Contacts of the helix formed by residues 341 - 368 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E GLN 5.4 0.2 - - - -
269E ASP* 3.8 34.3 - - + -
270E MET* 4.1 11.2 - - + -
273E ILE* 4.1 20.9 - - + -
331E ALA 3.8 16.6 - - - +
334E LEU* 3.8 10.8 - - + -
335E LYS* 3.6 38.6 - - + -
339E LYS 3.4 15.0 - - - -
340E PRO* 1.3 73.5 - - + +
342E ILE* 1.3 61.8 + - + +
344E GLU* 3.2 15.0 - - + -
345E ALA* 2.7 36.0 + - + +
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Residues in contact with ILE 342 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266E GLN* 6.5 0.2 - - + -
269E ASP* 3.5 40.4 - - + +
272E ARG* 5.4 1.5 + - - +
340E PRO* 5.3 3.3 - - + +
341E PHE* 1.3 81.9 - - + +
343E LYS* 1.3 63.2 + - - +
344E GLU* 3.7 0.4 + - - -
345E ALA* 3.9 1.9 - - - +
346E ALA* 3.0 23.6 + - - +
401E VAL* 3.6 14.6 - - + -
405E HIS* 3.4 41.5 - - + +
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Residues in contact with LYS 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330E ARG* 4.6 0.8 - - - +
342E ILE* 1.3 80.3 - - - +
344E GLU* 1.3 81.5 + - - +
346E ALA* 3.4 6.5 + - - +
347E MET* 2.9 45.4 + - + +
401E VAL* 5.1 2.0 - - - -
402E ILE* 4.1 19.9 - - + +
405E HIS* 4.0 31.9 - - + -
406E LEU* 4.7 13.8 - - + +
322G GLU* 2.7 41.7 + - - -
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Residues in contact with GLU 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327E LEU 4.1 2.8 - - - +
330E ARG* 3.7 36.3 + - - +
331E ALA* 3.6 16.2 - - - +
334E LEU* 3.4 34.6 - - + +
340E PRO 3.7 5.0 - - - +
341E PHE* 3.2 21.7 + - - +
342E ILE 3.7 0.3 + - - -
343E LYS* 1.3 94.2 + - - +
345E ALA* 1.3 59.2 + - - +
347E MET* 3.6 2.6 + - - +
348E ALA* 3.1 27.9 + - - +
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Residues in contact with ALA 345 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269E ASP* 3.4 29.6 - - - +
272E ARG* 3.9 10.5 - - + +
273E ILE* 4.0 14.1 - - + -
331E ALA* 3.7 9.7 - - - +
341E PHE* 2.7 26.2 + - + +
342E ILE 3.9 2.9 - - - +
344E GLU* 1.3 69.8 - - - +
346E ALA* 1.3 60.6 + - - +
348E ALA* 3.5 3.8 + - - +
349E LYS* 3.0 30.3 + - - +
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Residues in contact with ALA 346 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E ARG* 4.8 5.7 - - - +
342E ILE 3.0 18.1 + - - +
343E LYS 3.6 4.3 - - - +
345E ALA* 1.3 74.5 - - - +
347E MET* 1.3 63.7 + - - +
349E LYS* 3.5 0.6 + - - -
350E LEU* 3.0 27.2 + - - +
398E GLN* 3.2 29.2 - - - +
401E VAL* 4.0 16.4 - - + -
402E ILE* 3.9 16.8 - - + +
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Residues in contact with MET 347 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327E LEU* 4.4 9.4 - - + -
330E ARG* 3.4 23.6 - - - -
343E LYS* 2.9 31.1 + - + +
344E GLU* 3.7 6.3 - - - +
345E ALA 3.4 0.2 - - - -
346E ALA* 1.3 72.3 - - - +
348E ALA* 1.3 57.1 + - - +
350E LEU* 3.5 2.0 + - - +
351E ALA* 2.9 34.4 + - - +
402E ILE* 3.6 35.2 - - + -
318G ALA* 3.6 3.8 - - + -
319G LEU* 3.5 50.1 - - + +
322G GLU* 3.4 30.7 - - - +
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Residues in contact with ALA 348 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272E ARG 5.3 0.2 - - - +
