Contacts of the helix formed by residues 341 - 368 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266G GLN 5.2 0.4 - - - -
269G ASP* 3.7 30.1 - - + -
270G MET* 3.9 11.7 - - + -
273G ILE* 3.6 30.3 - - + -
331G ALA* 3.9 6.1 - - - +
334G LEU* 3.8 20.0 - - + -
335G LYS* 3.6 36.3 - - + -
339G LYS 3.4 13.5 - - - -
340G PRO* 1.3 74.4 - - + +
342G ILE* 1.3 63.1 + - + +
344G GLU* 3.3 14.4 - - + -
345G ALA* 2.8 30.3 + - + +
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Residues in contact with ILE 342 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269G ASP* 3.5 35.1 - - - +
272G ARG* 5.2 1.8 + - - +
340G PRO* 3.9 5.4 - - + +
341G PHE* 1.3 79.2 - - + +
343G LYS* 1.3 63.9 + - - +
344G GLU* 3.7 0.6 + - - -
345G ALA* 3.9 1.8 - - - +
346G ALA* 3.0 24.6 + - - +
401G VAL* 3.6 15.9 - - + -
405G HIS* 3.4 38.8 - - + +
502G COS 3.4 36.1 - - + +
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Residues in contact with LYS 343 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322E GLU* 2.7 40.8 + - - +
330G ARG* 4.8 1.2 - - - +
342G ILE* 1.3 81.5 - - - +
344G GLU* 1.3 76.7 + - - +
346G ALA* 3.4 6.9 + - - +
347G MET* 2.9 56.5 + - + +
401G VAL* 4.9 2.0 - - - -
402G ILE* 4.0 14.3 - - + +
405G HIS* 3.8 34.4 + - + -
406G LEU* 4.7 13.4 - - + +
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Residues in contact with GLU 344 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327G LEU* 4.2 2.8 - - - +
330G ARG* 3.6 39.8 + - - +
331G ALA* 3.7 13.2 - - + +
334G LEU* 3.4 34.8 - - + +
340G PRO 4.0 5.3 - - - +
341G PHE* 3.3 19.8 - - - +
342G ILE 3.2 0.7 + - - -
343G LYS* 1.3 94.8 + - - +
345G ALA* 1.3 60.3 + - - +
347G MET* 3.6 2.0 + - - +
348G ALA* 3.1 27.5 + - - +
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Residues in contact with ALA 345 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269G ASP* 3.3 31.0 - - - +
272G ARG* 4.1 10.8 - - + +
273G ILE* 4.1 8.7 - - + -
331G ALA* 3.8 8.9 - - - +
341G PHE* 2.8 31.3 + - + +
342G ILE 3.9 3.1 - - - +
344G GLU* 1.3 71.0 - - - +
346G ALA* 1.3 59.1 + - - +
348G ALA* 3.3 3.2 + - - +
349G LYS* 3.0 30.8 + - - +
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Residues in contact with ALA 346 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G ARG* 4.8 4.8 - - - +
342G ILE 3.0 18.1 + - - +
343G LYS 3.4 4.9 - - - +
345G ALA* 1.3 77.1 - - - +
347G MET* 1.3 56.6 + - - +
349G LYS* 3.5 1.0 + - - +
350G LEU* 2.9 32.2 + - - +
398G GLN* 3.3 29.0 - - - +
401G VAL* 4.0 16.4 - - + -
402G ILE* 3.8 18.4 - - + -
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Residues in contact with MET 347 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318E ALA* 3.8 4.3 - - + -
319E LEU* 3.8 44.0 - - + +
322E GLU* 3.4 45.3 - - - +
327G LEU* 4.3 6.1 - - + -
330G ARG* 3.4 15.3 - - - +
343G LYS* 2.9 32.4 + - + +
344G GLU* 3.8 6.5 - - - +
346G ALA* 1.3 74.5 - - - +
348G ALA* 1.3 56.8 + - - +
350G LEU* 3.7 1.9 - - - +
351G ALA* 2.8 32.7 + - - +
402G ILE* 3.8 35.0 - - + -
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Residues in contact with ALA 348 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G ARG 5.5 0.2 - - - +
273G ILE* 5.8 1.1 - - - -
276G ALA* 4.0 10.1 - - + -
