Contacts of the helix formed by residues 235 - 260 (chain A) in PDB entry 1OPT
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 ARG 235 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS* 5.8 5.8 - - - +
232A ARG* 5.6 1.5 - - - +
233A ALA* 3.1 10.1 + - - -
234A VAL* 1.3 70.4 - - + +
236A LEU* 1.3 62.3 + - - +
237A ILE* 3.6 2.0 - - - -
238A PHE* 3.3 39.0 + - - +
239A THR* 3.4 23.2 + - + +
296A ILE 3.3 18.5 + - - -
297A TYR* 3.0 69.1 + - + +
298A ALA 4.7 1.0 - - - -
300A VAL* 3.0 35.5 + - - +
301A GLY* 3.9 4.6 + - - +
302A GLU* 3.8 32.7 + - - +
313A GLN* 3.8 7.7 + - - +
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Residues in contact with LEU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE* 3.7 30.7 - - + -
123A THR* 4.6 8.1 - - - +
126A ARG* 4.3 20.9 - - + +
131A VAL* 5.2 13.9 - - + -
220A THR* 5.9 0.4 - - - +
222A LEU* 6.2 3.8 - - + -
234A VAL 2.9 12.1 + - - +
235A ARG* 1.3 71.4 - - - +
237A ILE* 1.3 68.1 + - + +
238A PHE 3.3 0.3 + - - -
239A THR* 4.1 9.0 - - + -
240A ILE* 3.2 51.1 + - + +
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Residues in contact with ILE 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A THR* 3.5 40.9 - - + +
222A LEU* 3.5 43.5 - - + +
223A ARG* 3.8 8.1 - - - +
232A ARG* 3.7 30.5 - - - +
233A ALA* 3.7 27.1 - - + +
235A ARG 3.4 0.8 + - - -
236A LEU* 1.3 79.7 - - + +
238A PHE* 1.3 56.1 + - - +
240A ILE* 3.4 14.8 - - - +
241A MET* 4.4 3.1 - - - +
312A PHE* 5.6 2.2 - - + -
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Residues in contact with PHE 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ARG* 4.0 5.6 - - - +
235A ARG* 3.3 14.4 + - - +
237A ILE* 1.3 77.1 - - - +
239A THR* 1.3 64.4 - - - +
240A ILE 3.4 0.2 - - - -
241A MET* 3.4 12.7 + - - +
242A ILE* 3.5 47.0 + - + +
300A VAL* 3.6 48.5 - - + -
304A PHE* 6.1 0.2 - + - -
313A GLN* 3.4 40.2 - - + +
314A LYS* 3.8 39.3 - - + -
315A HIS* 3.9 17.3 - - + -
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Residues in contact with THR 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 5.0 4.8 - - + +
235A ARG* 3.4 46.0 + - + +
236A LEU* 4.0 9.6 - - + +
238A PHE* 1.3 76.8 - - - +
240A ILE* 1.3 62.6 + - - +
242A ILE 4.9 0.2 - - - +
243A VAL* 3.3 32.3 + - - +
296A ILE* 3.6 24.1 - - - +
297A TYR* 4.1 21.9 + - + +
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Residues in contact with ILE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A THR* 3.2 46.4 - - + +
124A ILE* 4.0 26.2 - - + +
126A ARG* 5.7 2.2 - - + -
220A THR* 4.2 11.9 - - - +
236A LEU* 3.2 34.2 + - + +
237A ILE* 3.4 19.7 - - - +
239A THR* 1.3 77.0 - - - +
241A MET* 1.3 74.3 + - + +
243A VAL* 3.6 16.0 - - - +
244A TYR* 4.0 8.0 + - - +
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Residues in contact with MET 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 6.0 5.2 - - + -
217A ILE 5.0 1.6 - - - +
218A LEU* 3.7 23.3 - - + -
219A LYS 3.9 11.7 - - - +
220A THR* 3.6 39.3 - - + +
237A ILE 4.4 2.5 - - - +
238A PHE* 3.4 7.0 + - - +
240A ILE* 1.3 87.5 - - + +
242A ILE* 1.3 73.4 + - + +
244A TYR* 3.4 9.3 + - - +
245A PHE* 3.2 31.0 + - + -
315A HIS* 5.7 2.9 - - - +
317A ALA* 3.4 48.5 - - + +
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Residues in contact with ILE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A PHE* 3.5 56.4 + - + +
239A THR 3.9 0.2 + - - -
241A MET* 1.3 83.3 - - + +
243A VAL* 1.4 56.2 + - - +
245A PHE* 4.1 12.7 - - + +
246A LEU* 3.1 50.9 + - + +
296A ILE* 3.8 26.7 - - + -
300A VAL* 5.1 4.3 - - + -
315A HIS* 4.8 16.2 - - + +
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Residues in contact with VAL 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 5.8 7.0 - - + -
