Contacts of the helix formed by residues 228 - 256 (chain A) in PDB entry 4O6M
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 SER 228 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASN* 4.6 8.0 + - - -
226A MET 3.6 5.3 + - - -
227A GLU* 1.3 77.3 - - - +
229A LYS* 1.3 64.2 + - - +
230A TYR* 3.9 5.2 + - - +
231A GLY* 3.0 23.4 + - - -
232A ALA* 3.2 19.8 + - - +
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Residues in contact with LYS 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A SER* 1.3 69.9 - - - +
230A TYR* 1.3 59.9 + - - +
232A ALA* 3.3 6.7 + - - +
233A TRP* 2.9 28.4 + - - +
285B ALA* 3.5 28.4 - - - +
286B TYR* 3.7 49.1 + - + -
287B MET* 6.3 1.3 - - - -
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Residues in contact with TYR 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASN* 4.0 16.8 - - - -
228A SER* 3.3 5.3 + - - +
229A LYS* 1.3 78.6 - - - +
231A GLY* 1.3 55.0 + - - +
233A TRP* 3.3 24.7 + + - +
234A LEU* 2.7 67.1 + - + +
404A MPG 4.0 15.3 - - + +
286B TYR* 3.3 17.3 + - - +
336B ILE* 3.0 24.1 + - - +
339B LEU* 3.6 21.1 - - + +
340B ARG* 3.5 37.0 - - + +
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Residues in contact with GLY 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A PRO* 6.1 2.7 - - - -
175A ASN* 3.2 25.8 - - - +
178A THR* 4.7 3.3 + - - -
228A SER* 3.0 19.3 + - - -
230A TYR* 1.3 78.0 - - - +
232A ALA* 1.3 56.0 + - - +
234A LEU* 3.9 2.6 - - - +
235A ASP* 3.1 29.1 + - - +
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Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A SER 3.2 12.5 + - - +
229A LYS* 3.3 9.6 + - - +
231A GLY* 1.3 72.9 - - - +
233A TRP* 1.3 65.9 + - - +
235A ASP* 3.6 4.0 + - - +
236A GLY 3.4 15.6 + - - -
281B LYS* 3.5 15.3 + - - +
285B ALA* 4.4 10.5 - - + -
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Residues in contact with TRP 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A LYS 2.9 17.6 + - - +
230A TYR* 3.6 21.5 - + - +
232A ALA* 1.3 76.3 - - - +
234A LEU* 1.3 82.3 + - + +
236A GLY* 3.3 2.9 + - - -
237A VAL* 3.0 45.1 + - + +
278B THR* 3.0 40.4 + - + -
281B LYS* 3.5 20.6 - - + +
282B PHE* 3.4 33.2 - - + +
285B ALA* 4.2 4.2 - - + +
286B TYR* 4.2 8.3 - + + -
290B TYR* 6.2 2.4 - + - -
335B ARG* 4.0 8.5 - - + -
336B ILE* 3.7 47.1 - - + -
339B LEU* 3.5 23.3 - - + -
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASN* 4.4 11.0 - - - +
178A THR* 4.1 15.3 - - + -
179A VAL* 4.3 11.9 - - + -
230A TYR* 2.7 48.8 + - + +
231A GLY 3.9 3.8 - - - +
233A TRP* 1.3 84.7 - - + +
235A ASP* 1.3 63.1 + - - +
237A VAL* 3.3 1.6 + - + +
238A LEU* 2.9 45.6 + - + +
404A MPG 4.0 28.3 - - + -
336B ILE* 4.1 18.8 - - + -
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Residues in contact with ASP 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A THR* 3.6 17.0 - - - +
214A ASP* 3.1 13.5 - - - +
217A ASP* 2.9 13.7 - - - +
231A GLY 3.1 18.4 + - - +
232A ALA* 4.0 5.4 - - - +
233A TRP 3.3 0.2 - - - -
234A LEU* 1.3 76.3 - - - +
236A GLY* 1.3 59.5 + - - +
238A LEU* 3.9 0.5 - - - -
