Contacts of the helix formed by residues 233 - 256 (chain A) in PDB entry 2BU6
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 VAL 233 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A MET* 3.3 24.5 - - + -
159A MET* 4.1 7.6 - - + -
182A SER* 3.3 33.7 - - - +
183A ILE* 3.9 9.4 - - + -
232A TYR* 1.3 80.7 - - + +
234A PRO* 1.3 60.1 - - - +
235A SER* 4.1 7.4 - - - +
236A HIS* 2.9 51.8 + - + +
237A LEU 3.3 8.3 + - - -
332A PHE* 4.1 17.9 - - + -
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Residues in contact with PRO 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A HIS* 4.5 11.4 - - + +
182A SER 3.2 15.0 - - - +
184A ASP* 3.8 21.1 - - + +
187A CYS* 4.4 18.2 - - - -
192A VAL* 4.1 13.0 - - + +
232A TYR 3.0 14.3 - - - +
233A VAL* 1.3 81.2 - - - +
235A SER* 1.3 57.4 + - - +
237A LEU* 3.2 8.8 + - + +
238A TYR* 2.9 29.9 + - - +
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Residues in contact with SER 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A SER* 5.1 4.2 + - - -
233A VAL* 3.3 7.0 - - - +
234A PRO* 1.3 80.7 - - - +
236A HIS* 1.3 74.0 + - - +
238A TYR* 3.6 10.1 - - - +
239A HIS* 3.1 23.2 + - - +
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Residues in contact with HIS 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ILE* 4.2 3.8 - - + +
159A MET* 4.1 21.1 - - + +
162A ASN* 5.9 2.8 + - - -
182A SER* 5.4 0.2 + - - -
232A TYR* 4.2 10.9 + - + +
233A VAL* 2.9 38.0 + - + +
235A SER* 1.3 84.3 + - - +
237A LEU* 1.3 66.2 + - - +
239A HIS* 3.3 6.3 + - - +
240A MET* 3.2 28.5 + - - +
328A TYR* 3.4 46.3 + + + +
331A TYR* 4.0 24.8 - + - -
332A PHE* 4.6 4.0 - - - -
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Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A CYS* 4.5 12.1 - - - -
189A VAL* 4.1 23.6 - - + -
192A VAL* 3.9 26.0 - - + -
230A MET* 5.3 0.7 - - - -
232A TYR* 3.9 17.6 - - + -
233A VAL 3.3 1.6 + - - +
234A PRO* 3.2 10.2 + - + +
236A HIS* 1.3 76.6 - - - +
238A TYR* 1.3 63.6 + - - +
240A MET* 3.2 21.3 + - + +
241A LEU* 2.9 36.0 + - + +
278A ILE* 3.8 22.9 - - + -
350A ILE* 4.6 4.0 - - + -
352A LEU* 4.2 12.1 - - + -
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Residues in contact with TYR 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A VAL* 3.8 14.5 - - + +
195A ASP* 3.9 15.3 - - + -
196A ALA* 3.5 34.0 - - + +
199A MET* 3.1 35.2 - - - +
234A PRO 2.9 17.7 + - - +
235A SER* 3.6 10.8 - - - +
237A LEU* 1.3 76.3 - - - +
239A HIS* 1.3 60.2 + - - +
241A LEU* 3.2 4.0 + - - +
242A PHE* 2.8 54.4 + + + +
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Residues in contact with HIS 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A SER 3.1 12.7 + - - +
236A HIS* 3.3 10.1 + - - +
238A TYR* 1.3 85.0 - - + +
240A MET* 1.3 64.4 + - + +
242A PHE* 3.9 4.5 - - - +
243A GLU* 3.2 24.5 + - - +
321A GLY* 4.3 10.3 + - - -
324A ILE* 4.3 16.3 - - + +
325A SER* 3.4 20.1 + - - -
328A TYR* 4.1 31.8 + + + -
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Residues in contact with MET 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A TYR* 4.0 20.2 - - - +
236A HIS* 3.2 10.1 + - + +
237A LEU* 3.6 35.4 - - + +
238A TYR 3.2 0.2 - - - -
239A HIS* 1.3 78.2 - - + +
241A LEU* 1.3 63.7 + - - +
243A GLU* 3.3 4.7 + - - +
244A LEU* 3.1 27.1 + - - +
325A SER* 3.5 41.7 + - - +
328A TYR* 4.0 8.1 - - + -
329A ALA* 3.6 24.2 - - - +
336A LEU* 4.5 4.0 - - + -