324G ALA 4.9 0.7 - - - +
327G LEU* 3.7 13.4 - - - +
328G THR* 3.5 39.2 + - + +
331G ALA* 4.6 2.2 - - + -
344G GLU 3.1 18.7 + - - +
345G ALA* 3.3 7.4 + - - +
347G MET* 1.3 74.8 - - - +
349G LYS* 1.3 56.5 + - - +
351G ALA* 3.4 0.7 + - - +
352G ALA* 2.8 34.7 + - - +
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Residues in contact with LYS 349 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G ARG* 3.8 33.4 - - + +
275G ILE* 3.8 19.5 - - + -
276G ALA* 4.0 9.7 - - - +
345G ALA 3.0 16.5 + - - +
346G ALA 3.9 3.4 - - - +
348G ALA* 1.3 74.8 - - - +
350G LEU* 1.3 59.7 + - - +
352G ALA* 4.0 0.2 - - - +
353G SER* 2.9 37.5 + - - +
388G THR 2.8 27.8 + - - +
389G GLU* 3.9 9.9 + - - +
391G TYR 2.9 21.3 + - - -
392G GLU* 4.2 3.6 - - - -
393G GLY 2.6 26.4 + - - -
394G THR 4.5 1.6 - - - -
395G SER* 4.6 0.8 - - - +
398G GLN* 3.7 15.9 - - + +
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Residues in contact with LEU 350 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315E ALA* 6.1 0.9 - - + +
316E ASP* 4.8 1.3 - - - +
319E LEU* 3.7 23.6 - - + -
346G ALA 2.9 17.8 + - - +
347G MET 3.7 3.4 - - - +
349G LYS* 1.3 77.4 - - - +
351G ALA* 1.3 62.2 + - - +
353G SER* 3.1 16.7 + - - -
354G GLU* 3.1 25.0 + - - +
395G SER* 3.6 40.4 - - - +
398G GLN* 4.0 8.7 - - + -
399G ARG* 3.7 39.9 - - + +
402G ILE* 3.8 15.5 - - + -
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Residues in contact with ALA 351 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319E LEU* 4.4 11.2 - - + +
324G ALA* 4.0 12.7 - - + +
327G LEU* 3.4 26.0 - - + -
347G MET 2.8 21.2 + - - +
348G ALA 3.9 2.5 - - - +
350G LEU* 1.3 73.1 - - - +
352G ALA* 1.3 58.1 + - - +
354G GLU* 3.9 4.2 - - - +
355G ALA* 3.0 29.6 + - - +
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Residues in contact with ALA 352 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276G ALA* 3.6 31.4 - - + +
279G ALA* 3.5 9.6 - - + +
280G LEU* 4.1 7.9 - - + -
283G ALA* 5.3 0.3 - - - +
324G ALA* 3.7 17.9 - - + +
328G THR* 4.7 1.1 - - - +
348G ALA 2.8 23.1 + - - +
349G LYS 4.0 0.2 - - - +
351G ALA* 1.3 72.6 - - - +
353G SER* 1.3 59.9 + - - +
355G ALA* 3.2 3.5 + - - +
356G ALA* 2.8 31.9 + - - +
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Residues in contact with SER 353 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275G ILE* 5.8 0.4 - - - -
279G ALA* 3.7 3.7 - - - +
349G LYS* 2.9 25.8 + - - +
350G LEU* 3.1 9.7 + - - +
352G ALA* 1.3 78.3 - - - +
354G GLU* 1.3 64.7 + - - +
356G ALA* 3.4 2.9 + - - +
357G THR* 3.3 16.1 + - - -
388G THR* 3.2 49.7 + - - -
389G GLU* 3.8 18.4 - - - +
395G SER* 4.3 5.5 + - - -
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Residues in contact with GLU 354 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319E LEU* 5.7 1.7 - - - +
350G LEU* 3.1 24.2 + - - +
351G ALA* 4.1 3.8 - - - +
353G SER* 1.3 85.4 + - - +
355G ALA* 1.3 55.7 + - - +
357G THR* 3.4 2.4 + - - +
358G ALA* 3.0 30.4 + - - +
389G GLU* 3.5 23.0 - - - +
395G SER* 4.0 8.9 + - - +
399G ARG* 3.3 38.9 + - - -
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Residues in contact with ALA 355 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280G LEU* 6.1 0.4 - - + -
