Contacts of the helix formed by residues 277 - 301 (chain A) 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 TYR 277 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A PHE* 2.9 29.4 + + - -
136A PRO* 2.5 19.0 - - + +
137A PHE* 2.4 43.1 + + + +
138A ASP* 4.6 0.7 - - - -
210A ILE* 3.5 10.6 - - + +
273A LEU* 4.0 17.3 - - + -
274A ILE* 2.5 66.6 + - + +
276A LYS* 1.3 70.8 - - - +
278A MET* 1.3 58.9 + - - +
280A PHE* 2.7 62.7 + + + +
281A THR* 3.9 1.2 + - - -
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Residues in contact with MET 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A SER* 6.1 3.4 - - - +
273A LEU* 5.4 8.4 - - + +
275A GLY* 2.6 27.0 + - - +
277A TYR* 1.3 71.2 - - - +
279A LEU* 1.3 60.2 + - + +
281A THR* 2.6 41.6 + - + +
282A MET* 2.8 55.5 + - + +
220E PHE* 4.9 17.9 - - + +
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Residues in contact with LEU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A GLY 3.5 5.4 + - - +
276A LYS* 4.1 13.9 - - - +
277A TYR 3.3 1.0 - - - -
278A MET* 1.3 75.5 - - + +
280A PHE* 1.3 70.9 + - + +
282A MET* 3.0 52.5 + - + +
283A ILE* 3.2 28.5 + - + +
284A PHE* 4.6 0.7 - - - -
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Residues in contact with PHE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PHE* 6.6 0.2 - + - -
274A ILE* 6.1 0.4 - - + -
276A LYS 2.7 23.3 - - - -
277A TYR* 2.7 56.9 + + + +
279A LEU* 1.3 78.7 - - + +
281A THR* 1.3 59.7 + - - +
284A PHE* 2.5 64.7 + + + +
427A ALA* 5.8 10.3 - - + -
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Residues in contact with THR 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A VAL* 5.9 2.4 - - - +
264A ILE* 4.8 17.7 - - + +
277A TYR 3.9 0.8 + - - -
278A MET* 2.6 44.5 + - + +
280A PHE* 1.3 80.9 - - - +
282A MET* 1.3 76.4 + - - +
284A PHE* 4.2 7.2 - - - -
285A VAL* 2.6 40.2 + - + +
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Residues in contact with MET 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A MET* 2.8 57.7 + - + +
279A LEU* 3.0 42.1 + - + +
281A THR* 1.3 80.8 - - - +
283A ILE* 1.3 58.7 + - - +
285A VAL* 3.9 3.8 - - - -
286A ILE* 2.8 44.0 + - + +
220E PHE 5.2 4.9 - - - +
223E ILE* 4.7 28.0 - - + -
224E ASN* 5.8 1.3 - - - +
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Residues in contact with ILE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 3.2 25.7 + - + +
282A MET* 1.3 77.3 - - - +
284A PHE* 1.3 62.8 + - + +
286A ILE* 4.3 6.1 - - + -
287A SER* 2.6 41.6 + - - +
290A ILE* 5.8 6.5 - - + -
420A ILE* 6.4 2.7 - - + -
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Residues in contact with PHE 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A PHE* 5.1 5.5 - - - -
279A LEU 4.6 1.3 - - - -
280A PHE* 2.5 55.3 + + + +
281A THR* 3.6 4.7 - - - +
283A ILE* 1.3 85.7 - - + +
285A VAL* 1.3 62.7 + - - +
287A SER* 3.1 11.6 + - - -
288A SER* 3.3 9.7 + - - -
420A ILE* 5.5 7.8 - - + +
423A VAL 5.4 0.4 - - - -
424A SER* 3.0 54.1 - - - -
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Residues in contact with VAL 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A PHE* 5.8 2.5 - - - -
257A LEU* 2.9 40.4 - - + +
260A ILE* 6.2 1.1 - - + -
261A VAL* 5.6 8.1 - - + -
281A THR* 2.6 45.3 + - + +
282A MET* 2.8 7.6 - - - +
284A PHE* 1.3 75.8 - - - +
286A ILE* 1.3 80.9 + - + +
288A SER* 3.0 26.4 - - - -