273E ILE* 5.6 1.6 - - - -
276E ALA* 3.7 7.4 - - + +
324E ALA 4.9 0.7 - - - +
327E LEU* 3.7 15.2 - - - +
328E THR* 3.6 34.1 + - - +
331E ALA* 4.5 2.5 - - + -
344E GLU 3.1 18.4 + - - +
345E ALA* 3.6 9.0 - - - +
346E ALA 3.3 0.2 - - - -
347E MET* 1.3 72.5 - - - +
349E LYS* 1.3 59.8 + - - +
351E ALA* 4.0 0.5 - - - +
352E ALA* 2.9 34.8 + - - +
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Residues in contact with LYS 349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272E ARG* 3.6 32.8 - - + +
275E ILE* 4.2 18.1 - - + +
276E ALA* 3.8 10.1 - - - +
345E ALA 3.0 18.1 + - - +
346E ALA 4.0 3.1 - - - +
348E ALA* 1.3 76.0 - - - +
350E LEU* 1.3 53.6 + - - +
352E ALA* 4.3 0.2 - - - +
353E SER* 2.8 41.8 + - - +
388E THR 2.8 25.6 + - - +
389E GLU* 3.8 12.9 + - - +
391E TYR 3.0 23.1 + - - -
392E GLU* 4.2 3.1 - - - -
393E GLY 2.6 26.4 + - - -
394E THR* 4.5 1.6 - - - +
395E SER* 4.7 0.8 - - - +
398E GLN* 3.8 16.1 - - + +
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Residues in contact with LEU 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346E ALA 3.0 18.6 + - - +
347E MET 3.7 3.4 - - - +
349E LYS* 1.3 78.4 - - - +
351E ALA* 1.3 62.7 + - - +
353E SER* 3.0 17.8 + - - -
354E GLU* 3.1 27.7 + - - +
395E SER* 3.7 27.1 - - - +
398E GLN* 4.2 7.6 - - + -
399E ARG* 3.6 51.1 - - + +
402E ILE* 3.8 13.0 - - + -
315G ALA* 6.0 0.9 - - + +
316G ASP* 4.9 0.9 - - - +
319G LEU* 3.5 24.9 - - + -
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Residues in contact with ALA 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323E SER* 6.0 0.2 - - - +
324E ALA* 4.1 10.0 - - + +
327E LEU* 3.6 24.7 - - + -
347E MET 2.9 20.6 + - - +
348E ALA 4.2 1.6 - - - +
350E LEU* 1.3 74.6 - - - +
352E ALA* 1.3 56.9 + - - +
354E GLU* 3.9 4.6 - - - +
355E ALA* 2.9 30.8 + - - +
319G LEU* 4.4 12.8 - - + +
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Residues in contact with ALA 352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276E ALA* 3.4 32.3 - - + +
279E ALA* 3.5 14.1 - - + +
280E LEU* 4.0 8.5 - - + -
283E ALA* 5.4 0.5 - - - +
324E ALA* 3.7 19.6 - - + +
328E THR* 4.5 0.9 - - - +
348E ALA 2.9 19.1 + - - +
351E ALA* 1.3 76.8 - - - +
353E SER* 1.3 57.8 + - - +
355E ALA* 3.3 3.0 + - - +
356E ALA* 2.9 24.8 + - - +
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Residues in contact with SER 353 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E ILE* 5.8 0.4 - - - -
279E ALA* 3.9 3.5 - - - +
349E LYS* 2.8 25.8 + - - +
350E LEU* 3.0 14.0 + - - -
352E ALA* 1.3 77.1 - - - +
354E GLU* 1.3 63.0 + - - +
356E ALA 3.4 0.9 + - - -
357E THR* 3.2 18.4 + - - -
388E THR* 3.2 50.9 + - - -
389E GLU* 3.8 19.2 - - - +
395E SER* 4.4 2.8 + - - -
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Residues in contact with GLU 354 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350E LEU* 3.1 27.8 + - + +
351E ALA* 4.2 4.5 - - - +
353E SER* 1.3 78.5 + - - +
355E ALA* 1.3 57.2 + - - +
357E THR* 3.6 2.1 + - - +
358E ALA* 3.1 30.0 + - - +
389E GLU* 3.8 21.1 - - - +
395E SER* 4.0 7.8 + - - +
399E ARG* 3.1 39.6 + - - -
319G LEU* 5.6 1.7 - - - +