283G ALA* 5.1 2.0 - - + -
320G ALA* 3.9 31.6 - - + +
321G LEU* 4.8 2.0 - - + -
324G ALA* 4.5 2.2 - - + -
351G ALA 3.0 18.2 + - - +
352G ALA* 3.5 7.9 - - - +
354G GLU* 1.3 74.5 - - - +
356G ALA* 1.3 55.4 - - - +
358G ALA* 3.7 3.5 - - - +
359G ILE* 2.7 56.7 + - + +
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Residues in contact with ALA 356 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279G ALA* 3.6 28.7 - - + +
282G ILE* 4.6 1.5 - - + +
283G ALA* 3.8 17.8 - - + +
352G ALA 2.8 20.1 + - - +
353G SER 3.4 6.0 + - - +
355G ALA* 1.3 71.6 - - - +
357G THR* 1.3 57.4 + - - +
359G ILE* 4.2 0.3 - - - +
360G SER* 2.8 31.7 + - - -
385G ALA* 3.4 18.6 - - + +
388G THR* 4.2 2.5 - - - +
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Residues in contact with THR 357 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353G SER 3.3 4.2 + - - -
354G GLU 4.0 4.0 - - - +
355G ALA 3.3 0.4 - - - -
356G ALA* 1.3 76.1 - - - +
358G ALA* 1.3 60.1 + - - +
360G SER* 3.2 7.2 + - - -
361G HIS* 3.0 29.4 + - + +
382G TYR* 4.2 3.3 + - + -
385G ALA* 3.6 21.2 + - - +
386G ARG* 3.9 4.7 - - - +
389G GLU* 2.8 34.8 + - - +
361H HIS* 3.9 9.4 - - + +
382H TYR* 3.8 20.3 + - - +
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Residues in contact with ALA 358 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317G MET* 5.7 0.2 - - - -
320G ALA* 6.1 1.8 - - + -
354G GLU 3.0 18.0 + - - +
355G ALA* 3.9 4.9 - - - +
357G THR* 1.3 78.4 - - - +
359G ILE* 1.3 65.5 + - + +
361G HIS* 3.5 5.4 + - - +
362G GLN* 3.1 30.4 + - + +
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Residues in contact with ILE 359 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283G ALA* 3.6 41.1 - - + +
286G ALA* 4.1 2.9 - - + -
287G LEU* 4.0 13.0 - - + +
317G MET* 3.5 60.6 - - + +
320G ALA* 4.3 4.0 - - + -
321G LEU* 3.9 12.6 - - + +
355G ALA* 2.7 40.0 + - + +
356G ALA 4.2 1.8 - - - +
358G ALA* 1.3 73.6 - - + +
360G SER* 1.3 58.3 + - - +
362G GLN 3.3 1.2 + - - -
363G ALA* 2.8 27.2 + - - +
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Residues in contact with SER 360 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282G ILE* 5.3 0.9 - - - -
286G ALA* 4.2 13.0 - - - +
356G ALA 2.8 22.1 + - - -
357G THR* 3.2 6.2 + - - -
359G ILE* 1.3 72.7 - - - +
361G HIS* 1.3 67.5 + - - +
363G ALA* 3.3 3.8 + - - +
364G ILE* 3.1 26.3 + - - +
378G ALA 4.8 1.3 - - - +
381G HIS* 3.9 13.5 - - - -
382G TYR* 3.4 41.2 - - - +
385G ALA* 3.5 6.2 - - - +
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Residues in contact with HIS 361 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357G THR* 3.0 20.0 + - + +
358G ALA* 3.5 7.4 - - - +
360G SER* 1.3 78.6 + - - +
362G GLN* 1.3 83.5 + - - +
364G ILE* 3.3 3.2 + - - +
365G GLN* 3.1 12.1 + - - -
382G TYR* 3.5 28.9 - - + -
357H THR* 3.9 9.5 - - + +
386H ARG* 2.9 56.0 + - - +
389H GLU* 2.7 39.3 + - - -
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Residues in contact with GLN 362 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313G LYS* 3.0 42.5 + - + +
317G MET* 3.8 26.0 - - + -
358G ALA* 3.1 18.1 + - + +
359G ILE 3.8 3.8 - - - +
361G HIS* 1.3 111.3 + - - +
363G ALA* 1.3 65.7 + - - +
