Contacts of the helix formed by residues 341 - 368 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B LYS* 5.9 5.6 - - - -
266B GLN 5.1 1.1 - - - -
269B ASP* 3.5 40.6 - - + -
270B MET* 3.9 9.6 - - + -
273B ILE* 3.9 23.8 - - + -
331B ALA* 3.8 10.5 - - - +
334B LEU* 3.8 19.1 - - + -
335B LYS* 3.8 31.6 - - + -
339B LYS 3.5 13.9 - - - -
340B PRO* 1.3 75.0 - - + +
342B ILE* 1.3 62.8 + - + +
343B LYS 3.4 2.5 - - - -
344B GLU* 3.4 11.2 - - + -
345B ALA* 2.8 30.6 + - + +
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Residues in contact with ILE 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ASP* 3.4 37.4 - - - +
272B ARG* 5.4 1.4 + - - +
340B PRO* 5.1 5.7 - - + +
341B PHE* 1.3 80.6 - - + +
343B LYS* 1.3 62.0 + - - +
344B GLU* 3.8 1.0 + - - -
345B ALA* 3.7 2.1 - - - +
346B ALA* 3.1 22.9 + - - +
401B VAL* 3.8 15.0 - - + -
405B HIS* 3.2 40.2 - - + +
502B COS 3.7 29.6 - - + +
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Residues in contact with LYS 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ARG* 4.6 0.8 - - - +
342B ILE* 1.3 82.2 - - - +
344B GLU* 1.3 82.6 + - - +
346B ALA* 3.4 6.9 + - - +
347B MET* 2.9 51.8 + - + +
401B VAL* 4.9 1.8 - - - -
402B ILE* 4.2 20.0 - - + +
405B HIS* 3.7 34.9 - - + -
406B LEU* 4.6 12.1 - - + +
322D GLU* 3.0 38.4 + - - +
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Residues in contact with GLU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU* 4.2 3.1 - - - +
330B ARG* 3.5 39.6 + - - +
331B ALA* 3.8 13.1 - - + +
334B LEU* 3.4 34.7 - - + +
340B PRO 4.0 3.4 - - - +
341B PHE* 3.4 14.4 + - - +
342B ILE 3.8 0.3 + - - -
343B LYS* 1.3 101.1 + - - +
345B ALA* 1.3 59.3 + - - +
347B MET* 3.5 2.5 + - - +
348B ALA* 3.0 28.6 + - - +
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Residues in contact with ALA 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ASP* 3.5 29.6 - - - +
272B ARG* 4.0 12.6 - - + +
273B ILE* 4.2 7.4 - - + -
331B ALA* 3.8 9.8 - - - +
341B PHE* 2.8 30.4 + - + +
342B ILE 3.7 4.3 - - - +
344B GLU* 1.3 69.6 - - - +
346B ALA* 1.3 60.8 + - - +
348B ALA* 3.4 3.5 + - - +
349B LYS* 3.0 30.7 + - - +
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Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ARG* 4.8 4.4 - - - +
342B ILE 3.1 11.9 + - - +
343B LYS 3.5 9.0 - - - +
345B ALA* 1.3 78.9 - - - +
347B MET* 1.3 57.3 + - - +
349B LYS* 3.6 0.4 + - - -
350B LEU* 3.0 31.5 + - - +
398B GLN* 3.3 29.9 - - - +
401B VAL* 4.0 17.3 - - + -
402B ILE* 3.8 17.9 - - + -
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Residues in contact with MET 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B LEU* 4.3 6.3 - - + -
330B ARG* 3.5 25.6 - - - +
343B LYS* 2.9 32.2 + - + +
344B GLU* 3.7 5.8 - - - +
345B ALA 3.4 0.2 - - - -
346B ALA* 1.3 73.5 - - - +
348B ALA* 1.3 59.1 + - - +
350B LEU* 3.8 1.4 - - - +
351B ALA* 2.8 34.1 + - - +
402B ILE* 3.8 37.9 - - + -
318D ALA* 3.8 20.0 - - + +
319D LEU* 3.7 26.6 - - + +
322D GLU* 3.4 31.6 - - - +
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Residues in contact with ALA 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ILE* 5.7 1.6 - - - -
