Contacts of the helix formed by residues 341 - 368 (chain H) in PDB entry 2VIG
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 PHE 341 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266H GLN 5.1 0.9 - - - -
269H ASP* 3.7 35.2 - - + -
270H MET* 4.0 12.3 - - + -
273H ILE* 3.7 25.6 - - + -
331H ALA* 3.8 7.2 - - - +
334H LEU* 3.8 19.5 - - + -
335H LYS* 3.5 36.3 - - + -
339H LYS 3.6 13.9 - - - -
340H PRO* 1.3 75.0 - - + +
342H ILE* 1.3 65.4 + - + +
344H GLU* 3.4 11.9 - - + -
345H ALA* 2.8 35.7 + - + +
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Residues in contact with ILE 342 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266H GLN* 6.5 0.7 - - + -
269H ASP* 3.4 40.0 - - - +
272H ARG* 5.4 1.1 + - - +
340H PRO* 3.9 5.6 - - + +
341H PHE* 1.3 82.5 - - + +
343H LYS* 1.3 63.6 + - - +
344H GLU* 3.8 0.8 + - - -
345H ALA* 3.9 1.8 - - - +
346H ALA* 3.2 22.0 + - - +
401H VAL* 3.9 13.0 - - + -
405H HIS* 3.3 39.9 - - + +
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Residues in contact with LYS 343 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322F GLU* 2.8 40.6 + - - +
330H ARG* 4.9 0.6 - - - +
341H PHE 3.5 0.2 - - - -
342H ILE* 1.3 79.2 - - - +
344H GLU* 1.3 83.8 + - - +
346H ALA* 3.3 6.7 + - - +
347H MET* 3.0 54.3 + - + +
401H VAL* 5.0 2.2 - - - -
402H ILE* 4.2 13.9 - - + +
405H HIS* 3.8 33.8 - - + -
406H LEU* 4.6 15.8 - - + +
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Residues in contact with GLU 344 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327H LEU 4.2 3.1 - - - +
330H ARG* 3.6 37.2 + - - +
331H ALA* 3.7 11.8 - - + +
334H LEU* 3.3 34.6 - - + +
340H PRO* 3.8 6.0 - - - +
341H PHE* 3.4 20.6 + - - +
342H ILE 3.3 0.5 + - - -
343H LYS* 1.3 99.7 + - - +
345H ALA* 1.3 60.4 + - - +
347H MET* 3.6 2.8 + - - +
348H ALA* 3.1 22.7 + - - +
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Residues in contact with ALA 345 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269H ASP* 3.5 28.7 - - - +
272H ARG* 4.0 10.5 - - + +
273H ILE* 3.9 13.9 - - + -
331H ALA* 3.6 9.7 - - - +
341H PHE* 2.8 27.5 + - + +
342H ILE 3.9 3.4 - - - +
344H GLU* 1.3 70.6 - - - +
346H ALA* 1.3 59.7 + - - +
348H ALA* 3.3 4.1 + - - +
349H LYS* 3.0 30.0 + - - +
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Residues in contact with ALA 346 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272H ARG* 4.7 5.3 - - - +
342H ILE 3.2 17.3 + - - +
343H LYS 3.3 3.8 + - - +
345H ALA* 1.3 75.9 - - - +
347H MET* 1.3 57.7 + - - +
349H LYS* 3.9 0.6 - - - +
350H LEU* 2.9 32.9 + - - +
398H GLN* 3.2 30.4 - - - +
401H VAL* 3.9 17.5 - - + -
402H ILE* 3.9 18.2 - - + -
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Residues in contact with MET 347 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318F ALA* 3.9 17.9 - - + -
319F LEU* 3.9 26.4 - - + +
322F GLU* 3.2 33.0 - - - +
327H LEU* 4.4 4.9 - - + -
330H ARG* 3.3 27.6 - - - +
343H LYS* 3.0 33.8 + - + +
344H GLU 3.7 5.2 - - - +
345H ALA 3.3 0.2 - - - -
346H ALA* 1.3 75.0 - - - +
348H ALA* 1.3 53.6 + - - +
350H LEU* 3.8 0.7 - - - +
351H ALA* 2.8 38.6 + - - +
402H ILE* 3.7 38.8 - - + +
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Residues in contact with ALA 348 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273H ILE* 5.6 1.8 - - - -
