Contacts of the helix formed by residues 341 - 368 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D LYS* 6.2 2.0 - - - -
266D GLN 5.1 0.9 - - - -
269D ASP* 3.7 35.2 - - + -
270D MET* 4.0 12.3 - - + -
273D ILE* 3.9 22.0 - - + -
331D ALA* 3.9 8.5 - - - +
334D LEU* 3.8 18.8 - - + -
335D LYS* 3.7 37.0 - - + -
339D LYS 3.4 14.6 - - - -
340D PRO* 1.3 74.1 - - + +
342D ILE* 1.3 64.1 + - + +
343D LYS 3.5 2.2 - - - -
344D GLU* 3.4 11.7 - - - -
345D ALA* 2.9 28.9 + - + +
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Residues in contact with ILE 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D GLN* 6.5 0.7 - - + -
269D ASP* 3.6 38.0 - - - +
272D ARG* 5.5 1.3 + - - +
340D PRO* 5.2 5.5 - - + +
341D PHE* 1.3 82.5 - - + +
343D LYS* 1.3 63.6 + - - +
344D GLU* 3.9 0.6 + - - -
345D ALA* 3.9 2.2 - - - +
346D ALA* 3.1 22.5 + - - +
401D VAL* 3.8 13.0 - - + -
405D HIS* 3.4 41.7 - - + +
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Residues in contact with LYS 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B GLU* 2.9 37.7 + - - +
330D ARG* 4.8 0.6 - - - +
341D PHE 3.5 0.2 - - - -
342D ILE* 1.3 80.3 - - - +
344D GLU* 1.3 83.8 + - - +
346D ALA* 3.4 6.8 + - - +
347D MET* 2.9 46.9 + - + +
401D VAL* 4.9 3.6 - - - -
402D ILE* 4.0 16.9 - - + +
405D HIS* 3.8 30.6 - - + +
406D LEU* 4.8 11.5 - - + +
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Residues in contact with GLU 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327D LEU* 4.2 3.0 - - - +
330D ARG* 3.5 39.4 + - - +
331D ALA* 3.8 13.6 - - + +
334D LEU* 3.5 34.5 - - + +
340D PRO 3.9 4.5 - - - +
341D PHE* 3.4 19.9 + - - +
342D ILE 3.3 0.7 + - - -
343D LYS* 1.3 97.2 + - - +
345D ALA* 1.3 55.2 + - - +
347D MET* 3.5 3.2 + - - +
348D ALA* 3.0 28.4 + - - +
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Residues in contact with ALA 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D ASP* 3.4 29.4 - - - +
272D ARG* 4.0 9.6 - - + +
273D ILE* 3.9 14.4 - - + -
331D ALA* 3.8 9.7 - - + +
341D PHE* 2.9 23.5 + - + +
342D ILE 3.9 2.7 - - - +
344D GLU* 1.3 74.1 - - - +
346D ALA* 1.3 59.9 + - - +
348D ALA* 3.4 3.7 + - - +
349D LYS* 2.9 30.8 + - - +
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Residues in contact with ALA 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D ARG* 4.8 6.1 - - - +
342D ILE 3.1 17.0 + - - +
343D LYS 3.7 4.0 - - - +
345D ALA* 1.3 77.2 - - - +
347D MET* 1.3 56.9 + - - +
349D LYS* 3.5 0.8 + - - +
350D LEU* 2.9 32.6 + - - +
398D GLN* 3.2 29.5 - - - +
401D VAL* 3.8 21.5 - - + -
402D ILE* 3.8 14.0 - - + +
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Residues in contact with MET 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ALA* 3.8 20.6 - - + -
319B LEU* 3.6 25.4 - - + +
322B GLU* 3.3 33.4 - - - +
327D LEU* 3.8 7.7 - - + +
330D ARG* 3.3 27.1 - - - +
343D LYS* 2.9 29.0 + - + +
344D GLU* 3.6 6.3 - - - +
345D ALA 3.3 0.2 - - - -
346D ALA* 1.3 72.5 - - - +
348D ALA* 1.3 56.0 + - - +
350D LEU* 3.7 2.1 - - - +
351D ALA* 2.8 37.8 + - - +
402D ILE* 3.7 36.6 - - + -
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Residues in contact with ALA 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D ARG 5.4 0.4 - - - +