276B ALA* 3.8 9.0 - - + -
324B ALA 4.9 0.2 - - - +
327B LEU* 3.6 16.2 - - - +
328B THR* 3.5 36.1 + - - +
331B ALA* 4.5 2.9 - - + -
344B GLU 3.0 17.3 + - - +
345B ALA* 3.6 7.6 - - - +
346B ALA 3.4 0.2 - - - -
347B MET* 1.3 75.6 - - - +
349B LYS* 1.3 55.9 + - - +
351B ALA* 3.9 0.5 - - - +
352B ALA* 2.8 34.8 + - - +
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Residues in contact with LYS 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ARG* 3.7 31.4 - - + +
275B ILE* 4.1 17.7 - - + -
276B ALA* 3.9 10.1 - - - +
345B ALA 3.0 18.1 + - - +
346B ALA 4.0 2.9 - - - +
348B ALA* 1.3 76.0 - - - +
350B LEU* 1.3 59.8 + - - +
352B ALA* 4.1 0.2 - - - +
353B SER* 3.0 35.8 + - - +
388B THR 2.6 27.3 + - - +
389B GLU* 3.7 12.7 + - - +
391B TYR 3.0 22.7 + - - -
392B GLU* 4.3 3.6 - - - -
393B GLY 2.8 25.4 + - - -
394B THR 4.5 1.6 - - - -
395B SER* 4.6 1.0 + - - +
398B GLN* 3.8 16.5 - - + +
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Residues in contact with LEU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ALA 3.0 19.6 + - - +
347B MET 3.8 2.9 - - - +
349B LYS* 1.3 76.8 - - - +
351B ALA* 1.3 66.0 + - - +
353B SER* 3.1 5.1 + - - -
354B GLU* 3.1 57.9 + - - +
395B SER* 3.7 26.7 - - - +
398B GLN* 4.0 8.1 - - + -
399B ARG* 3.7 30.5 - - + +
402B ILE* 3.7 24.7 - - + -
315D ALA* 6.1 0.7 - - + +
316D ASP* 5.0 1.8 - - - +
319D LEU* 3.8 19.1 - - + -
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Residues in contact with ALA 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B ALA* 4.0 13.1 - - + +
327B LEU* 3.5 24.7 - - + -
347B MET 2.8 21.1 + - - +
348B ALA 4.0 1.8 - - - +
350B LEU* 1.3 73.9 - - - +
352B ALA* 1.3 61.6 + - - +
354B GLU* 4.0 3.9 - - - +
355B ALA* 3.1 25.6 + - - +
319D LEU* 4.4 11.8 - - + +
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Residues in contact with ALA 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ALA* 3.3 35.0 - - + +
279B ALA* 3.6 7.1 - - + +
280B LEU* 3.9 15.6 - - + +
283B ALA* 5.2 0.5 - - - +
324B ALA* 3.7 11.2 - - + -
328B THR* 4.4 0.9 - - - +
348B ALA 2.8 22.1 + - - +
351B ALA* 1.3 74.1 - - - +
353B SER* 1.3 58.7 + - - +
355B ALA* 3.4 3.7 + - - +
356B ALA* 2.9 28.9 + - - +
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Residues in contact with SER 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B ILE* 5.9 0.2 - - - -
279B ALA* 3.9 4.0 - - - +
349B LYS* 3.0 23.3 + - - +
350B LEU* 3.1 9.5 + - - -
352B ALA* 1.3 75.9 - - - +
354B GLU* 1.3 68.9 + - - +
356B ALA* 3.5 3.2 + - - +
357B THR* 3.2 17.3 + - - -
388B THR* 3.3 46.0 + - - -
389B GLU* 3.7 22.8 - - - +
395B SER* 4.1 2.9 + - - -
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Residues in contact with GLU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LEU* 3.1 31.5 + - + +
351B ALA* 4.2 3.3 - - - +
353B SER* 1.3 85.4 + - - +
355B ALA* 1.3 57.2 + - - +
357B THR* 3.5 2.5 + - - +
358B ALA* 3.0 29.5 + - - +
389B GLU* 3.7 19.3 - - - +
395B SER* 3.7 7.9 + - - +
399B ARG* 3.1 38.9 + - - -
319D LEU* 5.8 1.6 - - - +
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Residues in contact with ALA 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B LEU* 6.3 0.2 - - + -