276H ALA* 3.8 9.2 - - + -
324H ALA 4.9 0.4 - - - +
327H LEU* 3.6 15.8 - - - +
328H THR* 3.5 35.5 + - + +
331H ALA* 4.6 2.9 - - + -
344H GLU 3.1 15.2 + - - +
345H ALA* 3.6 7.6 - - - +
347H MET* 1.3 74.5 - - - +
349H LYS* 1.3 61.5 + - - +
351H ALA* 3.3 1.0 + - - +
352H ALA* 2.8 35.3 + - - +
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Residues in contact with LYS 349 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272H ARG* 3.6 32.5 - - + +
275H ILE* 3.9 17.7 - - + -
276H ALA* 3.9 11.2 - - - +
345H ALA 3.0 17.6 + - - +
346H ALA 3.9 2.9 - - - +
348H ALA* 1.3 75.3 - - - +
350H LEU* 1.3 65.2 + - - +
352H ALA* 4.2 0.3 - - - +
353H SER* 3.0 31.5 + - - +
388H THR 2.6 29.9 + - - +
389H GLU* 3.8 10.5 + - - +
391H TYR 3.0 20.9 + - - -
392H GLU* 4.1 3.4 - - - -
393H GLY 2.6 26.8 + - - -
394H THR 4.5 1.6 - - - -
395H SER* 4.6 1.0 - - - +
398H GLN* 3.7 13.9 - - + +
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Residues in contact with LEU 350 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315F ALA* 6.0 0.9 - - + +
316F ASP* 4.8 2.5 - - - +
319F LEU* 3.6 23.1 - - + -
346H ALA 2.9 19.0 + - - +
347H MET 3.8 1.8 - - - +
349H LYS* 1.3 77.7 - - - +
351H ALA* 1.3 66.0 + - - +
353H SER* 3.1 17.6 + - - -
354H GLU* 3.2 22.3 + - - +
395H SER* 3.6 37.0 - - - +
398H GLN* 3.9 11.4 - - + -
399H ARG* 3.6 38.1 - - + +
402H ILE* 3.8 16.8 - - + -
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Residues in contact with ALA 351 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319F LEU* 4.4 10.3 - - + -
323H SER* 6.5 0.2 - - - -
324H ALA* 4.1 11.1 - - + +
327H LEU* 3.4 25.8 - - + -
347H MET 2.8 23.2 + - - +
348H ALA 3.9 1.6 - - - +
350H LEU* 1.3 74.4 - - - +
352H ALA* 1.3 62.9 + - - +
354H GLU* 3.6 4.3 + - - +
355H ALA* 3.1 25.1 + - - +
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Residues in contact with ALA 352 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276H ALA* 3.3 33.2 - - + +
279H ALA* 3.5 7.9 - - + +
280H LEU* 3.9 17.5 - - + -
283H ALA* 5.3 0.7 - - - +
324H ALA* 3.7 10.8 - - + -
328H THR* 4.6 0.9 - - - +
348H ALA 2.8 20.3 + - - +
351H ALA* 1.3 74.6 - - - +
353H SER* 1.3 58.4 + - - +
355H ALA* 3.5 3.0 + - - +
356H ALA* 2.8 30.5 + - - +
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Residues in contact with SER 353 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H ILE* 5.8 0.2 - - - -
279H ALA* 3.8 3.9 - - - +
349H LYS* 3.0 17.7 + - - +
350H LEU* 3.1 14.6 + - - -
352H ALA* 1.3 77.6 - - - +
354H GLU* 1.3 63.3 + - - +
356H ALA* 3.3 2.8 + - - +
357H THR* 3.2 25.1 + - - -
388H THR* 3.3 48.6 + - - -
389H GLU* 3.7 14.8 - - - +
395H SER* 4.1 5.7 + - - -
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Residues in contact with GLU 354 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350H LEU* 3.2 26.1 + - - +
351H ALA* 4.3 3.6 - - - +
353H SER* 1.3 81.0 + - - +
355H ALA* 1.3 56.3 + - - +
357H THR* 3.5 2.9 + - - +
358H ALA* 2.8 36.7 + - - +
389H GLU* 3.5 23.0 - - - +
395H SER* 3.8 6.9 + - - +
399H ARG* 3.1 41.6 + - - -
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Residues in contact with ALA 355 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280H LEU* 6.3 0.2 - - + -
283H ALA* 5.2 1.3 - - + -