289A ILE* 3.2 12.9 + - + +
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Residues in contact with ILE 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A MET* 2.8 46.4 + - + +
283A ILE* 4.0 4.3 - - - +
285A VAL* 1.3 92.9 - - + +
287A SER* 1.3 51.0 + - - +
289A ILE* 2.6 28.9 - - + +
290A ILE* 2.6 49.4 + - + +
223E ILE* 5.0 7.4 - - + +
227E ALA* 4.1 28.5 - - + -
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Residues in contact with SER 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ILE* 2.6 27.4 + - - -
284A PHE* 3.1 6.0 + - - -
286A ILE* 1.3 68.9 - - - +
288A SER* 1.3 55.8 + - - +
289A ILE 2.7 5.6 - - - -
290A ILE* 3.7 13.0 - - - +
291A VAL* 2.6 59.9 + - - +
416A LEU* 5.1 1.7 - - - +
420A ILE* 4.0 27.2 - - - +
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Residues in contact with SER 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A PHE* 3.8 39.7 - - - -
229A THR* 4.8 3.9 + - - +
253A LEU* 4.4 14.2 - - - +
254A THR* 5.1 0.9 + - - -
257A LEU* 4.6 9.7 - - - +
284A PHE 3.3 3.6 + - - -
285A VAL* 3.0 19.9 + - - -
287A SER* 1.3 77.6 - - - +
289A ILE* 1.3 54.4 - - - +
291A VAL* 4.3 3.3 - - - +
292A THR* 2.4 41.1 + - - +
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Residues in contact with ILE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A THR* 3.2 28.9 - - + +
257A LEU* 5.7 4.0 - - + -
285A VAL* 3.4 15.5 - - + +
286A ILE* 2.6 31.9 - - + +
287A SER 2.7 0.2 - - - -
288A SER* 1.3 80.6 - - - +
290A ILE* 1.3 68.6 + - + +
292A THR* 2.3 24.0 + - + +
293A VAL* 3.2 14.1 + - + +
227E ALA 5.2 2.5 - - - +
231E LEU* 3.9 46.5 - - + +
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ILE* 5.8 6.3 - - + -
286A ILE* 2.6 39.9 + - + +
287A SER* 3.7 12.8 - - - +
289A ILE* 1.3 75.6 - - + +
291A VAL* 1.3 60.2 + - + +
293A VAL* 2.9 30.1 - - + +
294A VAL* 3.1 10.3 + - - +
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Residues in contact with VAL 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A THR* 4.9 7.2 - - + -
233A PHE* 4.4 9.4 - - + -
287A SER* 2.6 48.4 + - - +
288A SER* 4.3 2.9 - - - +
290A ILE* 1.3 68.5 - - + +
292A THR* 1.3 53.9 + - - +
294A VAL* 2.9 8.4 - - + +
295A VAL* 2.4 66.6 + - + +
413A VAL* 3.9 23.1 - - + -
416A LEU* 4.4 18.8 - - + -
417A ILE* 6.2 0.2 - - + -
420A ILE* 5.6 2.0 - - + -
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Residues in contact with THR 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A THR* 5.2 12.3 - - + +
232A VAL* 5.8 0.4 - - + -
250A LEU* 3.1 30.7 - - + -
253A LEU* 5.4 7.0 - - + -
254A THR* 5.8 2.5 - - - +
288A SER* 2.4 28.8 + - - +
289A ILE* 2.3 35.3 + - + +
291A VAL* 1.3 74.7 - - - +
293A VAL* 1.3 59.3 + - - -
295A VAL* 4.1 1.1 - - - -
296A ILE* 2.4 48.4 + - + +
231E LEU* 5.7 1.6 - - - +
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Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ILE* 3.5 11.4 - - + +
290A ILE* 2.9 27.4 - - + +
292A THR* 1.3 79.1 + - - +
294A VAL* 1.3 56.4 + - + +
296A ILE* 4.2 3.8 - - - -
297A ASN* 2.6 40.6 + - - +
231E LEU* 4.8 6.3 - - + +
234E SER* 3.1 32.5 - - - +
235E LEU* 4.7 0.4 - - - +
238E LEU* 3.5 29.9 - - + +
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Residues in contact with VAL 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ILE 3.7 9.4 - - - +
291A VAL* 2.9 18.6 + - + +
292A THR 2.7 4.5 + - - -