273D ILE* 5.7 2.0 - - - -
276D ALA* 3.6 8.1 - - + -
324D ALA 4.9 1.0 - - - +
327D LEU* 3.7 13.1 - - - +
328D THR* 3.6 37.8 + - + +
331D ALA* 4.6 2.7 - - + -
344D GLU 3.0 18.3 + - - +
345D ALA* 3.6 7.9 - - - +
346D ALA 3.4 0.2 - - - -
347D MET* 1.3 74.4 - - - +
349D LYS* 1.3 57.1 + - - +
352D ALA* 2.8 35.9 + - - +
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Residues in contact with LYS 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D ARG* 3.7 30.7 - - + +
275D ILE* 4.0 18.2 - - + -
276D ALA* 3.7 9.8 - - - +
345D ALA 2.9 17.8 + - - +
346D ALA 3.9 3.1 - - - +
348D ALA* 1.3 76.1 - - - +
350D LEU* 1.3 53.6 + - - +
352D ALA* 4.2 0.2 - - - +
353D SER* 2.8 40.5 + - - +
388D THR 2.8 27.5 + - - +
389D GLU* 4.0 8.1 - - - +
391D TYR 2.8 23.3 + - - -
392D GLU* 4.2 5.2 - - - -
393D GLY 2.6 26.4 + - - -
394D THR* 4.5 2.0 - - - +
395D SER* 4.7 0.8 + - - +
398D GLN* 3.8 17.0 - - + +
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Residues in contact with LEU 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B ALA* 6.0 0.7 - - + +
316B ASP* 4.8 1.6 - - - +
319B LEU* 3.7 20.0 - - + -
346D ALA 2.9 18.4 + - - +
347D MET 3.7 3.8 - - - +
349D LYS* 1.3 77.9 - - - +
351D ALA* 1.3 62.1 + - - +
353D SER* 3.1 16.1 + - - -
354D GLU* 3.1 22.0 + - - +
395D SER* 3.6 37.5 - - - +
398D GLN* 4.1 9.2 - - + -
399D ARG* 3.7 42.8 - - + +
402D ILE* 3.7 18.8 - - + -
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Residues in contact with ALA 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 4.5 11.4 - - + +
323D SER* 6.0 0.4 - - - +
324D ALA* 4.1 13.7 - - + -
327D LEU* 3.4 24.5 - - + -
347D MET 2.8 20.7 + - - +
348D ALA 4.0 1.6 - - - +
350D LEU* 1.3 72.8 - - - +
352D ALA* 1.3 58.0 + - - +
354D GLU* 3.3 3.8 + - - +
355D ALA* 2.9 31.0 + - - +
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Residues in contact with ALA 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D ALA* 3.3 33.7 - - + +
279D ALA* 3.6 10.2 - - + +
280D LEU* 4.2 8.1 - - + +
283D ALA* 5.2 0.3 - - - +
324D ALA* 3.7 18.3 - - + +
328D THR* 4.6 1.3 - - - +
348D ALA 2.8 21.3 + - - +
349D LYS 4.2 0.2 - - - +
351D ALA* 1.3 73.3 - - - +
353D SER* 1.3 56.7 + - - +
355D ALA* 3.3 4.9 + - - +
356D ALA* 2.8 28.8 + - - +
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Residues in contact with SER 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D ILE* 5.8 0.2 - - - -
279D ALA* 3.9 4.5 - - - -
349D LYS* 2.8 25.6 + - - +
350D LEU* 3.1 8.3 + - - -
352D ALA* 1.3 74.9 - - - +
354D GLU* 1.3 67.0 + - - +
356D ALA* 3.4 2.9 + - - +
357D THR* 3.3 17.3 + - - -
388D THR* 3.2 47.0 + - - -
389D GLU* 3.7 20.5 - - - +
395D SER* 4.1 5.4 + - - -
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Residues in contact with GLU 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B LEU* 5.8 1.2 - - - +
350D LEU* 3.1 25.0 + - - +
351D ALA* 4.1 3.0 - - - +
353D SER* 1.3 81.7 + - - +
355D ALA* 1.3 62.1 + - - +
357D THR* 3.5 3.5 + - - +
358D ALA* 3.1 22.8 + - - +
389D GLU* 3.4 25.9 - - + +
395D SER* 3.9 8.4 + - - +
399D ARG* 3.0 42.2 + - - -
