Contacts of the helix formed by residues 293 - 317 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B THR 4.1 0.2 + - - -
292B LEU* 1.3 79.4 - - - +
294B LEU* 1.3 64.3 + - - +
295B ALA* 4.0 3.8 - - - -
296B ASP* 3.0 33.5 + - - +
297B GLN* 3.0 21.0 + - - +
383B GLU* 3.3 21.9 + - - -
384B ASP* 6.3 0.2 - - - +
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Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU 3.8 0.2 + - - -
293B SER* 1.3 73.2 - - - +
295B ALA* 1.3 62.1 + - - +
297B GLN* 3.5 24.5 + - - +
298B MET* 3.1 33.5 + - + +
1328H LEU* 4.7 23.1 - - + +
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B SER* 3.2 1.5 - - - +
294B LEU* 1.3 79.0 - - - +
296B ASP* 1.3 57.1 + - - +
298B MET* 3.4 13.7 + - + +
299B SER* 3.0 30.4 + - - -
381B HIS 5.9 1.8 - - - +
383B GLU* 3.1 32.1 - - + +
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Residues in contact with ASP 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B LEU* 4.1 20.1 - - + +
293B SER* 3.0 27.1 + - - +
295B ALA* 1.3 77.3 - - - +
297B GLN* 1.3 64.3 + - - +
299B SER* 3.1 4.6 + - - -
300B LEU* 3.0 29.9 + - + +
381B HIS 4.2 1.2 - - - +
382B ILE* 3.4 18.8 - - + +
383B GLU* 2.7 32.4 + - - +
384B ASP* 3.2 28.9 + - - +
388B VAL* 5.0 2.9 - - + -
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Residues in contact with GLN 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B LYS* 5.2 3.1 - - - +
289B PHE* 3.4 48.9 + - + +
290B SER* 3.3 19.6 + - - +
292B LEU* 3.1 26.2 + - + +
293B SER 3.0 16.2 + - - +
294B LEU* 3.8 21.1 - - - +
295B ALA 3.4 0.2 - - - -
296B ASP* 1.3 75.1 - - - +
298B MET* 1.3 62.8 + - - +
300B LEU* 3.7 0.4 + - - -
301B LEU* 3.3 30.7 + - - +
1328H LEU* 3.4 29.5 - - + +
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Residues in contact with MET 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B LEU* 3.1 22.4 + - + +
295B ALA* 3.5 11.0 - - + +
296B ASP 3.1 0.2 - - - -
297B GLN* 1.3 79.0 - - - +
299B SER* 1.3 59.7 + - - +
301B LEU* 3.5 1.9 + - - +
302B GLN* 2.9 42.4 + - - +
1321H GLU* 4.6 23.3 - - - +
1324H ILE* 4.2 12.3 - - + +
1325H ARG* 3.7 57.0 - - + +
1328H LEU* 3.9 17.0 - - + -
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Residues in contact with SER 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ALA 3.0 16.8 + - - -
296B ASP* 3.1 8.0 + - - -
298B MET* 1.3 73.7 - - - +
300B LEU* 1.3 66.0 + - - +
302B GLN* 3.2 15.3 + - - +
303B SER* 3.1 25.8 + - - -
379B SER* 3.6 18.1 + - - -
381B HIS* 3.6 27.0 + - - +
382B ILE* 4.0 14.8 - - - -
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B PHE* 4.2 14.6 - - + -
292B LEU* 4.0 23.1 - - + -
296B ASP 3.0 17.7 + - - +
297B GLN 4.1 3.1 - - - +
299B SER* 1.3 76.0 - - - +
301B LEU* 1.3 57.4 + - - +
303B SER* 3.3 0.7 + - - -
304B ALA* 2.9 28.8 + - - +
374B LEU* 3.5 30.3 - - + +
375B ALA* 4.4 8.7 - - - +
377B SER* 3.2 16.3 + - - +
378B ASP 6.0 0.9 - - - +
379B SER* 4.9 3.8 - - - +
382B ILE* 3.5 29.2 - - + -
388B VAL* 4.1 24.2 - - + -
391B LEU* 4.5 3.8 - - + -
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B LEU* 6.1 1.6 - - + -
279B ILE* 4.6 19.1 - - + -
280B ILE* 4.3 22.7 - - + -
283B ALA* 4.4 15.7 - - + -
289B PHE* 4.0 15.7 - - + -
297B GLN 3.3 20.0 + - - +
298B MET 3.7 3.8 - - - +
299B SER 3.2 0.4 - - - -
300B LEU* 1.3 79.8 - - - +
302B GLN* 1.3 57.9 + - - +
303B SER 3.1 0.2 + - - -
305B TRP* 2.9 38.8 + - + +
308B ILE* 5.1 2.7 - - + -
374B LEU* 4.0 15.7 - - + -
1324H ILE* 3.8 33.9 - - + -
1328H LEU* 4.3 10.1 - - + -