350A ILE* 3.8 27.1 - - + -
352A LEU* 4.1 3.4 - - + -
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Residues in contact with LEU 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A VAL* 4.1 6.1 - - + -
193A VAL* 3.7 40.2 - - + +
196A ALA* 3.7 12.3 - - + -
237A LEU* 2.9 39.7 + - + +
238A TYR 3.8 0.2 - - - +
240A MET* 1.3 75.7 - - - +
242A PHE* 1.3 57.8 + - - +
244A LEU* 3.3 9.2 + - + +
245A PHE* 2.8 49.4 + - + -
267A VAL* 5.6 2.2 - - + -
278A ILE* 4.1 20.2 - - + -
280A MET* 5.6 5.8 - - + -
350A ILE* 4.0 20.2 - - + -
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Residues in contact with PHE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ALA* 3.6 23.7 - - + +
199A MET* 3.6 18.8 - - + -
200A ALA* 3.5 28.3 - - + -
203A LEU* 3.6 20.6 - - + -
238A TYR* 2.8 40.5 + + + +
239A HIS* 3.9 5.4 - - - +
241A LEU* 1.3 73.9 - - - +
243A GLU* 1.3 58.2 + - - +
245A PHE* 3.8 1.9 - - - +
246A LYS* 2.9 69.4 + - + +
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Residues in contact with GLU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A HIS* 3.2 12.7 + - + +
240A MET 3.6 4.7 - - - +
242A PHE* 1.3 81.9 - - + +
244A LEU* 1.3 62.8 + - + +
246A LYS* 3.3 29.0 + - - +
247A ASN* 3.2 44.1 + - - +
321A GLY* 3.2 42.6 + - - +
322A LEU* 3.8 7.2 + - + +
325A SER* 3.5 17.7 - - - +
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Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A MET 3.1 12.4 + - - +
241A LEU* 3.8 7.4 - - + +
243A GLU* 1.3 77.5 - - + +
245A PHE* 1.3 60.2 + - - +
247A ASN* 3.2 8.6 + - + +
248A ALA 3.0 13.5 + - - -
280A MET* 2.7 36.8 - - + +
322A LEU* 3.8 28.9 - - + -
325A SER* 6.0 0.2 - - - -
336A LEU* 4.3 15.3 - - + -
338A LEU* 4.5 2.9 - - + -
348A ALA* 3.9 32.1 - - + +
350A ILE* 3.8 36.6 - - + -
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Residues in contact with PHE 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A VAL* 3.3 42.2 - - + -
196A ALA* 3.8 6.3 - - + -
197A TYR* 3.6 39.9 - + + -
200A ALA* 3.8 17.9 - - + -
214A LEU* 3.8 22.4 - - + -
241A LEU* 2.8 39.9 + - + +
242A PHE 3.8 2.0 - - - +
244A LEU* 1.3 73.4 - - - +
246A LYS* 1.3 56.6 + - - +
248A ALA* 3.3 0.5 + - - +
249A MET* 2.9 38.2 + - + +
265A ILE* 4.0 16.8 - - + -
267A VAL* 4.0 6.7 - - + -
280A MET* 3.6 19.9 - - - +
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Residues in contact with LYS 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ALA* 4.2 9.8 - - + +
203A LEU* 4.9 9.2 - - + +
242A PHE* 2.9 64.6 + - + +
243A GLU* 3.6 28.8 + - - +
244A LEU 3.3 0.2 - - - -
245A PHE* 1.3 76.4 - - - +
247A ASN* 1.3 58.8 + - - +
249A MET* 3.9 3.6 - - - +
250A ARG* 3.1 29.2 + - - +
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Residues in contact with ASN 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A GLU* 3.2 33.8 + - - +
244A LEU* 3.2 8.6 + - + +
246A LYS* 1.3 76.7 - - - +
248A ALA* 1.3 61.1 + - - +
250A ARG* 3.8 11.1 - - - +
251A ALA* 3.0 32.1 + - - +
322A LEU* 4.0 29.7 - - - +
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Residues in contact with ALA 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A LEU 3.0 6.0 + - - +
245A PHE 3.9 0.7 - - - +
247A ASN* 1.3 77.4 - - - +
249A MET* 1.3 55.2 + - - +
251A ALA* 4.2 1.5 - - - +
252A THR* 2.6 37.8 + - - -
265A ILE* 3.6 19.9 - - + +
280A MET* 3.2 31.9 - - + -
282A ASP* 3.6 28.0 - - + +