293A VAL* 1.3 80.6 - - + +
295A VAL* 1.3 84.2 + - + +
297A ASN* 4.2 10.3 - - - +
298A THR* 2.5 51.6 + - - +
409A ILE* 6.0 4.7 - - + -
413A VAL* 5.9 3.4 - - + -
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Residues in contact with VAL 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A VAL* 3.6 36.1 - - + +
233A PHE* 4.7 16.4 - - + -
236A PRO* 6.1 0.2 - - + -
291A VAL* 2.4 64.7 + - + +
292A THR* 2.7 1.5 + - - +
294A VAL* 1.3 78.5 - - + +
296A ILE* 1.3 55.1 + - + +
298A THR* 3.3 6.8 - - - +
299A HIS* 2.4 39.5 + - + +
409A ILE* 5.4 17.6 - - + +
413A VAL* 4.9 5.8 - - + -
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Residues in contact with ILE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A VAL* 4.4 5.6 - - + -
243A MET 5.8 1.8 - - - +
246A SER* 5.8 0.2 - - - -
250A LEU* 3.1 49.4 - - + -
292A THR* 2.4 70.1 + - + +
293A VAL* 3.7 4.3 - - - +
295A VAL* 1.3 73.2 - - + +
297A ASN* 1.3 59.3 + - - +
298A THR 3.1 1.1 - - - -
299A HIS* 3.0 28.9 - - + +
300A HIS* 2.8 46.3 + - + +
238E LEU* 5.4 8.5 - - + -
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Residues in contact with ASN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A VAL 2.6 24.6 + - - +
294A VAL* 3.7 11.9 + - - +
296A ILE* 1.3 76.0 - - - +
298A THR* 1.3 54.7 + - - +
300A HIS* 3.0 12.4 - - - +
301A ARG* 2.4 31.1 + - - +
238E LEU* 4.5 16.8 - - + +
242E LEU* 5.9 1.6 - - + -
245E GLN* 2.7 39.3 + - - +
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Residues in contact with THR 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A VAL* 2.5 34.4 + - - +
295A VAL* 3.5 4.9 - - - +
297A ASN* 1.3 72.3 + - - +
299A HIS* 1.3 68.3 + - - +
300A HIS 2.8 2.0 - - - -
301A ARG* 2.7 65.6 + - - +
405A VAL* 5.8 1.1 - - + -
409A ILE* 4.2 27.8 - - + +
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Residues in contact with HIS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A VAL* 3.4 29.2 + - + +
235A LEU* 5.3 2.7 - - + +
236A PRO* 3.5 31.3 - - + +
243A MET* 4.2 35.1 + - + +
246A SER* 4.7 11.3 - - - -
295A VAL* 2.4 36.9 + - + +
296A ILE* 3.0 36.3 - - + +
298A THR* 1.3 70.6 - - - +
300A HIS* 1.3 55.3 - + + +
301A ARG* 4.5 4.9 + - - +
306A HIS* 2.1 36.0 + + - +
406A ILE* 6.0 2.5 - - - -
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Residues in contact with HIS 300 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A MET* 5.1 13.1 + - + +
244A THR 5.6 0.2 + - - -
247A ILE* 5.3 4.9 - - + +
250A LEU* 6.0 1.1 - - + +
296A ILE* 2.8 30.2 + - + +
297A ASN* 3.0 14.4 - - - +
299A HIS* 1.3 78.8 + - + +
301A ARG* 1.3 47.9 + - - -
302A SER 2.5 20.3 + - - -
306A HIS* 2.5 31.0 - - + +
238E LEU* 5.6 6.0 - - + +
242E LEU* 3.4 39.9 - - + +
245E GLN* 3.3 26.1 - - + +
246E ALA 4.9 1.1 - - - +
250E LYS* 4.5 13.8 - - - -
253E LEU* 3.8 23.2 - - + +
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Residues in contact with ARG 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A ASN* 2.4 18.4 + - - +
298A THR* 2.7 60.2 + - - +
299A HIS* 4.5 4.0 + - - +
300A HIS* 1.3 60.6 - - - +
302A SER* 1.3 65.6 + - - +
303A PRO* 4.1 4.2 - - - +
400A LYS 5.3 0.4 + - - -
401A TYR* 6.1 1.0 - - - +
402A VAL* 4.6 16.8 + - - +
405A VAL* 3.3 27.2 - - - +
406A ILE* 3.0 37.5 - - - +
245E GLN* 4.0 21.5 - - - +
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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