320H ALA* 4.1 26.9 - - + +
321H LEU* 5.0 1.3 - - + -
324H ALA* 4.6 1.8 - - + -
351H ALA 3.1 18.7 + - - +
352H ALA* 3.6 7.6 - - - +
354H GLU* 1.3 75.9 - - - +
356H ALA* 1.3 59.9 + - - +
358H ALA* 4.4 5.4 - - - +
359H ILE* 2.8 53.3 + - + +
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Residues in contact with ALA 356 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279H ALA* 3.6 27.8 - - + +
282H ILE* 4.5 2.4 - - + +
283H ALA* 3.9 17.7 - - + +
352H ALA 2.8 20.3 + - - +
353H SER 3.3 5.8 + - - +
355H ALA* 1.3 71.8 - - - +
357H THR* 1.3 52.4 + - - +
359H ILE* 4.1 0.7 - - - +
360H SER* 2.8 39.5 + - - -
385H ALA* 3.6 18.5 - - + +
388H THR* 4.3 3.1 - - - +
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Residues in contact with THR 357 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361G HIS* 3.9 13.9 - - + +
382G TYR* 4.0 15.0 + - - +
353H SER 3.2 7.9 + - - -
354H GLU* 3.8 4.0 - - - +
356H ALA* 1.3 76.2 - - - +
358H ALA* 1.3 66.2 + - - +
360H SER* 3.2 6.6 + - - -
361H HIS* 3.1 24.7 + - + +
382H TYR* 4.3 4.3 + - + -
385H ALA* 3.6 20.8 + - - +
386H ARG* 4.0 3.6 - - - -
389H GLU* 2.8 32.1 + - - +
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Residues in contact with ALA 358 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317H MET* 5.7 0.2 - - - -
320H ALA* 6.0 2.9 - - + -
354H GLU 2.8 22.2 + - - +
355H ALA* 3.9 5.8 - - - +
357H THR* 1.3 74.3 - - - +
359H ILE* 1.3 65.1 + - + +
361H HIS* 3.5 5.6 + - - +
362H GLN* 3.1 29.1 + - + +
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Residues in contact with ILE 359 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283H ALA* 3.6 40.2 - - + +
286H ALA* 4.0 3.1 - - + -
287H LEU* 3.9 12.3 - - + +
317H MET* 3.5 61.8 - - + +
320H ALA* 4.1 5.4 - - + -
321H LEU* 3.9 20.0 - - + +
355H ALA* 2.8 32.7 + - + +
356H ALA 4.2 1.6 - - - +
358H ALA* 1.3 70.3 - - + +
360H SER* 1.3 54.7 + - - +
362H GLN 3.3 0.9 + - - -
363H ALA* 2.7 33.6 + - - +
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Residues in contact with SER 360 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282H ILE* 5.3 1.1 - - - -
286H ALA* 4.1 12.3 - - - -
356H ALA 2.8 23.8 + - - -
357H THR* 3.2 9.4 + - - -
359H ILE* 1.3 74.0 - - - +
361H HIS* 1.3 67.5 + - - +
363H ALA* 3.2 4.1 + - - +
364H ILE* 3.1 26.3 + - - +
378H ALA 4.7 1.9 - - - +
381H HIS* 3.8 14.1 - - - -
382H TYR* 3.4 39.8 - - - -
385H ALA* 3.7 2.5 - - - +
----------------------------------------------------------
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Residues in contact with HIS 361 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357G THR* 3.9 8.7 - - + +
386G ARG* 2.9 57.2 + - - +
389G GLU* 2.7 38.0 + - - -
357H THR* 3.1 19.5 + - + +
358H ALA* 3.6 7.0 - - - +
360H SER* 1.3 79.5 + - - +
362H GLN* 1.3 84.3 + - - +
364H ILE* 3.3 1.4 + - - +
365H GLN* 3.1 8.4 + - - -
382H TYR* 3.4 30.2 - + + -
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Residues in contact with GLN 362 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313H LYS* 2.7 44.7 + - + +
317H MET* 3.9 24.5 - - + -
358H ALA* 3.1 16.8 + - + +
359H ILE 3.3 3.3 + - - +
361H HIS* 1.3 108.9 + - - +
363H ALA* 1.3 60.8 + - - +
365H GLN* 3.5 9.0 - - - +
366H ILE* 2.9 36.1 + - + +