120A ILE* 3.6 39.2 - - + +
123A THR* 4.8 8.1 - - + -
239A THR* 3.3 31.2 + - - +
240A ILE* 3.6 12.1 - - - +
242A ILE* 1.4 73.0 - - - +
244A TYR* 1.3 65.7 + - - +
246A LEU* 4.2 0.8 - - - -
247A PHE* 3.3 17.0 + - - +
289A HIS* 4.3 4.1 + - - +
293A ASN* 4.4 17.5 - - - +
296A ILE* 4.1 22.6 - - + +
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Residues in contact with TYR 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ILE* 4.2 7.2 - - + +
124A ILE* 4.2 14.8 - - + -
214A TYR* 3.7 36.1 - + + -
215A SER* 2.9 24.0 + - - -
218A LEU* 3.7 34.8 - - + +
240A ILE 4.0 8.3 + - - +
241A MET* 3.4 12.0 + - - +
243A VAL* 1.3 79.9 - - - +
245A PHE* 1.3 90.7 + + - +
247A PHE* 3.4 13.1 + - - +
248A TRP* 3.2 49.6 - + - -
318A LYS* 5.5 2.0 + - - -
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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
----------------------------------------------------------
218A LEU* 5.1 1.1 - - + -
241A MET* 3.2 30.8 + - + +
242A ILE* 3.6 11.8 + - + +
244A TYR* 1.3 99.8 - + - +
246A LEU* 1.3 59.6 + - + +
248A TRP* 3.4 20.2 + + - +
249A ALA* 3.7 10.7 + - - +
315A HIS* 3.8 22.0 - + - -
317A ALA* 3.7 31.6 - - + -
318A LYS* 3.8 28.5 - - - -
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Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A ILE* 3.1 29.5 + - + +
243A VAL 4.8 0.9 - - - +
245A PHE* 1.3 74.2 - - + +
247A PHE* 1.4 62.1 + - - +
248A TRP 3.5 0.2 - - - -
249A ALA* 4.9 11.4 - - + -
250A PRO* 3.3 18.1 - - - +
289A HIS* 3.5 13.1 - - - +
292A ILE* 4.1 32.8 - - + +
296A ILE* 3.8 26.2 - - + -
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Residues in contact with PHE 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 3.5 28.9 - - + -
116A ILE* 5.2 0.4 - - + -
117A PHE* 3.7 28.7 - + + -
120A ILE* 3.8 15.5 - - + -
214A TYR* 5.5 1.6 - + + -
243A VAL 3.3 15.3 + - - +
244A TYR* 3.4 12.0 + - - +
246A LEU* 1.4 75.3 - - - +
248A TRP* 1.3 96.0 + + - +
250A PRO* 3.4 2.9 - - - +
251A TYR* 3.3 62.6 + + + -
255A LEU* 4.9 5.4 - - + -
289A HIS* 3.6 27.0 + + - +
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Residues in contact with TRP 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PHE* 4.0 1.3 - + - -
207A LEU* 3.8 13.5 - - + -
211A VAL* 3.5 32.8 - - + -
214A TYR* 4.0 11.7 - + - -
244A TYR* 3.2 56.9 + + - -
245A PHE* 3.4 10.8 + + - +
247A PHE* 1.3 107.0 - + - +
249A ALA* 1.3 65.0 + - - +
251A TYR 4.5 0.7 - - - +
252A ASN* 3.4 64.3 + - - +
253A ILE* 4.9 0.5 - - - +
255A LEU* 4.2 16.2 - - + -
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Residues in contact with ALA 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A PHE 3.7 11.1 + - - +
246A LEU* 4.6 13.7 - - + +
248A TRP* 1.3 75.8 - - - +
250A PRO* 1.4 65.8 - - + +
253A ILE* 3.4 19.1 - - - +
285A LEU* 4.4 6.3 - - - +
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Residues in contact with PRO 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU 3.3 22.9 - - - +
247A PHE 3.4 9.0 - - - +
249A ALA* 1.4 90.7 - - + +
251A TYR* 1.3 81.7 + - + +
252A ASN 3.7 1.1 - - - -
253A ILE* 3.6 10.7 + - - +
254A VAL* 3.6 21.0 + - - +
285A LEU* 3.6 39.3 - - + +
286A GLY 5.2 0.2 - - - +
288A THR* 3.7 12.1 - - - +
289A HIS* 4.7 7.0 - - + -
292A ILE* 6.1 1.1 - - + -
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Residues in contact with TYR 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A PHE* 3.1 43.3 - + + -
247A PHE* 3.3 64.6 + + + +
248A TRP* 3.7 3.3 + - + -
250A PRO* 1.3 76.9 - - + +
252A ASN* 1.3 59.9 + - - +
253A ILE 3.5 0.2 - - - -
254A VAL* 4.1 16.8 - - + +
255A LEU* 3.1 45.0 + - + +
286A GLY* 2.7 36.9 + - - -
289A HIS* 3.2 39.8 + + + +
