Contacts of the helix formed by residues 293 - 318 (chain F) in PDB entry 2GPV
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 293 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291F THR 3.9 0.6 + - - -
292F LEU* 1.3 77.2 - - - +
294F LEU* 1.3 65.8 + - - +
295F ALA 4.2 2.0 - - - -
296F ASP* 3.2 26.9 + - - +
297F GLN* 2.9 20.3 + - - +
383F GLU* 3.3 25.8 + - - +
384F ASP* 5.4 3.7 - - - +
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Residues in contact with LEU 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F LEU 3.8 0.8 + - - -
293F SER* 1.3 71.3 - - - +
295F ALA* 1.3 55.7 + - - +
297F GLN* 2.9 24.4 + - + +
298F MET* 2.8 50.2 + - + +
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Residues in contact with ALA 295 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293F SER* 3.3 1.2 + - - -
294F LEU* 1.3 79.5 - - - +
296F ASP* 1.3 58.1 + - - +
298F MET* 3.8 14.3 + - - +
299F SER* 2.9 29.7 + - - -
381F HIS 5.7 1.3 - - - +
383F GLU* 3.4 37.5 - - + +
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Residues in contact with ASP 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F LEU* 4.5 9.5 - - + +
293F SER* 3.2 22.6 + - - +
294F LEU 3.1 0.6 - - - -
295F ALA* 1.3 77.9 - - - +
297F GLN* 1.3 65.7 + - - +
298F MET 3.2 1.6 - - - -
299F SER* 3.1 4.1 + - - -
300F LEU* 3.0 31.0 + - - +
381F HIS 4.0 2.4 - - - +
382F ILE* 3.4 19.6 - - + +
383F GLU* 2.7 27.2 + - - +
384F ASP* 2.8 34.7 + - - +
388F VAL* 4.3 9.6 - - + +
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Residues in contact with GLN 297 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284F LYS* 5.4 5.7 - - - +
289F PHE* 3.4 53.1 + - + +
290F SER* 3.3 19.5 + - - +
292F LEU* 2.6 28.9 + - + +
293F SER 2.9 17.3 + - - +
294F LEU* 3.5 24.0 - - + +
296F ASP* 1.3 76.9 - - - +
298F MET* 1.3 64.0 + - + +
300F LEU* 3.9 1.3 - - - +
301F LEU* 3.2 31.7 + - + +
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Residues in contact with MET 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294F LEU* 2.8 33.2 + - + +
295F ALA* 3.9 12.3 - - - +
297F GLN* 1.3 77.4 - - + +
299F SER* 1.3 54.7 + - - +
301F LEU* 3.4 6.9 + - + +
302F GLN* 2.6 39.5 + - + +
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Residues in contact with SER 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295F ALA 2.9 23.6 + - - -
296F ASP* 3.1 6.2 + - - -
298F MET* 1.3 75.7 - - - +
300F LEU* 1.3 63.0 + - - +
302F GLN* 3.3 10.5 + - - +
303F SER* 2.9 27.2 + - - -
379F SER* 3.6 25.2 + - - -
381F HIS* 3.6 18.0 + - - +
382F ILE* 4.0 10.8 - - - -
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Residues in contact with LEU 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289F PHE* 4.0 22.0 - - + -
292F LEU* 4.1 19.1 - - + -
296F ASP 3.0 18.9 + - - +
297F GLN 3.9 3.4 - - - +
299F SER* 1.3 74.8 - - - +
301F LEU* 1.3 53.1 + - - +
303F SER* 3.1 2.1 + - - -
304F ALA* 2.7 37.8 + - - +
374F LEU* 3.7 27.4 - - + +
375F ALA* 4.2 14.6 - - - +
377F SER* 3.3 17.3 + - - +
378F ASP 5.5 2.5 - - - +
379F SER* 5.2 2.7 - - - +
382F ILE* 3.9 23.3 - - + -
388F VAL* 4.2 11.4 - - + -
391F LEU* 4.5 10.5 - - + -
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Residues in contact with LEU 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279F ILE* 4.6 19.3 - - + +
280F ILE* 4.0 32.5 - - + -
283F ALA* 4.2 15.7 - - + -
289F PHE* 4.1 15.7 - - + -
297F GLN* 3.2 19.7 + - + +
298F MET* 3.8 6.1 - - + +
300F LEU* 1.3 76.6 - - - +
302F GLN* 1.3 65.2 + - - +
304F ALA 4.3 0.2 - - - +
305F TRP* 3.0 36.6 + - + +
308F ILE* 5.0 3.4 - - + -
374F LEU* 3.7 21.1 - - + -
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Residues in contact with GLN 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298F MET 2.6 23.9 + - - +