365G GLN* 3.3 9.6 + - - +
366G ILE* 3.0 29.4 + - + +
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Residues in contact with ALA 363 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286G ALA* 3.5 31.0 - - + +
289G CYS* 5.3 2.2 - - - -
290G ALA* 4.1 15.7 - - + +
317G MET* 4.0 1.1 - - + +
359G ILE 2.8 16.8 + - - +
360G SER* 3.3 9.4 + - - +
362G GLN* 1.3 74.4 - - - +
364G ILE* 1.3 64.3 + - - +
366G ILE* 3.4 1.0 + - - +
367G LEU* 3.2 28.8 + - - +
378G ALA* 4.4 13.5 - - + -
381G HIS* 6.3 0.2 - - + -
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Residues in contact with ILE 364 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360G SER 3.1 14.2 + - - +
361G HIS 3.4 7.9 - - - +
363G ALA* 1.3 75.3 - - - +
365G GLN* 1.3 61.8 + - - +
367G LEU* 3.3 4.7 + - - +
368G GLY* 3.1 22.3 + - - +
371G GLY* 3.7 35.7 - - - +
372G TYR* 5.1 0.7 - - - -
378G ALA* 4.0 15.3 - - - +
379G GLU* 4.1 6.3 - - - -
382G TYR* 3.7 38.1 - - + -
231H LEU* 4.2 4.5 - - + -
386H ARG* 3.5 32.1 - - + +
390H ILE* 4.0 12.5 - - + +
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Residues in contact with GLN 365 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313G LYS* 4.4 6.7 - - - +
361G HIS* 3.1 8.7 + - - +
362G GLN* 3.6 21.5 - - - +
363G ALA 3.3 0.4 - - - -
364G ILE* 1.3 80.0 - - - +
366G ILE* 1.3 60.9 + - - +
368G GLY* 3.1 10.8 + - - -
386H ARG* 2.7 40.7 + - - +
389H GLU* 3.1 28.3 + - - +
390H ILE* 4.0 6.6 - - - +
394H THR* 3.9 7.2 - - - +
395H SER* 3.8 8.8 - - - +
396H GLU* 2.9 40.3 + - - +
501H FAD 2.8 20.2 + - - +
----------------------------------------------------------
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Residues in contact with ILE 366 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290G ALA* 3.8 28.9 - - + +
293G TYR* 4.0 1.1 - - + -
294G ALA* 3.9 18.2 - - + +
304G LEU* 3.7 12.6 - - + +
310G ILE* 4.3 11.2 - - + -
313G LYS* 3.9 27.6 - - + -
314G LEU* 3.6 31.0 - - + -
317G MET* 3.9 14.4 - - - -
362G GLN 3.0 21.0 + - - +
363G ALA 3.9 4.0 - - - +
365G GLN* 1.3 73.8 - - - +
367G LEU* 1.3 58.9 + - + +
501H FAD 3.0 30.7 - - - +
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Residues in contact with LEU 367 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289G CYS* 4.0 10.3 - - - +
290G ALA* 4.3 14.1 - - - -
293G TYR* 3.6 52.8 + - + -
363G ALA 3.2 13.2 + - - +
364G ILE 3.3 2.2 + - - +
366G ILE* 1.3 76.0 - - + +
368G GLY* 1.3 63.0 + - - +
369G GLY 3.4 0.9 + - - -
370G MET* 3.4 18.7 + - + +
371G GLY* 3.3 17.0 - - - +
376G MET* 3.7 40.2 - - + -
378G ALA* 3.8 20.0 - - + -
501H FAD 4.3 5.5 + - - +
----------------------------------------------------------
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Residues in contact with GLY 368 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364G ILE 3.1 10.1 + - - +
365G GLN* 3.1 12.7 + - - -
366G ILE 3.2 1.0 + - - -
367G LEU* 1.3 73.4 - - - +
369G GLY* 1.3 66.4 + - - +
371G GLY* 2.9 14.7 + - - -
390H ILE* 3.8 23.8 - - - +
394H THR* 5.2 0.9 - - - -
501H FAD 3.8 21.1 - - - -
----------------------------------------------------------
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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