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Residues in contact with GLN 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B MET* 2.9 34.6 + - - +
299B SER* 3.7 14.6 + - - +
301B LEU* 1.3 76.2 - - - +
303B SER* 1.3 58.1 - - - +
305B TRP* 3.0 25.4 + - - +
381B HIS* 5.3 7.4 - - - -
1320H LEU* 4.4 12.4 - - + +
1321H GLU* 3.4 38.9 + - + +
1324H ILE* 3.8 17.2 - - + +
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Residues in contact with SER 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B SER 3.1 9.8 + - - -
301B LEU 3.1 0.4 - - - -
302B GLN* 1.3 80.7 - - - +
304B ALA* 1.3 57.1 + - - +
305B TRP* 3.6 3.1 + - - -
306B MET* 5.0 1.2 + - - +
307B GLU* 4.5 9.0 - - - +
377B SER* 3.2 34.5 + - - +
378B ASP 4.8 0.2 - - - -
379B SER* 3.4 25.4 + - - -
425B ARG* 6.0 0.3 - - - -
428B SER* 5.0 5.0 + - - -
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Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B LEU 2.9 16.4 + - - +
303B SER* 1.3 75.8 - - - +
305B TRP* 1.3 65.7 + - - +
306B MET 3.4 2.7 - - - -
307B GLU* 3.1 11.4 + - + +
308B ILE* 3.0 26.8 + - + +
373B ALA 3.6 13.7 - - - +
374B LEU* 3.6 20.2 - - + +
377B SER* 3.5 18.4 - - - -
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Residues in contact with TRP 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ALA* 5.6 0.2 - - + -
276B LEU* 4.1 34.1 - - + -
279B ILE* 4.6 6.0 - - + +
301B LEU* 2.9 19.4 + - + +
302B GLN* 3.0 29.6 + - - -
303B SER 4.4 2.2 - - - -
304B ALA* 1.3 76.2 - - - +
306B MET* 1.3 92.9 + - + +
308B ILE* 3.2 10.8 + - - +
309B LEU* 3.0 35.0 + - + +
432B VAL* 4.4 21.0 - - + +
435B PHE* 5.8 4.5 - + - -
436B TYR* 5.0 10.8 - + - -
501B OHT 3.7 49.6 - + - -
1320H LEU* 3.3 31.9 - - + +
1324H ILE* 5.5 0.4 - - + -
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Residues in contact with MET 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B SER 5.0 1.1 + - - +
304B ALA 3.4 0.6 - - - -
305B TRP* 1.3 102.2 - - + +
307B GLU* 1.3 56.6 + - - +
309B LEU* 3.5 9.2 + - - +
310B ILE* 3.0 36.1 + - + +
428B SER* 3.5 19.7 - - - +
431B ALA* 3.5 47.1 - - + +
432B VAL* 3.8 17.0 - - + +
435B PHE* 5.2 2.5 - - + -
501B OHT 3.6 49.8 - - + -
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Residues in contact with GLU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B SER 4.5 6.5 + - - +
304B ALA* 3.1 17.3 + - - +
306B MET* 1.3 76.9 - - - +
308B ILE* 1.3 59.2 + - - +
311B LEU* 3.0 28.8 + - - +
373B ALA* 3.7 31.6 - - + +
377B SER* 5.2 2.3 - - - -
421B LEU* 4.9 4.2 - - - +
424B LEU* 3.6 27.8 - - + +
425B ARG* 2.8 51.1 + - - -
428B SER* 3.4 24.8 + - - +
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Residues in contact with ILE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B ILE* 3.6 44.9 - - + -
282B TRP* 4.0 17.5 - - + -
301B LEU* 5.1 2.2 - - + -
304B ALA* 3.0 27.9 + - + +
305B TRP* 3.7 6.3 - - - +
307B GLU* 1.3 75.0 - - + +
309B LEU* 1.3 67.2 + - - +
311B LEU* 3.2 6.3 + - - +
312B GLY* 2.8 21.7 + - - -
370B LYS* 3.8 39.3 - - + +
373B ALA* 5.2 2.9 - - + -
374B LEU* 4.3 19.7 - - + -
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ALA* 3.9 12.1 - - + +
275B GLU* 3.6 34.9 - - + +
276B LEU* 4.6 5.2 - - + +
279B ILE* 3.5 23.1 - - + -
305B TRP* 3.0 30.9 + - + +
306B MET* 3.7 11.0 - - - +
307B GLU 3.5 0.2 - - - -
308B ILE* 1.3 75.4 - - - +
310B ILE* 1.3 62.9 + - - +
312B GLY* 3.3 2.4 + - - -
313B VAL* 3.2 21.1 + - - +
316B ARG* 4.7 0.7 + - - -
501B OHT 3.6 58.1 + - + +
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Residues in contact with ILE 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B MET* 3.0 27.6 + - + +