283B ALA* 5.3 1.6 - - + -
320B ALA* 4.0 37.0 - - + +
321B LEU* 4.6 1.6 - - + +
324B ALA* 4.6 2.5 - - + -
351B ALA 3.1 19.2 + - - +
352B ALA* 3.5 7.0 - - - +
354B GLU* 1.3 75.6 - - - +
356B ALA* 1.3 57.4 + - - +
358B ALA* 4.0 3.1 - - - +
359B ILE* 2.8 49.2 + - + +
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Residues in contact with ALA 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B ALA* 3.5 31.6 - - + +
282B ILE* 4.5 1.9 - - + +
283B ALA* 3.9 18.0 - - + +
352B ALA 2.9 13.7 + - - +
353B SER 3.8 6.5 - - - +
354B GLU 3.4 0.4 - - - -
355B ALA* 1.3 75.3 - - - +
357B THR* 1.3 57.1 + - - +
359B ILE* 4.3 0.3 - - - +
360B SER* 3.0 32.6 + - - -
385B ALA* 3.5 18.0 - - + +
388B THR* 4.3 3.4 - - - +
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Residues in contact with THR 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361A HIS* 3.8 11.9 - - + +
382A TYR* 3.8 19.9 + - - +
353B SER 3.2 11.6 + - - -
354B GLU 4.0 2.9 - - - -
355B ALA 3.2 0.2 - - - -
356B ALA* 1.3 74.2 - - - +
358B ALA* 1.3 61.3 + - - +
360B SER* 3.1 6.9 + - - -
361B HIS* 3.0 29.9 + - + +
382B TYR* 4.2 3.5 + - + -
385B ALA* 3.9 19.6 + - - +
386B ARG* 3.9 4.3 - - - -
389B GLU* 2.8 32.9 + - - +
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Residues in contact with ALA 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B MET* 5.6 0.4 - - - -
320B ALA* 6.1 2.9 - - + -
354B GLU 3.0 17.9 + - - +
355B ALA* 4.0 4.7 - - - +
357B THR* 1.3 79.3 - - - +
359B ILE* 1.3 59.0 + - + +
361B HIS* 3.5 7.3 + - - +
362B GLN* 3.0 32.7 + - + +
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Residues in contact with ILE 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B ALA* 3.6 40.2 - - + +
286B ALA* 4.1 2.7 - - + -
287B LEU* 4.0 12.8 - - + +
317B MET* 3.4 61.7 - - + +
320B ALA* 4.4 4.5 - - + -
321B LEU* 3.9 14.6 - - + +
355B ALA* 2.8 41.3 + - + +
356B ALA 4.3 1.6 - - - +
358B ALA* 1.3 71.3 - - + +
360B SER* 1.3 55.4 + - - +
362B GLN 3.1 1.2 + - - -
363B ALA* 2.8 31.7 + - - +
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Residues in contact with SER 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ILE* 5.2 0.9 - - - -
286B ALA* 4.1 13.0 - - - +
356B ALA 3.0 22.3 + - - -
357B THR* 3.1 6.8 + - - -
359B ILE* 1.3 73.0 - - - +
361B HIS* 1.3 68.1 + - - +
363B ALA* 3.2 4.0 + - - +
364B ILE* 3.1 27.0 + - - +
378B ALA 4.7 0.9 - - - +
381B HIS* 3.8 14.1 - - - -
382B TYR* 3.3 40.2 - - - +
385B ALA* 3.7 5.6 - - - +
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Residues in contact with HIS 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A THR* 3.8 9.8 - - + +
386A ARG* 2.9 54.8 + - - +
389A GLU* 2.7 38.2 + - - -
357B THR* 3.0 20.8 + - + +
358B ALA* 3.5 8.1 - - - +
360B SER* 1.3 79.6 + - - +
362B GLN* 1.3 84.3 + - - +
364B ILE* 3.4 0.9 + - - +
365B GLN* 3.1 11.6 + - - -
382B TYR* 3.4 30.0 - + + -
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Residues in contact with GLN 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LYS* 2.8 48.2 + - + +
317B MET* 3.8 26.9 - - + -
358B ALA 3.0 19.6 + - - +