239A ASP* 3.0 48.3 + - - +
401A CA 2.5 30.6 - - - -
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Residues in contact with GLY 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ALA 3.4 4.9 + - - -
233A TRP 3.3 6.1 + - - -
234A LEU 3.3 0.2 - - - -
235A ASP* 1.3 80.4 + - - +
237A VAL* 1.3 59.5 + - - +
239A ASP* 3.3 2.7 + - - -
240A ARG* 3.1 38.5 + - - -
277B TYR* 3.5 19.1 - - - -
281B LYS* 4.1 11.7 - - - -
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Residues in contact with VAL 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A TRP* 3.0 51.4 + - + +
234A LEU* 3.3 4.7 + - + +
236A GLY* 1.3 76.2 - - - +
238A LEU* 1.3 63.7 + - + +
240A ARG* 3.1 6.1 + - - +
241A TYR* 3.1 45.1 + - + -
274B MET* 4.0 7.2 - - + -
277B TYR* 3.9 19.7 - - + -
278B THR* 4.2 10.1 - - + -
281B LYS* 4.7 0.7 - - + -
336B ILE* 3.9 23.3 - - + -
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Residues in contact with LEU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A THR* 4.0 16.4 - - + +
179A VAL* 4.4 10.3 - - + -
182A PHE* 3.8 39.9 - - + -
234A LEU* 2.9 43.5 + - + +
235A ASP 4.2 2.0 - - - +
237A VAL* 1.3 77.0 - - + +
239A ASP* 1.3 62.0 + - - +
241A TYR* 3.2 11.9 + - + +
242A SER* 2.8 32.6 + - - -
404A MPG 4.3 17.3 - - + -
336B ILE* 4.3 23.6 - - + -
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Residues in contact with ASP 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ASP* 4.9 3.6 - - - +
178A THR* 5.8 0.2 - - - +
210A HIS* 4.7 3.3 - - - -
214A ASP* 3.2 32.8 - - - +
235A ASP* 3.0 33.1 + - - +
236A GLY* 3.6 6.8 - - - +
237A VAL 3.2 0.4 - - - -
238A LEU* 1.3 78.8 - - - +
240A ARG* 1.3 76.9 + - - +
242A SER* 3.3 0.7 + - - -
243A ASP* 2.9 35.3 + - - +
301A ARG* 3.6 30.7 + - - +
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Residues in contact with ARG 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A GLY* 3.1 25.1 + - - -
237A VAL* 3.1 10.0 + - - +
239A ASP* 1.3 87.4 + - - +
241A TYR* 1.3 65.5 + - - +
243A ASP* 3.3 23.2 + - - -
244A PHE* 3.1 24.9 + - - +
272A SER 5.2 0.6 + - - -
273A LEU* 3.6 27.3 - - + +
276A ALA* 3.3 24.7 - - + +
280A ASP* 4.2 3.4 + - - -
301A ARG* 3.7 5.3 - - - +
304A ARG* 3.9 0.8 - - - +
411A SO4 3.2 24.0 + - - -
270B PHE* 4.3 2.2 - - - -
274B MET* 3.6 26.0 - - + -
277B TYR* 3.1 43.5 + - + -
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Residues in contact with TYR 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PHE* 3.7 20.2 - + + -
237A VAL* 3.1 45.4 + - + -
238A LEU* 3.5 13.2 - - + +
240A ARG* 1.3 76.7 - - - +
242A SER* 1.3 58.4 + - - +
244A PHE* 3.7 0.7 - - - +
245A ILE* 2.9 48.7 + - + +
270B PHE* 3.6 32.1 - + - -
274B MET* 3.9 12.1 - - + -
278B THR* 6.0 0.2 - - + -
329B ASN* 4.6 4.7 + - - -
332B ALA* 3.3 29.3 - - + +
333B LEU* 3.6 29.8 + - + +
336B ILE* 4.1 6.7 - - + -
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Residues in contact with SER 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PHE* 3.3 12.4 - - - -
185A SER* 2.7 34.9 + - - -
210A HIS* 4.1 6.2 - - - -
238A LEU 2.8 23.1 + - - -