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Residues in contact with ALA 355 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283E ALA* 4.7 1.8 - - + -
320E ALA* 4.1 34.5 - - + +
321E LEU* 4.7 2.0 - - + +
324E ALA* 4.6 2.2 - - + -
351E ALA 2.9 19.9 + - - +
352E ALA* 3.6 7.4 - - - +
353E SER 3.3 0.2 - - - -
354E GLU* 1.3 75.2 - - - +
356E ALA* 1.3 59.7 + - - +
358E ALA* 4.6 4.0 - - - -
359E ILE* 2.8 44.7 + - + +
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Residues in contact with ALA 356 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279E ALA* 3.7 26.9 - - + +
282E ILE* 4.5 1.9 - - + +
283E ALA* 4.0 17.3 - - - +
352E ALA 2.9 16.9 + - - +
353E SER 3.4 5.4 + - - +
355E ALA* 1.3 74.9 - - - +
357E THR* 1.3 57.7 + - - +
359E ILE* 4.3 0.3 - - - +
360E SER* 2.8 32.9 + - - -
385E ALA* 3.4 19.3 - - + +
388E THR* 4.3 2.5 - - - +
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Residues in contact with THR 357 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353E SER 3.2 8.4 + - - -
354E GLU 4.1 2.7 - - - +
355E ALA 3.4 0.2 - - - -
356E ALA* 1.3 78.1 - - - +
358E ALA* 1.3 65.0 + - - +
360E SER* 3.2 7.5 + - - -
361E HIS* 3.0 24.5 + - + +
382E TYR* 4.2 4.6 + - + -
385E ALA* 3.8 19.6 + - - +
386E ARG* 3.9 4.7 - - - -
389E GLU* 2.7 32.2 + - - +
361F HIS* 3.8 15.9 - - + +
382F TYR* 3.9 15.2 + - - +
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Residues in contact with ALA 358 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317E MET* 5.6 0.4 - - - -
320E ALA* 6.2 2.2 - - + -
354E GLU 3.1 19.0 + - - +
355E ALA* 4.0 4.9 - - - +
357E THR* 1.3 79.7 - - - +
359E ILE* 1.3 63.7 + - + +
361E HIS* 3.4 5.0 + - - +
362E GLN* 3.1 30.1 + - + +
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Residues in contact with ILE 359 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283E ALA* 3.6 34.5 - - + +
286E ALA* 4.2 2.5 - - + -
287E LEU* 4.0 9.4 - - + +
317E MET* 3.2 67.7 - - + +
320E ALA* 4.4 4.3 - - + -
321E LEU* 3.8 24.2 - - + +
355E ALA* 2.8 34.0 + - + +
356E ALA 4.3 1.6 - - - +
358E ALA* 1.3 73.7 - - + +
360E SER* 1.3 57.3 + - - +
362E GLN 3.4 0.9 + - - -
363E ALA* 2.9 25.1 + - - +
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Residues in contact with SER 360 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282E ILE* 5.2 1.6 - - - -
286E ALA* 4.1 13.0 - - - +
356E ALA 2.8 24.5 + - - -
357E THR* 3.2 7.8 + - - -
359E ILE* 1.3 73.9 - - - +
361E HIS* 1.3 64.0 + - - +
363E ALA* 3.3 3.3 + - - +
364E ILE* 3.1 26.9 + - - +
378E ALA 4.7 1.0 - - - +
381E HIS* 3.8 14.8 - - - -
382E TYR* 3.3 38.4 - - - -
385E ALA* 3.6 6.5 - - - +
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Residues in contact with HIS 361 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357E THR* 3.0 20.6 + - + +
358E ALA* 3.6 7.0 - - - +
360E SER* 1.3 76.9 + - - +
362E GLN* 1.3 79.5 + - - +
364E ILE* 3.3 2.9 + - - +
365E GLN* 3.1 12.4 + - - -
382E TYR* 3.5 31.2 - + + -
357F THR* 3.7 10.3 - - + +
386F ARG* 2.7 55.3 + - - +
389F GLU* 2.7 38.5 + - - -
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Residues in contact with GLN 362 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313E LYS* 2.8 44.4 + - + +
317E MET* 3.8 24.9 - - + -
358E ALA* 3.1 17.5 + - + +