359B ILE 3.1 4.0 + - - +
361B HIS* 1.3 106.0 + - - +
363B ALA* 1.3 60.9 + - - +
365B GLN* 3.6 10.1 - - - +
366B ILE* 2.9 34.6 + - + +
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Residues in contact with ALA 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ALA* 3.5 29.2 - - + +
289B CYS* 5.5 1.1 - - - -
290B ALA* 4.1 15.3 - - + +
317B MET* 3.9 1.0 - - + +
359B ILE 2.8 14.1 + - - +
360B SER* 3.2 14.6 + - - +
362B GLN* 1.3 73.4 - - - +
364B ILE* 1.3 65.0 + - - +
366B ILE* 3.4 1.2 + - - +
367B LEU* 3.1 31.5 + - + +
378B ALA* 4.4 12.6 - - + -
381B HIS* 6.2 0.2 - - + -
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Residues in contact with ILE 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A LEU* 4.3 8.3 - - + -
386A ARG* 3.6 31.0 - - + +
390A ILE* 4.0 13.6 - - + +
360B SER 3.1 14.3 + - - +
361B HIS 3.6 1.6 - - - +
363B ALA* 1.3 73.5 - - - +
365B GLN* 1.3 62.1 + - - +
367B LEU* 3.3 2.8 + - - +
368B GLY* 3.2 21.7 + - - +
371B GLY* 3.7 33.2 - - - +
372B TYR* 4.9 1.8 - - - -
378B ALA* 3.9 13.9 - - + +
379B GLU* 4.0 10.3 - - - -
382B TYR* 3.5 43.7 - - + -
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Residues in contact with GLN 365 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386A ARG* 2.7 42.9 + - - +
389A GLU* 3.0 28.6 + - - +
390A ILE* 4.0 5.7 - - - +
394A THR* 3.9 6.7 - - - +
395A SER* 3.7 9.0 + - - +
396A GLU* 2.9 40.4 + - - +
501A FAD 2.6 27.3 + - - +
313B LYS* 4.3 7.0 - - - +
361B HIS* 3.1 13.0 + - - +
362B GLN* 3.6 21.8 - - - +
363B ALA 3.2 0.4 - - - -
364B ILE* 1.3 77.9 - - - +
366B ILE* 1.3 57.8 + - - +
368B GLY* 3.1 8.3 + - - +
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Residues in contact with ILE 366 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A FAD 3.0 29.9 - - - +
290B ALA* 4.0 18.4 - - + +
293B TYR* 4.8 0.4 - - + -
294B ALA* 3.8 29.6 - - + +
304B LEU* 3.6 12.6 - - + +
310B ILE* 4.0 12.8 - - + -
313B LYS* 4.0 27.4 - - + -
314B LEU* 3.9 29.2 - - + -
317B MET* 4.0 12.3 - - - -
362B GLN 2.9 21.6 + - - +
363B ALA 3.9 3.6 - - - +
364B ILE 3.3 0.2 - - - -
365B GLN* 1.3 74.9 - - - +
367B LEU* 1.3 61.9 + - + +
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Residues in contact with LEU 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A FAD 4.2 5.5 + - - +
289B CYS* 4.0 9.2 - - - -
290B ALA* 4.2 15.7 - - - -
293B TYR* 3.6 49.3 + - + -
363B ALA 3.1 19.3 + - - +
364B ILE 3.7 0.2 - - - +
365B GLN 3.3 0.2 - - - -
366B ILE* 1.3 76.1 - - + +
368B GLY* 1.3 62.2 + - - +
369B GLY 3.5 0.7 + - - -
370B MET* 3.4 16.1 + - + +
371B GLY* 3.4 18.8 - - - +
376B MET* 3.5 42.6 - - + -
378B ALA* 3.8 20.0 - - + -
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Residues in contact with GLY 368 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ILE* 3.9 21.9 - - - +
394A THR* 5.3 1.1 - - - -
501A FAD 3.7 20.9 - - - -
364B ILE 3.2 7.1 + - - +
365B GLN 3.1 16.2 + - - -
366B ILE 3.2 1.0 + - - -
367B LEU* 1.3 73.0 - - - +
369B GLY* 1.3 61.8 + - - +
371B GLY* 2.9 20.4 + - - -
372B 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).
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