - - +
296N ILE* 2.7 34.5 + - + +
298N THR* 1.3 72.6 - - - +
300N HIS* 1.3 54.7 + + - +
301N ARG* 4.2 10.5 + - - +
302N SER* 5.6 0.2 + - - -
306N HIS 2.3 22.8 - - - +
406N ILE* 4.5 7.4 - - + +
409N ILE* 6.5 1.1 - - + -
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Residues in contact with HIS 300 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249M LEU* 6.0 7.6 - - + -
252M GLU* 3.1 17.9 - - + +
253M SER* 4.8 3.1 - - - -
256M LYS* 3.9 33.3 - - + +
243N MET* 3.6 38.5 + - + +
244N THR* 4.6 1.3 - - - -
247N ILE* 3.9 22.6 - - + +
296N ILE* 2.4 49.9 + - + +
297N ASN* 3.5 4.9 - - - +
299N HIS* 1.3 68.7 - + + -
301N ARG* 1.3 48.9 + - - +
302N SER 2.6 18.6 + - - +
306N HIS* 2.6 44.2 + - + +
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Residues in contact with ARG 301 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252M GLU* 2.9 25.1 - - - +
297N ASN 2.7 9.0 + - - +
298N THR* 2.6 65.3 + - + +
299N HIS* 4.2 6.0 + - - +
300N HIS* 1.3 69.5 - - - +
302N SER* 1.3 67.9 + - - +
303N PRO* 4.0 3.5 - - - +
400N LYS 5.5 4.4 + - - -
401N TYR* 6.4 0.2 - - - +
402N VAL* 5.9 3.4 - - - +
405N VAL* 3.2 45.1 - - - +
406N ILE* 3.9 22.6 - - - +
409N ILE* 5.3 1.8 - - - +
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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