359E ILE 3.8 3.4 - - - +
361E HIS* 1.3 105.1 + - - +
363E ALA* 1.3 59.8 + - - +
365E GLN* 3.6 10.6 - - - +
366E ILE* 2.9 33.0 + - + +
396F GLU* 5.4 0.4 + - - -
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Residues in contact with ALA 363 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286E ALA* 3.5 33.0 - - + +
289E CYS* 5.4 1.3 - - - -
290E ALA* 4.0 16.4 - - + +
317E MET* 4.0 1.0 - - + +
359E ILE 2.9 16.9 + - - +
360E SER* 3.3 7.2 + - - +
362E GLN* 1.3 73.4 - - - +
364E ILE* 1.3 67.5 + - - +
366E ILE* 3.3 1.4 + - - -
367E LEU* 3.1 28.8 + - - +
378E ALA* 4.4 12.3 - - + -
381E HIS* 6.4 0.2 - - + -
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Residues in contact with ILE 364 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360E SER 3.1 11.3 + - - +
361E HIS 3.4 7.0 - - - +
363E ALA* 1.3 77.0 - - - +
365E GLN* 1.3 60.7 + - - +
367E LEU* 3.3 3.5 + - - +
368E GLY* 3.1 21.8 + - - +
371E GLY* 3.7 32.3 - - - +
372E TYR* 5.0 1.1 - - - -
378E ALA* 3.8 15.5 - - - +
379E GLU* 4.1 8.3 - - - -
382E TYR* 3.5 43.7 - - + -
231F LEU* 4.4 3.8 - - + -
386F ARG* 3.5 30.5 - - + +
390F ILE* 3.9 13.0 - - + +
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Residues in contact with GLN 365 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313E LYS* 4.4 6.3 - - - +
361E HIS* 3.1 11.4 + - - +
362E GLN* 3.6 21.5 - - - +
363E ALA 3.2 0.4 - - - -
364E ILE* 1.3 77.0 - - - +
366E ILE* 1.3 58.1 + - - +
368E GLY* 3.1 12.5 + - - +
386F ARG* 3.0 34.3 + - - +
389F GLU* 3.0 29.2 + - - +
390F ILE* 3.9 5.9 - - - +
394F THR* 3.8 8.1 - - - +
395F SER* 3.7 9.1 - - - +
396F GLU* 2.8 42.1 + - - +
501F FAD 2.7 22.4 + - - +
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Residues in contact with ILE 366 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290E ALA* 3.8 33.0 - - + +
293E TYR* 3.9 1.6 - - + -
294E ALA* 4.1 17.3 - - + +
304E LEU* 3.6 11.2 - - + +
310E ILE* 4.2 11.9 - - + -
313E LYS* 3.9 26.7 - - + -
314E LEU* 3.8 30.5 - - + -
317E MET* 4.0 11.4 - - - -
362E GLN 2.9 20.9 + - - +
363E ALA 3.3 4.5 + - - +
365E GLN* 1.3 76.4 - - - +
367E LEU* 1.3 58.5 + - + +
501F FAD 3.1 28.2 - - - +
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Residues in contact with LEU 367 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289E CYS* 4.1 15.3 - - - +
290E ALA* 4.2 8.5 - - - -
293E TYR* 3.5 52.4 + - + -
363E ALA 3.1 17.7 + - - +
365E GLN 3.2 0.2 - - - -
366E ILE* 1.3 76.9 - - - +
368E GLY* 1.3 61.7 + - - +
369E GLY 3.4 0.9 + - - -
370E MET* 3.4 14.7 + - + +
371E GLY* 3.4 19.3 - - - +
376E MET* 3.7 37.5 - - + -
378E ALA* 3.8 23.8 - - + -
501F FAD 4.4 5.7 + - - +
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Residues in contact with GLY 368 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364E ILE 3.1 8.5 + - - +
365E GLN* 3.1 16.2 + - - -
366E ILE 3.3 0.6 - - - -
367E LEU* 1.3 77.6 - - - +
369E GLY* 1.3 64.4 + - - -
371E GLY* 3.0 12.0 + - - -
390F ILE* 3.9 23.6 - - - +
394F THR* 5.3 1.1 - - - -
501F FAD 3.8 21.3 - - - -
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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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