307B GLU 4.1 2.5 - - - +
309B LEU* 1.3 73.4 - - - +
311B LEU* 1.3 67.0 + - - +
312B GLY 3.0 1.5 + - - -
313B VAL* 3.2 9.2 - - + +
314B VAL* 2.8 35.5 + - + +
349B ILE* 4.3 18.8 - - + -
352B LEU* 4.1 9.2 - - + -
424B LEU* 3.7 17.9 - - + -
427B THR* 3.9 15.7 - - + -
428B SER* 3.7 27.8 - - - +
431B ALA* 3.9 19.5 - - + -
501B OHT 4.9 6.5 - - + -
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLU 3.0 18.9 + - - +
308B ILE* 3.8 3.1 - - - +
310B ILE* 1.3 76.1 - - - +
312B GLY* 1.3 56.7 + - - +
314B VAL* 3.7 6.1 - - + +
315B TYR* 2.9 25.1 + - - +
356B TYR* 3.9 35.0 - - + +
361B LEU* 5.7 3.4 - - + -
366B PHE* 3.4 23.5 - - + +
369B LEU* 3.8 17.9 - - + +
370B LYS* 3.6 40.8 - - + +
373B ALA* 4.8 1.3 - - + -
421B LEU* 5.8 0.9 - - + -
424B LEU* 4.0 26.2 - - + -
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Residues in contact with GLY 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B ILE 2.8 13.2 + - - -
309B LEU* 3.5 4.3 - - - -
310B ILE 3.0 1.0 - - - -
311B LEU* 1.3 72.4 - - - +
313B VAL* 1.3 65.9 + - - -
314B VAL 2.9 1.7 + - - -
315B TYR* 3.0 4.9 + - - +
316B ARG* 3.0 42.4 + - - +
366B PHE* 3.9 16.3 - - - -
370B LYS* 5.4 0.4 - - - -
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Residues in contact with VAL 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B LEU 3.2 13.7 + - - +
310B ILE* 3.2 24.7 - - + +
312B GLY* 1.3 71.2 - - - +
314B VAL* 1.3 57.2 + - - +
316B ARG* 3.3 25.1 - - - +
317B SER* 2.5 43.2 + - - +
324B LEU* 4.1 21.3 - - + -
325B VAL 3.9 10.1 - - - +
326B TYR* 3.9 24.5 - - + -
349B ILE* 4.3 11.7 - - + -
501B OHT 4.0 11.9 - - + -
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Residues in contact with VAL 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ILE* 2.8 27.1 + - + +
311B LEU* 3.7 8.7 - - + +
313B VAL* 1.3 75.3 - - - +
315B TYR* 1.3 66.3 + - - +
317B SER* 3.1 12.6 + - - -
318B LEU* 3.4 15.6 + - + +
349B ILE* 3.4 37.7 - - + +
352B LEU* 3.9 18.4 - - + +
353B VAL* 4.1 12.8 - - + +
356B TYR* 3.6 33.7 - - + -
361B LEU* 5.9 0.7 - - + -
424B LEU* 5.7 0.2 - - + -
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Residues in contact with TYR 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B LEU 2.9 9.2 + - - +
312B GLY 3.7 2.5 - - - +
314B VAL* 1.3 76.9 - - - +
316B ARG* 1.3 72.1 + - + +
317B SER 3.1 0.9 + - - -
318B LEU* 3.3 43.8 + - + +
319B SER* 5.1 0.7 + - - -
361B LEU* 4.3 10.0 + - + -
362B GLU* 4.0 4.4 - - - -
363B LYS* 3.2 60.8 + - + +
366B PHE* 3.6 48.7 - + + -
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Residues in contact with ARG 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LYS* 6.4 1.6 - - - -
275B GLU* 3.9 17.7 + - - -
312B GLY* 3.0 36.7 + - - +
313B VAL* 3.3 20.3 - - - +
315B TYR* 1.3 84.1 - - + +
317B SER* 1.3 59.4 + - - +
318B LEU 3.5 0.6 + - - -
319B SER* 4.2 4.3 + - - -
320B PHE* 4.0 12.6 - - - -
325B VAL* 3.0 41.8 + - + +
326B TYR 2.8 29.2 + - - -
327B ALA* 4.6 2.9 - - - +
328B ASP* 5.9 1.1 - - - -
366B PHE* 6.3 0.7 - - + -
501B OHT 3.3 22.2 + - - -
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Residues in contact with SER 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B VAL 2.5 22.7 + - - -
314B VAL 3.1 5.6 + - - -
315B TYR 3.0 1.0 - - - -
316B ARG* 1.3 76.7 - - - +
318B LEU* 1.3 62.2 + - - +
319B SER 3.3 3.4 - - - -
320B PHE* 3.0 29.7 + - - +
323B GLU 3.6 15.7 - - - +
324B LEU* 3.3 7.6 - - - +
325B VAL 2.9 22.8 + - - +
353B VAL* 3.9 20.7 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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