Contacts of the helix formed by residues 293 - 317 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A THR 3.9 1.0 + - - -
292A LEU* 1.3 75.8 - - - +
294A LEU* 1.3 65.9 + - - +
295A ALA* 4.2 2.5 - - - -
296A ASP* 3.0 22.9 + - - +
297A GLN* 3.0 20.1 + - - +
383A GLU* 2.7 29.5 + - - +
384A ASP* 5.8 0.7 - - - +
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Residues in contact with LEU 294 (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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292A LEU 3.7 1.0 + - - +
293A SER* 1.3 73.2 - - - +
295A ALA* 1.3 56.4 + - - +
297A GLN* 3.6 26.5 - - - +
298A MET* 3.0 34.0 + - + +
1328G LEU* 4.5 22.1 - - + +
1329G MET* 6.2 5.4 - - - -
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Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A SER* 3.1 1.6 - - - -
294A LEU* 1.3 79.0 - - - +
296A ASP* 1.3 58.8 + - - +
298A MET* 3.3 11.2 - - - +
299A SER* 2.9 33.3 + - - +
383A GLU* 4.2 24.5 - - + +
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Residues in contact with ASP 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A LEU* 4.4 18.7 - - + +
293A SER* 3.0 20.1 + - - +
295A ALA* 1.3 77.2 - - - +
297A GLN* 1.3 66.6 + - - +
299A SER* 3.0 5.7 + - - -
300A LEU* 2.9 30.4 + - + +
381A HIS 4.2 2.8 - - - +
382A ILE* 3.7 17.8 - - + +
383A GLU* 2.8 31.5 + - - +
384A ASP* 2.9 34.3 + - - +
388A VAL* 4.6 3.7 - - + +
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Residues in contact with GLN 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LYS* 5.4 2.8 - - - +
289A PHE* 3.3 55.6 + - + +
290A SER* 3.4 16.8 + - - +
292A LEU* 2.7 28.5 + - + +
293A SER 3.0 12.4 + - - +
294A LEU* 3.6 23.4 - - - +
296A ASP* 1.3 75.0 - - - +
298A MET* 1.3 64.4 + - - +
300A LEU* 3.3 0.8 + - - -
301A LEU* 3.2 28.7 + - - +
1328G LEU* 3.4 25.3 - - + +
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Residues in contact with MET 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A LEU* 3.0 19.1 + - + +
295A ALA* 3.3 12.8 - - - +
297A GLN* 1.3 78.2 - - - +
299A SER* 1.3 52.7 + - - +
301A LEU* 3.3 2.8 + - - +
302A GLN* 2.8 56.9 + - - +
1321G GLU* 5.0 10.1 - - + +
1324G ILE* 3.8 19.9 - - + +
1325G ARG* 4.0 42.2 - - - +
1328G LEU* 3.7 21.5 - - + +
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Residues in contact with SER 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ALA* 2.9 20.1 + - - +
296A ASP* 3.0 6.2 + - - -
298A MET* 1.3 74.0 - - - +
300A LEU* 1.3 66.1 + - - +
302A GLN* 3.7 12.3 + - - +
303A SER* 3.4 15.2 + - - -
379A SER* 3.6 30.4 + - - -
381A HIS* 4.1 17.2 + - - +
382A ILE* 4.2 11.7 - - - -
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Residues in contact with LEU 300 (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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289A PHE* 4.2 11.9 - - + -
292A LEU* 4.1 24.9 - - + -
296A ASP 2.9 18.2 + - - +
297A GLN 3.9 3.6 - - - +
299A SER* 1.3 74.4 - - - +
301A LEU* 1.3 66.7 + - - +
303A SER 3.2 1.6 + - - -
304A ALA* 3.0 23.9 + - - +
374A LEU* 3.7 22.0 - - + +
375A ALA* 4.6 6.3 - - - +
377A SER* 3.4 22.3 + - - +
378A ASP 6.1 0.4 - - - +
379A SER* 4.7 1.6 - - - +
382A ILE* 3.3 34.5 - - + -
388A VAL* 4.4 16.8 - - + -
391A LEU* 4.2 15.3 - - + -
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Residues in contact with LEU 301 (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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279A ILE* 4.2 20.2 - - + -
280A ILE* 3.9 40.8 - - + -
283A ALA* 4.3 11.9 - - + -
289A PHE* 4.1 17.9 - - + -
297A GLN 3.2 15.0 + - - +
298A MET 3.6 6.5 - - - +
300A LEU* 1.3 78.1 - - - +
302A GLN* 1.3 63.2 + - - +
304A ALA 4.6 0.2 - - - +
305A TRP* 3.0 35.2 + - + +
308A ILE* 5.0 3.1 - - + -
374A LEU* 4.0 14.8 - - + -
1324G ILE* 4.0 16.7 - - + +
1328G LEU* 4.4 17.7 - - + -