299F SER* 3.5 10.9 - - - +
301F LEU* 1.3 71.3 - - - +
303F SER* 1.3 65.0 + - - +
305F TRP* 3.2 23.4 + - - -
379F SER* 4.9 4.3 + - - -
381F HIS* 5.8 4.0 - - - -
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Residues in contact with SER 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F SER 2.9 17.3 + - - -
300F LEU 3.5 3.1 - - - -
302F GLN* 1.3 85.2 + - - +
304F ALA* 1.3 60.3 + - - +
305F TRP* 3.5 2.3 + - - -
306F MET* 4.9 1.7 + - - +
307F GLU* 4.5 7.1 - - - +
377F SER* 3.5 27.5 + - - -
379F SER* 3.6 21.2 - - - -
428F SER* 5.2 4.5 + - - -
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Residues in contact with ALA 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300F LEU 2.7 20.7 + - - +
303F SER* 1.3 72.2 - - - +
305F TRP* 1.3 66.5 + - - +
306F MET 3.1 3.9 + - - -
307F GLU* 3.1 22.1 + - + +
308F ILE* 3.2 15.7 + - + +
373F ALA 3.8 4.7 - - - +
374F LEU* 3.7 27.6 - - + -
377F SER* 3.5 19.3 - - - -
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Residues in contact with TRP 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276F LEU* 3.8 29.1 - - + +
279F ILE* 5.0 2.9 - - + +
301F LEU* 3.0 24.1 + - + +
302F GLN* 3.2 30.0 + - - -
303F SER 4.6 2.6 + - - -
304F ALA* 1.3 77.0 - - - +
306F MET* 1.3 97.5 + - + +
308F ILE* 3.2 10.9 + - - +
309F LEU* 3.1 49.8 + - + +
432F VAL* 4.4 15.4 - - + +
435F PHE* 5.5 5.2 - + - -
436F TYR* 4.2 18.9 + + - -
505F OHT 3.8 37.7 - + - -
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Residues in contact with MET 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303F SER 4.9 1.7 + - - +
304F ALA 3.2 0.8 - - - -
305F TRP* 1.3 102.1 - - + +
307F GLU* 1.3 57.5 + - - +
309F LEU* 3.2 9.6 + - - +
310F ILE* 2.9 45.0 + - + +
428F SER* 3.5 27.4 - - - +
431F ALA* 3.8 23.6 - - + +
432F VAL* 3.6 25.8 - - + +
435F PHE* 5.1 2.0 - - + -
505F OHT 3.6 46.0 - - + -
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Residues in contact with GLU 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303F SER 4.5 9.3 - - - +
304F ALA* 3.1 15.9 + - - +
306F MET* 1.3 76.6 - - - +
308F ILE* 1.3 56.5 + - - +
310F ILE* 3.9 1.1 - - - -
311F LEU* 3.0 30.8 + - - +
373F ALA* 4.2 25.0 - - + +
377F SER* 5.0 3.1 - - - +
421F LEU* 5.1 3.1 - - - +
424F LEU* 3.7 31.8 - - + +
425F ARG* 2.8 46.1 + - - +
428F SER* 3.2 27.4 + - - +
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Residues in contact with ILE 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279F ILE* 3.8 37.8 - - + +
282F TRP* 4.0 19.7 - - + -
301F LEU* 5.0 1.6 - - + -
304F ALA* 3.2 19.8 + - + +
305F TRP* 3.6 8.5 - - - +
306F MET 3.2 0.6 - - - -
307F GLU* 1.3 74.6 - - - +
309F LEU* 1.3 66.3 + - - +
311F LEU* 4.3 4.5 - - - +
312F GLY* 3.2 17.5 + - - -
370F LYS* 4.1 35.8 - - + +
373F ALA* 4.9 7.2 - - + -
374F LEU* 3.9 33.2 - - + -
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Residues in contact with LEU 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F ALA* 4.0 12.6 - - + +
275F GLU* 3.6 44.1 - - + +
276F LEU* 4.5 5.4 - - + -
279F ILE* 3.9 12.6 - - + -
305F TRP* 3.1 47.9 + - + +
306F MET* 3.2 9.2 + - - +
308F ILE* 1.3 77.7 - - - +
310F ILE* 1.3 57.0 + - - +
312F GLY* 3.1 4.3 + - - -
313F VAL 3.1 22.0 + - - -
505F OHT 3.5 47.9 + - + +
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Residues in contact with ILE 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F MET* 2.9 32.4 + - + +
307F GLU* 4.1 3.4 - - - +
308F ILE 3.3 0.2 - - - -
309F LEU* 1.3 72.9 - - - +
311F LEU* 1.3 60.2 + - - +
312F GLY 3.1 1.6 - - - -
313F VAL* 2.9 12.0 - - + +
314F VAL* 2.9 31.4 + - + +
349F ILE* 4.4 22.0 - - + -
352F LEU* 4.3 16.4 - - + -
424F LEU* 3.9 17.0 - - + -
427F THR* 4.2 9.0 - - + +
428F SER* 3.7 31.9 - - - +