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Residues in contact with ALA 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D LEU* 6.4 0.4 - - + -
283D ALA* 5.1 1.6 - - + -
320D ALA* 4.1 27.4 - - + +
321D LEU* 5.0 1.6 - - + -
324D ALA* 4.7 1.3 - - + -
351D ALA 2.9 18.1 + - - +
352D ALA* 3.4 8.3 - - - +
354D GLU* 1.3 73.5 - - - +
356D ALA* 1.3 55.2 + - - +
358D ALA* 3.1 5.0 + - - +
359D ILE* 2.6 57.8 + - + +
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Residues in contact with ALA 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279D ALA* 3.7 25.4 - - + +
282D ILE* 4.6 2.4 - - + +
283D ALA* 4.0 17.5 - - + +
352D ALA 2.8 19.4 + - - +
353D SER 3.4 6.7 + - - +
355D ALA* 1.3 71.1 - - - +
357D THR* 1.3 57.7 + - - +
359D ILE* 4.3 0.2 - - - +
360D SER* 2.8 33.8 + - - -
385D ALA* 3.4 18.4 - - + +
388D THR* 4.2 4.3 - - - +
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Residues in contact with THR 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361C HIS* 3.8 10.8 - - + +
382C TYR* 3.7 21.2 + - - +
353D SER 3.3 7.5 + - - -
354D GLU 3.9 4.3 - - - +
355D ALA 3.2 0.6 - - - -
356D ALA* 1.3 78.5 - - - +
358D ALA* 1.3 58.3 + - - +
360D SER* 3.3 6.3 + - - -
361D HIS* 3.1 28.5 + - + +
382D TYR* 4.3 2.6 + - + -
385D ALA* 3.6 20.7 + - - +
386D ARG* 4.0 3.1 - - - -
389D GLU* 2.7 32.0 + - - +
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Residues in contact with ALA 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D MET* 5.6 0.9 - - - -
354D GLU 3.1 15.3 + - - +
355D ALA* 3.1 7.6 + - - +
357D THR* 1.3 74.3 - - - +
359D ILE* 1.3 67.1 + - + +
361D HIS* 3.5 4.6 + - - +
362D GLN* 3.1 30.5 + - + +
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Residues in contact with ILE 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D ALA* 3.6 42.8 - - + +
286D ALA* 4.2 2.9 - - + -
287D LEU* 4.0 12.1 - - + +
317D MET* 3.4 61.7 - - + +
320D ALA* 4.4 4.0 - - + -
321D LEU* 3.9 14.4 - - + +
355D ALA* 2.6 34.9 + - + +
356D ALA 4.3 1.6 - - - +
358D ALA* 1.3 73.5 - - + +
360D SER* 1.3 57.6 + - - +
362D GLN 3.3 0.9 + - - -
363D ALA* 2.9 26.7 + - - +
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Residues in contact with SER 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D ILE* 5.2 1.1 - - - -
286D ALA* 4.1 12.5 - - - +
356D ALA 2.8 22.7 + - - -
357D THR* 3.3 5.7 + - - -
359D ILE* 1.3 73.5 - - - +
361D HIS* 1.3 67.2 + - - +
363D ALA* 3.3 3.3 + - - +
364D ILE* 3.1 26.5 + - - +
378D ALA 4.7 1.6 - - - +
381D HIS* 3.8 15.0 - - - -
382D TYR* 3.3 39.8 - - - -
385D ALA* 3.6 5.9 - - - +
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Residues in contact with HIS 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C THR* 3.8 10.3 - - + +
386C ARG* 2.9 54.2 + - - +
389C GLU* 2.7 38.1 + - - -
357D THR* 3.1 19.9 + - + +
358D ALA* 3.7 6.7 - - - +
360D SER* 1.3 77.0 + - - +
362D GLN* 1.3 89.6 + - - +
364D ILE* 3.2 3.6 + - - +
365D GLN* 3.1 7.8 + - - -
382D TYR* 3.5 29.1 - + + -
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Residues in contact with GLN 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396C GLU* 5.4 0.2 + - - -
313D LYS* 3.0 42.4 + - + +
317D MET* 3.8 28.9 - - + -
358D ALA* 3.1 18.7 + - + +