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Residues in contact with GLN 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A MET* 2.8 43.5 + - - +
299A SER* 3.7 12.6 + - - +
300A LEU 3.2 0.4 - - - -
301A LEU* 1.3 77.1 - - - +
303A SER* 1.3 58.3 + - - +
305A TRP* 3.1 21.2 + - - -
381A HIS* 5.3 10.9 - - - -
1320G LEU* 5.1 6.9 - - + +
1321G GLU* 3.6 27.3 + - - +
1324G ILE* 4.0 15.0 - - + +
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Residues in contact with SER 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A SER 3.4 6.8 + - - -
300A LEU 3.2 0.8 + - - -
301A LEU 3.2 0.4 - - - -
302A GLN* 1.3 81.0 - - - +
304A ALA* 1.3 58.1 + - - +
305A TRP* 3.7 3.8 + - - -
306A MET* 5.1 0.9 + - - +
307A GLU* 4.3 9.7 - - - +
377A SER* 3.4 40.5 + - - +
378A ASP 4.5 0.2 - - - -
379A SER* 3.5 20.4 - - - -
428A SER* 5.0 5.5 + - - -
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Residues in contact with ALA 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A LEU 3.0 14.6 + - - +
303A SER* 1.3 74.8 - - - +
305A TRP* 1.3 67.1 + - - +
306A MET 3.2 3.4 - - - -
307A GLU* 3.0 14.4 + - + +
308A ILE* 2.9 30.1 + - + +
373A ALA 3.8 6.3 - - - +
374A LEU* 3.8 22.2 - - + +
377A SER* 3.6 17.3 - - - -
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Residues in contact with TRP 305 (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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276A LEU* 3.8 32.5 - - + -
279A ILE* 4.5 4.0 - - + +
301A LEU* 3.0 21.3 + - + +
302A GLN* 3.1 30.0 + - - -
303A SER 4.4 2.6 + - - -
304A ALA* 1.3 79.1 - - - +
306A MET* 1.3 96.6 + - + +
308A ILE* 3.0 11.0 + - - +
309A LEU* 2.8 37.6 + - + +
432A VAL* 4.3 24.0 - - + +
435A PHE* 6.0 5.2 - + - -
436A TYR* 6.1 2.9 - + - -
500A OHT 4.0 36.3 - + - -
1320G LEU* 3.7 35.9 - - + +
1324G ILE* 5.5 2.2 - - + -
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Residues in contact with MET 306 (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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303A SER 5.1 0.9 + - - +
304A ALA 3.2 0.8 - - - -
305A TRP* 1.3 106.0 - - + +
307A GLU* 1.3 58.4 + - - +
309A LEU* 4.4 7.2 - - - -
310A ILE* 2.9 49.6 + - + +
428A SER* 3.7 18.8 - - - +
431A ALA* 3.8 20.6 - - + -
432A VAL* 3.8 28.5 - - + +
435A PHE* 5.3 2.7 - - + -
500A OHT 3.6 47.1 - - + -
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Residues in contact with GLU 307 (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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303A SER 4.3 9.9 + - - +
304A ALA* 3.0 17.2 + - - +
306A MET* 1.3 77.8 - - - +
308A ILE* 1.3 56.6 + - - +
311A LEU* 2.9 31.4 + - - +
373A ALA* 3.9 26.0 - - + +
377A SER* 5.6 1.8 - - - -
421A LEU* 5.3 2.4 - - - +
424A LEU* 3.6 31.9 - - + +
425A ARG* 2.8 48.4 + - - +
428A SER* 3.5 21.7 + - - +
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Residues in contact with ILE 308 (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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279A ILE* 3.9 37.2 - - + +
282A TRP* 4.2 13.5 - - + -
301A LEU* 5.0 2.0 - - + -
304A ALA* 2.9 35.9 + - + +
305A TRP* 3.5 7.2 - - - +
307A GLU* 1.3 74.1 - - - +
309A LEU* 1.3 65.7 + - - +
311A LEU* 3.4 5.6 + - - +
312A GLY* 3.0 19.1 + - - -
370A LYS* 3.7 41.9 - - + +
373A ALA* 4.9 4.3 - - + -
374A LEU* 4.2 22.9 - - + -
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Residues in contact with LEU 309 (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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272A ALA* 4.0 24.0 - - + +
275A GLU* 3.3 47.6 - - + +
276A LEU* 4.2 6.5 - - + +
279A ILE* 3.8 15.9 - - + -
305A TRP* 2.8 40.5 + - + +
306A MET* 3.9 6.3 - - - +
308A ILE* 1.3 73.1 - - - +
310A ILE* 1.3 58.4 + - - +
312A GLY* 2.9 19.1 + - - -
313A VAL* 3.2 11.8 + - - +
500A OHT 3.8 35.2 + - + +