239A ASP* 3.6 0.7 + - - -
241A TYR* 1.3 74.2 - - - +
243A ASP* 1.3 63.2 + - - +
245A ILE* 4.7 3.1 - - - -
246A ILE* 2.9 33.6 + - - +
301A ARG* 3.3 22.0 - - - -
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Residues in contact with ASP 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ASP 2.9 16.3 + - - +
240A ARG* 3.3 22.9 + - - +
242A SER* 1.3 74.2 - - - +
244A PHE* 1.3 62.5 + - - +
246A ILE* 4.0 5.3 - - - +
247A VAL* 3.3 29.6 + - - +
269A ALA* 6.0 0.7 - - - -
272A SER* 4.1 19.8 - - - +
273A LEU* 4.7 4.3 - - + -
301A ARG* 2.9 29.1 + - - +
304A ARG* 2.9 32.1 + - - -
305A LEU* 4.3 9.4 - - - +
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Residues in contact with PHE 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ARG 3.1 17.5 + - - +
241A TYR 3.7 1.3 - - - +
243A ASP* 1.3 77.6 - - - +
245A ILE* 1.3 69.0 + - + +
247A VAL* 3.3 4.8 + - - +
248A PHE* 2.8 59.0 + + - +
269A ALA* 4.3 17.9 - - + -
273A LEU* 4.6 12.0 - - + +
266B PHE* 3.5 43.3 - + - -
267B LEU* 4.2 11.4 - - + -
270B PHE* 3.4 53.4 - + + -
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Residues in contact with ILE 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A PHE* 4.5 6.1 - - + -
185A SER* 6.0 0.2 - - - +
186A LEU* 3.7 30.3 - - + -
189A SER* 3.5 22.2 - - - +
241A TYR* 2.9 40.6 + - + +
242A SER* 4.0 3.1 - - - +
244A PHE* 1.3 85.4 - - + +
246A ILE* 1.3 64.2 + - - +
248A PHE* 3.7 7.4 - - + +
249A SER* 2.9 33.8 + - - +
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Residues in contact with ILE 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A SER* 4.2 13.5 - - - +
189A SER* 3.4 19.1 - - - +
192A PHE* 4.2 12.7 - - + -
207A ILE* 3.8 24.5 - - + -
210A HIS* 4.8 2.2 - - + -
242A SER* 2.9 29.5 + - - +
243A ASP* 4.0 5.6 - - - +
245A ILE* 1.3 77.6 - - - +
247A VAL* 1.3 62.9 + - - +
249A SER* 3.3 2.9 + - - -
250A ILE* 3.1 34.3 + - + +
301A ARG* 5.0 0.2 - - - +
305A LEU* 4.3 21.1 - - + -
308A ILE* 3.9 27.4 - - + -
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Residues in contact with VAL 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ASP 3.3 18.8 + - - +
244A PHE 3.8 2.5 - - - +
246A ILE* 1.3 79.8 - - + +
248A PHE* 1.3 55.3 + - - +
250A ILE* 3.3 3.0 + - - +
251A THR* 2.8 45.3 + - - +
265A GLY 3.4 25.8 - - - +
268A ALA* 4.2 3.1 - - + -
269A ALA* 3.8 19.3 - - + +
272A SER* 4.5 15.3 - - - +
308A ILE* 5.1 9.2 - - + -
321A LEU* 4.0 24.5 - - + -
324A ILE* 5.5 3.8 - - + -
266B PHE* 4.8 1.8 - - + -
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Residues in contact with PHE 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A PHE* 2.8 51.3 + + + +
245A ILE* 3.7 9.4 - - + +
247A VAL* 1.3 72.4 - - - +
249A SER* 1.3 58.6 + - - +
251A THR* 3.7 1.2 - - - -
252A TYR* 2.9 34.1 + + + +
262A TRP* 3.9 30.3 - + - -
263B ILE* 3.9 28.5 - - + -
266B PHE* 3.9 33.2 - + + -
267B LEU* 4.2 16.8 - - + -
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Residues in contact with SER 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A SER* 3.4 38.3 + - - -
192A PHE* 4.2 6.2 - - - +