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Residues in contact with ASN 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A TRP* 3.4 53.6 + - - +
251A TYR* 1.3 74.2 - - - +
253A ILE* 1.3 65.1 + - + +
255A LEU* 5.2 0.9 - - - -
256A LEU* 3.2 50.8 + - + +
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Residues in contact with ILE 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A TRP 4.9 0.4 - - - +
249A ALA 3.4 25.4 - - - +
250A PRO 3.6 6.3 + - - +
251A TYR 3.5 0.4 - - - -
252A ASN* 1.3 80.0 - - + +
254A VAL* 1.4 60.4 + - - +
256A LEU* 4.6 0.6 - - - +
257A LEU* 3.2 32.9 + - + +
282A THR* 4.1 21.3 - - + +
285A LEU* 4.0 22.9 - - + -
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Residues in contact with VAL 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 6.6 0.2 - - + -
113A PHE* 4.5 20.2 - - + -
197A LYS* 6.0 1.6 - - - +
250A PRO 3.6 15.0 + - - +
251A TYR* 3.8 13.9 + - + +
252A ASN 3.6 0.2 - - - -
253A ILE* 1.4 76.8 - - + +
255A LEU* 1.3 61.6 + - + +
257A LEU* 4.0 0.5 - - - +
258A ASN* 3.0 48.4 + - + +
282A THR* 3.6 35.4 - - + +
283A GLU* 5.7 1.1 - - - -
285A LEU* 5.5 0.9 - - + -
286A GLY* 3.8 19.3 - - - +
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Residues in contact with LEU 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 6.4 1.1 - - + -
113A PHE* 6.4 1.3 - - + -
197A LYS* 4.1 21.0 + - - +
202A GLY 5.4 5.4 - - - +
203A LEU* 4.8 8.1 - - + +
207A LEU* 3.8 43.5 - - + -
247A PHE* 4.9 4.3 - - + -
248A TRP* 4.2 13.7 - - + -
251A TYR* 3.1 34.8 + - + +
252A ASN* 5.2 0.7 - - - -
254A VAL* 1.3 76.2 - - + +
256A LEU* 1.3 62.6 + - + +
258A ASN* 4.4 3.0 - - - +
259A THR* 3.5 25.5 + - - +
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Residues in contact with LEU 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ASN* 3.2 40.2 + - + +
253A ILE* 4.6 0.9 - - - +
255A LEU* 1.3 76.7 - - + +
257A LEU* 1.3 55.6 + - - +
259A THR* 3.9 5.8 - - + +
260A PHE* 2.9 28.2 + - - -
261A GLN* 3.5 30.6 - - + +
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Residues in contact with LEU 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A PHE* 4.9 3.8 - - - -
253A ILE* 3.2 25.0 + - + +
254A VAL 4.1 1.1 - - - +
256A LEU* 1.3 72.4 - - - +
258A ASN* 1.3 64.7 + - - +
260A PHE* 3.3 44.5 + - + +
277A GLN 3.2 27.6 - - - +
278A ALA* 4.4 4.5 - - - -
279A MET* 3.6 37.9 - - + +
282A THR* 3.5 26.2 - - + +
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Residues in contact with ASN 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ILE* 5.3 2.7 - - - +
189A PHE* 3.4 23.8 - - - -
194A GLN* 4.5 13.6 + - - +
197A LYS* 3.7 46.6 - - + +
199A VAL* 3.7 12.6 - - - +
254A VAL* 3.0 41.9 + - - +
255A LEU 4.5 1.1 - - - +
256A LEU 3.7 0.2 - - - -
257A LEU* 1.3 73.7 - - - +
259A THR* 1.3 55.6 + - - +
279A MET* 3.9 29.3 - - - +
282A THR* 4.9 1.2 - - - +
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Residues in contact with THR 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A TYR* 5.3 6.2 - - - +
189A PHE* 4.5 8.2 - - - -
197A LYS* 5.4 0.4 - - - +
199A VAL* 3.5 27.3 - - - +
203A LEU* 3.8 28.5 - - + +
255A LEU 3.5 20.1 + - - +
256A LEU* 3.9 8.7 - - + +
258A ASN* 1.3 76.4 - - - +
260A PHE* 1.3 64.0 + - - +
261A GLN* 3.0 33.6 + - + +
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Residues in contact with PHE 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A TYR* 5.8 7.4 - + + -
189A PHE* 5.0 9.2 - - + -
256A LEU 2.9 23.1 + - - -
257A LEU* 3.3 41.6 + - + +
259A THR* 1.3 70.4 - - - +
261A GLN* 1.3 51.4 + - - +
262A GLU* 2.8 31.1 + - - +
263A PHE 5.5 0.7 - - - -
264A PHE* 3.8 46.8 - + + -
275A LEU* 4.9 22.4 - - + -
277A GLN 5.5 2.5 - - - -
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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