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Residues in contact with ILE 310 (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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306A MET* 2.9 33.2 + - + +
307A GLU 4.1 1.3 - - - +
309A LEU* 1.3 76.6 - - - +
311A LEU* 1.3 61.9 + - - +
313A VAL* 3.1 15.8 - - - +
314A VAL* 3.1 17.7 - - + +
345A LEU* 5.9 0.2 - - + -
349A ILE* 4.6 19.1 - - + -
352A LEU* 4.0 17.7 - - + -
424A LEU* 3.8 18.8 - - + -
427A THR* 4.1 13.9 - - + -
428A SER* 3.9 12.8 - - - -
431A ALA* 3.7 30.5 - - + -
500A OHT 4.8 10.1 - - + -
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A GLU 2.9 19.9 + - - +
308A ILE* 4.0 3.8 - - - +
309A LEU 3.2 0.2 - - - -
310A ILE* 1.3 75.4 - - - +
312A GLY* 1.3 62.9 + - - +
314A VAL* 3.6 7.2 + - + +
315A TYR* 3.2 13.3 + - - +
356A TYR* 3.8 36.8 - - + +
361A LEU* 5.4 3.4 - - + -
366A PHE* 3.1 30.1 - - + +
369A LEU* 4.2 11.4 - - + +
370A LYS* 3.7 38.4 - - + +
373A ALA* 5.0 1.6 - - + -
421A LEU* 6.2 0.2 - - + -
424A LEU* 4.0 27.6 - - + -
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Residues in contact with GLY 312 (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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275A GLU* 5.6 0.4 - - - -
308A ILE 3.0 10.1 + - - -
309A LEU* 2.9 10.1 + - - -
311A LEU* 1.3 74.2 - - - +
313A VAL* 1.3 64.8 + - - -
315A TYR* 3.2 11.4 + - - +
316A ARG* 3.2 32.9 + - - +
366A PHE* 3.9 17.4 - - - -
370A LYS* 5.4 0.7 - - - -
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Residues in contact with VAL 313 (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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309A LEU 3.2 5.4 + - - +
310A ILE* 3.1 30.1 - - + +
312A GLY* 1.3 73.6 - - - +
314A VAL* 1.3 58.7 + - - +
315A TYR 3.2 0.2 + - - -
316A ARG* 3.3 24.8 + - - +
317A SER* 2.6 40.6 + - - +
324A LEU* 4.1 15.3 - - + -
325A VAL 3.5 20.4 - - - +
326A TYR* 4.1 30.3 - - + +
349A ILE* 4.4 11.9 - - + -
500A OHT 4.2 3.8 - - + -
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Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ILE 3.1 19.8 + - - +
311A LEU* 3.7 10.5 - - + +
312A GLY 3.2 0.6 - - - -
313A VAL* 1.3 77.1 - - - +
315A TYR* 1.3 66.2 + - - +
317A SER* 3.1 11.1 + - - -
318A LEU* 3.4 11.2 + - + +
349A ILE* 3.7 23.8 - - + +
352A LEU* 3.8 24.7 - - + +
353A VAL* 3.6 25.9 - - + +
356A TYR* 3.8 33.0 - - + -
361A LEU* 5.8 0.9 - - + -
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Residues in contact with TYR 315 (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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311A LEU 3.2 4.2 + - - +
312A GLY 3.2 2.8 + - - +
314A VAL* 1.3 78.6 - - - +
316A ARG* 1.3 64.3 + - + +
318A LEU* 2.9 61.0 + - + +
361A LEU* 4.3 9.8 + - + -
362A GLU* 4.2 4.8 - - - -
363A LYS* 3.4 61.8 + - + +
366A PHE* 3.5 51.4 - + + -
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Residues in contact with ARG 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LYS* 6.3 4.7 - - - +
275A GLU* 3.6 16.8 + - - -
312A GLY* 3.2 29.5 + - - +
313A VAL* 3.4 26.3 - - - +
315A TYR* 1.3 85.8 - - + +
317A SER* 1.3 58.8 + - - +
318A LEU 3.4 0.4 + - - -
319A SER* 5.0 0.9 + - - -
320A PHE* 3.9 9.5 - - - -
325A VAL* 3.2 37.8 + - + +
326A TYR* 2.8 30.0 + - - +
327A ALA* 4.7 2.9 - - - +
366A PHE* 6.3 0.7 - - + -
500A OHT 3.3 20.0 + - - -
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Residues in contact with SER 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A VAL* 2.6 28.0 + - - +
314A VAL 3.4 6.1 - - - -
315A TYR 2.9 0.8 + - - -
316A ARG* 1.3 77.2 - - - +
318A LEU* 1.3 63.6 + - - +
319A SER 3.4 2.0 - - - -
320A PHE* 3.1 23.2 + - - +
323A GLU 3.9 13.8 - - - +
324A LEU* 3.6 4.0 - - - +
325A VAL* 3.2 26.2 + - - -
353A VAL* 3.7 22.2 - - - +
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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