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Residues in contact with MET 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A TYR* 3.2 45.1 - - + +
200A ALA* 3.5 36.8 - - + +
201A LYS* 3.6 17.7 - - + +
204A CYS* 3.8 23.6 - - + -
211A SER* 5.3 0.7 - - - -
212A PRO* 4.0 17.9 - - + +
245A PHE* 2.9 22.4 + - + +
246A LYS* 3.9 4.5 - - - +
248A ALA* 1.3 76.1 - - - +
250A ARG* 1.3 65.2 + - - +
252A THR* 3.2 1.0 + - - -
253A VAL* 2.9 30.6 + - - +
265A ILE* 3.7 13.0 - - + -
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Residues in contact with ARG 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A TYR* 3.6 27.7 + - + +
246A LYS 3.1 15.8 + - - +
247A ASN* 3.8 12.1 - - - +
248A ALA 3.5 0.2 - - - -
249A MET* 1.3 81.2 - - - +
251A ALA* 1.3 59.2 + - + +
253A VAL* 3.9 0.5 - - - +
254A GLU* 2.5 75.0 + - - +
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Residues in contact with ALA 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ASN 3.0 19.5 + - - +
248A ALA* 4.2 3.6 - - - +
250A ARG* 1.3 78.6 - - + +
252A THR* 1.3 63.2 + - - +
254A GLU* 4.4 3.5 - - - +
255A SER* 2.8 31.7 + - - -
282A ASP* 5.0 3.4 - - - +
284A GLY* 3.3 21.3 - - - +
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Residues in contact with THR 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A PRO* 4.2 11.0 - - + -
248A ALA 2.6 23.9 + - - -
249A MET 3.8 2.9 - - - -
251A ALA* 1.3 75.8 - - - +
253A VAL* 1.3 63.7 - - - +
255A SER* 3.2 2.1 + - - -
256A HIS* 3.0 28.4 + - + +
262A LEU* 3.9 15.6 - - + +
263A PRO* 3.4 39.7 - - + +
265A ILE* 4.3 5.5 - - - +
282A ASP* 3.9 16.5 - - - +
283A ARG 4.3 2.2 + - - +
284A GLY* 3.7 10.7 + - - -
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Residues in contact with VAL 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A CYS* 3.9 23.8 - - - -
208A TYR* 3.5 38.4 - - + -
210A ALA* 3.9 16.2 - - + +
212A PRO* 4.2 13.0 - - + -
249A MET 2.9 19.2 + - - +
250A ARG 3.9 2.5 - - - +
252A THR* 1.3 77.1 - - - +
254A GLU* 1.3 64.3 + - - +
256A HIS* 3.3 12.1 + - - +
257A GLU* 3.4 16.8 + - + +
262A LEU* 4.0 15.2 - - + +
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Residues in contact with GLU 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A TYR* 2.8 30.5 + - + +
250A ARG* 2.5 58.7 + - - +
251A ALA* 4.4 3.2 - - - +
253A VAL* 1.3 76.8 - - - +
255A SER* 1.3 60.8 + - - +
256A HIS 3.4 0.9 + - - -
257A GLU* 3.6 33.5 + - - +
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Residues in contact with SER 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ALA 2.8 22.8 + - - -
252A THR 3.2 0.5 + - - -
254A GLU* 1.3 76.4 - - - +
256A HIS* 1.3 89.1 + - - +
257A GLU 3.6 0.7 - - - -
258A SER 5.5 0.2 + - - -
284A GLY* 3.3 22.3 - - - -
285A GLY* 4.1 6.1 - - - -
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Residues in contact with HIS 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A THR* 3.0 14.2 + - + +
253A VAL 3.3 6.9 + - - +
254A GLU 3.2 1.2 - - - -
255A SER* 1.3 102.6 + - - +
257A GLU* 1.3 56.1 + - - +
258A SER 3.0 6.1 - - - -
259A SER* 2.9 40.9 + - - +
261A ILE* 3.7 19.4 - - + +
262A LEU* 4.3 8.0 - - + +
263A PRO* 3.5 32.2 - - + +
283A ARG* 3.0 29.3 - - - +
285A GLY* 5.1 0.7 - - - -
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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) + - + + + + + -
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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