359D ILE 3.9 0.4 - - - +
361D HIS* 1.3 106.8 + - - +
363D ALA* 1.3 56.8 + - - +
365D GLN* 3.3 11.5 + - - +
366D ILE* 2.9 33.9 + - + +
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Residues in contact with ALA 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D ALA* 3.5 29.6 - - + +
289D CYS* 5.5 2.0 - - + -
290D ALA* 4.0 15.3 - - + +
317D MET* 4.1 1.3 - - + +
359D ILE 2.9 16.8 + - - +
360D SER* 3.5 10.8 - - - +
361D HIS 3.2 0.2 - - - -
362D GLN* 1.3 71.6 - - - +
364D ILE* 1.3 66.6 + - - +
366D ILE* 3.3 1.7 + - - +
367D LEU* 3.1 30.7 + - - +
378D ALA* 4.5 10.5 - - + -
381D HIS* 6.3 0.2 - - + -
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Residues in contact with ILE 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C LEU* 4.4 4.3 - - + -
386C ARG* 3.5 31.4 - - + +
390C ILE* 4.0 13.4 - - + +
360D SER 3.1 10.3 + - - +
361D HIS 3.4 7.0 - - - +
363D ALA* 1.3 79.5 - - - +
365D GLN* 1.3 61.5 + - - +
367D LEU* 3.3 4.3 + - - +
368D GLY* 3.1 21.7 + - - +
371D GLY* 3.7 27.6 - - - +
372D TYR* 5.1 0.7 - - - -
378D ALA* 3.9 18.8 - - + +
379D GLU* 4.1 9.6 - - - -
382D TYR* 3.6 44.4 - - + -
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Residues in contact with GLN 365 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C ARG* 2.8 35.7 + - - +
389C GLU* 3.0 28.9 + - - +
390C ILE* 4.1 5.5 - - - +
394C THR* 4.0 6.3 - - - +
395C SER* 3.7 9.9 + - - +
396C GLU* 2.9 39.6 + - - +
501C FAD 2.7 21.8 + - - +
313D LYS* 4.4 6.3 - - - +
361D HIS* 3.1 11.4 + - - +
362D GLN* 3.5 21.8 - - - +
363D ALA 3.2 0.4 - - - -
364D ILE* 1.3 77.2 - - - +
366D ILE* 1.3 58.6 + - - +
368D GLY* 3.1 12.1 + - - -
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Residues in contact with ILE 366 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501C FAD 3.2 27.4 - - - +
290D ALA* 3.8 39.7 - - + +
293D TYR* 3.9 2.2 - - + -
294D ALA* 4.0 15.7 - - + -
304D LEU* 3.7 11.2 - - + +
310D ILE* 4.2 12.8 - - + -
313D LYS* 3.9 25.8 - - + -
314D LEU* 3.8 21.1 - - + -
317D MET* 3.9 13.0 - - - -
362D GLN 2.9 20.8 + - - +
363D ALA 3.8 4.0 - - - +
364D ILE 3.3 0.2 - - - -
365D GLN* 1.3 76.4 - - - +
367D LEU* 1.3 59.8 + - + +
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Residues in contact with LEU 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501C FAD 4.4 4.8 + - - +
289D CYS* 4.0 9.0 - - - +
290D ALA* 4.2 15.7 - - - -
293D TYR* 3.6 50.9 + - + -
363D ALA 3.1 16.7 + - - +
364D ILE 3.3 5.8 + - - +
366D ILE* 1.3 75.7 - - + +
368D GLY* 1.3 62.7 + - - +
369D GLY 3.5 0.3 + - - -
370D MET* 3.4 16.1 + - + +
371D GLY* 3.5 15.0 - - - +
376D MET* 3.6 37.0 - - + -
378D ALA* 3.7 25.8 - - + -
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Residues in contact with GLY 368 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C ILE* 3.7 26.3 - - - +
394C THR* 5.3 1.3 - - - -
501C FAD 3.9 20.4 - - - -
364D ILE 3.1 9.8 + - - +
365D GLN* 3.1 13.1 + - - -
366D ILE 3.3 1.0 + - - -
367D LEU* 1.3 73.4 - - - +
369D GLY* 1.3 62.0 + - - +
371D GLY* 2.9 18.9 + - - -
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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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