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Residues in contact with ALA 363 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286H ALA* 3.5 31.0 - - + +
289H CYS* 5.4 2.5 - - + -
290H ALA* 4.1 15.9 - - + +
317H MET* 4.1 1.3 - - + +
359H ILE 2.7 20.8 + - - +
360H SER* 3.2 8.9 + - - +
362H GLN* 1.3 70.3 - - - +
364H ILE* 1.3 65.0 + - - +
366H ILE* 3.4 1.4 + - - +
367H LEU* 3.1 29.5 + - - +
378H ALA* 4.5 12.8 - - + -
381H HIS* 6.4 0.2 - - + -
----------------------------------------------------------
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Residues in contact with ILE 364 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231G LEU* 4.5 4.0 - - + -
386G ARG* 3.7 29.4 - - + +
390G ILE* 3.9 14.3 - - + +
360H SER 3.1 10.2 + - - +
361H HIS 3.5 7.4 - - - +
363H ALA* 1.3 75.4 - - - +
365H GLN* 1.3 63.9 + - - +
367H LEU* 3.2 3.1 + - - +
368H GLY* 3.0 21.5 + - - +
371H GLY* 3.6 35.4 - - - +
372H TYR* 4.3 1.6 - - - +
378H ALA* 3.9 14.1 - - + +
379H GLU* 4.1 7.0 - - - -
382H TYR* 3.7 41.3 - - + -
----------------------------------------------------------
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Residues in contact with GLN 365 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386G ARG* 2.8 40.9 + - - +
389G GLU* 3.1 26.8 + - - +
390G ILE* 3.9 7.8 - - - +
394G THR* 4.1 6.3 - - - +
395G SER* 3.9 10.6 + - - +
396G GLU* 2.8 40.3 + - - +
501G FAD 2.7 21.9 + - - +
313H LYS* 4.4 6.7 - - - +
361H HIS* 3.1 12.6 + - - +
362H GLN* 3.2 20.4 + - - +
364H ILE* 1.3 77.6 - - - +
366H ILE* 1.3 58.3 + - - +
368H GLY* 3.1 12.3 + - - -
----------------------------------------------------------
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Residues in contact with ILE 366 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501G FAD 3.1 30.5 - - - +
290H ALA* 3.8 31.2 - - + +
293H TYR* 4.0 1.5 - - + -
294H ALA* 3.9 17.9 - - + +
304H LEU* 3.5 11.3 - - + +
310H ILE* 4.0 12.1 - - + -
313H LYS* 3.9 33.7 - - + -
314H LEU* 3.8 28.5 - - + -
317H MET* 4.0 8.7 - - - -
362H GLN 2.9 19.5 + - - +
363H ALA 3.9 3.8 - - - +
365H GLN* 1.3 74.8 - - - +
367H LEU* 1.3 60.6 + - + +
----------------------------------------------------------
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Residues in contact with LEU 367 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501G FAD 4.5 5.1 + - - +
289H CYS* 4.0 8.7 - - - +
290H ALA* 4.1 16.4 - - - -
293H TYR* 3.6 49.7 + - + -
363H ALA 3.1 18.2 + - - +
366H ILE* 1.3 76.5 - - + +
368H GLY* 1.3 62.9 + - - +
369H GLY 3.6 0.3 + - - -
370H MET* 3.4 17.2 + - + +
371H GLY* 3.4 17.9 - - - +
376H MET* 3.6 34.3 - - + -
378H ALA* 3.7 28.5 - - + -
----------------------------------------------------------
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Residues in contact with GLY 368 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390G ILE* 4.0 21.7 - - - +
394G THR* 5.3 1.1 - - - -
501G FAD 3.8 21.3 - - - -
364H ILE 3.0 12.3 + - - +
365H GLN 3.1 12.8 + - - -
366H ILE 3.2 0.8 + - - -
367H LEU* 1.3 75.3 - - - +
369H GLY* 1.3 61.4 + - - +
371H GLY* 2.9 17.0 + - - -
372H TYR 3.8 1.9 + - - -
----------------------------------------------------------
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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