193A LEU* 3.8 22.8 - - - +
245A ILE* 2.9 24.6 + - - +
246A ILE 3.6 4.0 - - - -
248A PHE* 1.3 77.9 - - - +
250A ILE* 1.3 61.7 + - - +
252A TYR* 3.6 0.6 + - - -
253A VAL* 3.3 27.7 + - - +
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Residues in contact with ILE 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A PHE* 3.8 46.0 - - + -
246A ILE* 3.1 24.5 + - + +
247A VAL* 3.7 5.2 - - - +
249A SER* 1.3 75.9 - - - +
251A THR* 1.3 64.3 + - - +
253A VAL* 3.4 5.6 + - - +
254A LEU* 3.0 42.1 + - + +
308A ILE* 4.3 14.4 - - + -
317A PRO* 3.8 24.0 - - + +
320A ALA* 5.7 0.2 - - + -
321A LEU* 3.8 24.2 - - + -
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Residues in contact with THR 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A VAL* 2.8 25.3 + - - +
248A PHE* 3.7 6.5 - - - -
250A ILE* 1.3 78.0 - - - +
252A TYR* 1.3 57.2 + - - +
254A LEU* 3.2 4.6 + - - +
255A SER* 2.8 29.3 + - - -
261A TYR 3.3 23.8 - - - +
262A TRP* 3.5 33.0 - - + -
265A GLY* 3.2 24.1 - - - -
321A LEU* 3.6 11.6 - - - +
266B PHE* 4.2 4.9 - - + -
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Residues in contact with TYR 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 4.0 19.1 - - + -
248A PHE* 2.9 25.0 + + + +
249A SER* 3.8 6.3 - - - +
251A THR* 1.3 76.3 - - - +
253A VAL* 1.3 67.0 + - + +
255A SER* 2.7 23.7 + - - -
256A ALA* 3.8 3.5 + - - +
262A TRP* 4.0 25.3 - + + -
263B ILE* 4.2 22.7 - - + -
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Residues in contact with VAL 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A PHE 3.5 23.3 - - - +
193A LEU* 3.7 23.1 - - + +
195A ASN* 3.4 37.4 + - + +
249A SER 3.3 14.1 + - - +
250A ILE* 3.8 7.4 - - - +
251A THR 3.3 0.2 - - - -
252A TYR* 1.3 80.4 - - + +
254A LEU* 1.3 68.9 + - + +
256A ALA* 3.3 20.8 + - - +
257A SER* 4.3 1.9 + - - -
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Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ILE* 3.0 34.7 + - + +
251A THR 3.7 3.4 - - - +
253A VAL* 1.3 79.8 - - + +
255A SER* 1.3 64.7 + - - +
257A SER* 2.9 30.4 + - - +
258A ASN 3.1 8.2 + - - +
261A TYR* 3.9 25.1 - - + -
317A PRO* 5.2 7.6 - - + -
318A SER* 3.4 44.2 - - - +
321A LEU* 3.9 11.4 - - + -
----------------------------------------------------------
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Residues in contact with SER 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A THR 2.8 18.4 + - - -
252A TYR* 2.7 21.3 + - - -
254A LEU* 1.3 72.4 - - - +
256A ALA* 1.3 62.4 + - - +
257A SER 3.2 0.4 + - - -
258A ASN 3.6 22.2 + - - -
259A PRO* 3.7 9.0 - - - +
261A TYR* 4.5 2.0 - - - +
262A TRP* 3.2 48.2 + - - -
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Residues in contact with ALA 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195A ASN* 6.2 2.0 - - - +
252A TYR 3.8 2.7 + - - +
253A VAL* 3.3 14.5 + - - +
254A LEU 3.1 0.8 - - - -
255A SER* 1.3 82.8 + - - +
257A SER* 1.3 58.9 + - - +
259A PRO* 5.8 0.3 - - - +
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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