431F ALA* 4.0 14.4 - - + -
505F OHT 4.6 9.4 - - + -
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Residues in contact with LEU 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307F GLU 3.0 18.1 + - - +
308F ILE* 4.3 4.0 - - - +
310F ILE* 1.3 76.1 - - - +
312F GLY* 1.3 56.7 + - - +
314F VAL* 3.7 7.1 - - + +
315F TYR* 2.9 25.7 + - - +
356F TYR* 3.7 38.6 - - + +
361F LEU* 5.6 2.9 - - + -
366F PHE* 3.4 28.7 - - + +
369F LEU* 4.1 10.8 - - + -
370F LYS* 3.6 39.7 - - + +
373F ALA* 5.3 0.9 - - + -
424F LEU* 4.0 24.4 - - + +
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Residues in contact with GLY 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275F GLU* 5.6 1.1 - - - -
308F ILE 3.2 12.7 + - - -
309F LEU* 3.1 8.8 + - - -
310F ILE 3.1 1.0 - - - -
311F LEU* 1.3 79.7 - - - +
313F VAL* 1.3 61.5 + - - +
315F TYR* 3.4 2.6 + - - +
316F ARG* 2.9 39.5 + - - +
366F PHE* 4.0 15.2 - - - -
370F LYS* 5.3 1.1 - - - -
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Residues in contact with VAL 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309F LEU 3.1 4.9 + - - +
310F ILE* 2.9 34.3 - - + +
312F GLY* 1.3 71.3 - - - +
314F VAL* 1.3 60.6 + - - +
316F ARG* 3.4 20.8 + - - +
317F SER* 2.7 37.1 + - - +
324F LEU* 4.3 7.0 - - + -
325F VAL 3.4 27.8 - - - +
326F TYR* 3.7 34.5 - - + +
349F ILE* 4.3 15.3 - - + -
505F OHT 4.1 4.5 - - + +
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Residues in contact with VAL 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310F ILE* 2.9 27.8 + - + +
311F LEU* 3.7 9.6 - - + +
313F VAL* 1.3 72.9 - - - +
315F TYR* 1.3 67.8 + - - +
317F SER* 2.8 14.7 + - - -
318F LEU* 3.3 13.1 + - + +
349F ILE* 3.7 33.4 - - + +
352F LEU* 3.9 11.0 - - + -
353F VAL* 3.9 25.8 - - + +
356F TYR* 3.6 33.0 - - + -
361F LEU* 6.0 0.2 - - + -
424F LEU* 5.8 0.2 - - + -
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Residues in contact with TYR 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311F LEU* 2.9 11.6 + - + +
312F GLY 3.8 1.3 - - - +
314F VAL* 1.3 74.7 - - - +
316F ARG* 1.3 69.8 + - + +
317F SER 3.2 0.7 + - - -
318F LEU* 3.5 43.9 + - + +
361F LEU* 3.9 11.9 + - + -
362F GLU* 4.0 5.6 - - - -
363F LYS* 3.3 57.2 + - + +
366F PHE* 3.5 62.6 - + + -
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Residues in contact with ARG 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248F LYS* 6.5 0.7 - - - -
275F GLU* 3.7 14.1 + - - -
312F GLY* 2.9 31.6 + - - +
313F VAL* 3.4 23.6 - - - +
314F VAL 3.2 0.8 - - - -
315F TYR* 1.3 82.5 - - + +
317F SER* 1.3 58.1 + - - +
318F LEU 3.6 0.4 + - - -
319F SER* 5.0 2.5 + - - -
320F PHE* 3.9 9.7 - - - -
325F VAL* 3.1 43.0 + - + +
326F TYR 3.1 25.0 + - - -
327F ALA* 4.6 3.7 - - - +
328F ASP* 5.8 2.7 - - - +
366F PHE* 5.8 1.0 - - + -
505F OHT 3.6 15.8 + - - -
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Residues in contact with SER 317 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313F VAL 2.7 22.4 + - - -
314F VAL 2.8 6.9 + - - -
316F ARG* 1.3 76.9 - - - +
318F LEU* 1.3 62.7 + - - +
319F SER 3.4 2.7 - - - -
320F PHE* 3.0 22.8 + - - +
323F GLU 3.6 18.0 - - - +
324F LEU* 3.4 4.9 - - - +
325F VAL* 2.7 29.4 + - - -
353F VAL* 3.7 23.1 - - - +
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Residues in contact with LEU 318 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314F VAL* 3.3 12.2 + - + +
315F TYR* 3.5 46.9 + - + +
316F ARG 3.6 0.2 - - - -
317F SER* 1.3 75.9 - - - +
319F SER* 1.3 58.6 + - - +
320F PHE 3.2 4.2 + - - +
353F VAL* 3.9 21.3 - - + +
356F TYR* 3.7 27.6 - - + +
357F LYS* 3.2 37.7 - - + +
361F LEU* 4.0 25.6 - - + +
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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