Contacts of the helix formed by residues 376 - 401 (chain B) in PDB entry 2XWU
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 ALA 376 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B GLU* 1.3 78.2 - - + +
377B GLU* 1.3 67.8 - - + +
379B GLN* 3.4 7.2 + - - +
380B ALA* 3.0 25.9 + - - +
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Residues in contact with GLU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B ALA* 1.3 77.9 - - + +
378B LYS* 1.3 61.4 + - + +
380B ALA* 4.5 3.8 - - - -
381B VAL* 2.7 46.4 + - + +
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Residues in contact with LYS 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B LEU 3.7 12.9 + - - -
325B ASP* 4.0 13.7 + - - +
327B VAL* 3.7 29.6 - - + +
374B PHE* 3.6 44.6 - - + -
375B GLU 3.5 9.2 + - - +
376B ALA 3.4 0.8 - - - -
377B GLU* 1.3 76.8 - - + +
379B GLN* 1.3 63.2 + - - +
381B VAL* 5.0 1.8 - - - -
382B TYR* 3.0 37.6 + - + +
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Residues in contact with GLN 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ILE* 3.5 21.2 - - + +
372B LEU* 3.8 25.9 + - + +
374B PHE* 2.8 35.0 + - - +
375B GLU* 3.8 9.2 + - - +
376B ALA 3.4 9.6 + - - +
377B GLU 3.3 0.6 - - - -
378B LYS* 1.3 79.1 - - - +
380B ALA* 1.3 58.7 + - - +
382B TYR 3.9 0.2 - - - -
383B GLN* 3.0 35.7 + - + +
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Residues in contact with ALA 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B ALA 3.0 18.2 + - - +
377B GLU* 3.9 3.8 - - - +
379B GLN* 1.3 75.8 - - - +
381B VAL* 1.3 66.5 + - + +
383B GLN* 3.4 7.6 + - - +
384B GLN* 3.2 21.0 + - - +
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Residues in contact with VAL 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B GLU* 2.7 36.0 + - + +
378B LYS* 4.4 1.8 - - - +
380B ALA* 1.3 73.7 - - + +
382B TYR* 1.3 64.5 + - + +
384B GLN* 3.2 16.0 + - + +
385B VAL* 3.2 20.7 + - + +
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Residues in contact with TYR 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B LEU 4.7 0.7 + - - -
324B LEU* 2.8 50.2 + - + +
327B VAL* 3.9 16.1 - - + -
330B TRP* 3.9 29.9 - + + +
333B PHE* 6.0 0.2 - + - -
371B ILE* 4.0 20.8 - - + +
374B PHE* 3.6 25.1 - + + -
378B LYS* 3.0 35.5 + - + +
381B VAL* 1.3 79.6 - - + +
383B GLN* 1.3 56.8 + - - +
385B VAL* 3.2 9.0 + - + -
386B TYR* 3.0 57.9 + + - +
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Residues in contact with GLN 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ILE* 4.2 11.9 - - - +
372B LEU* 4.5 9.4 - - - +
379B GLN* 3.0 23.4 + - + +
380B ALA* 3.5 9.2 - - - +
382B TYR* 1.3 74.7 - - - +
384B GLN* 1.3 65.3 + - - +
385B VAL 3.1 0.2 - - - -
386B TYR* 4.6 1.1 - - - +
387B ARG* 2.8 72.3 + - + +
437B MET* 3.5 39.5 + - - +
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Residues in contact with GLN 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B ALA 3.2 10.5 + - - +
381B VAL* 3.2 11.6 + - + +
383B GLN* 1.3 79.2 - - - +
385B VAL* 1.3 63.3 + - + +
387B ARG* 4.8 3.5 - - - +
388B PRO* 3.5 15.9 - - - +
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Residues in contact with VAL 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B TRP* 4.3 26.0 - - + -
334B LEU* 4.3 20.1 - - + +
381B VAL* 3.2 20.8 + - + +
382B TYR* 3.2 14.7 + - + +
383B GLN 3.1 0.4 - - - -
384B GLN* 1.3 81.5 - - + +
386B TYR* 1.3 85.1 + - + +
388B PRO* 3.4 13.2 - - - +
389B VAL* 3.4 12.1 - - - +
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Residues in contact with TYR 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B LEU* 4.3 8.0 - - + +
330B TRP 4.6 2.4 + - - -
333B PHE* 3.3 25.0 - + - -
334B LEU* 3.3 39.5 + - + +
337B VAL* 3.8 18.1 - - + +
367B LEU* 4.0 13.7 - - + -
371B ILE* 3.5 27.4 - - + -
382B TYR* 3.0 45.0 + + - +
383B GLN* 5.1 2.2 - - - -
385B VAL* 1.3 87.7 - - + +
387B ARG* 1.3 59.6 + - - +
388B PRO* 3.2 2.7 - - - -
389B VAL* 3.2 19.6 + - + +
390B TYR* 2.9 39.5 + - + -
437B MET* 5.7 1.6 - - - -
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Residues in contact with ARG 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B GLN* 2.8 49.9 + - - +
384B GLN* 4.8 2.5 - - - +
386B TYR* 1.3 74.8 - - - +
388B PRO* 1.3 68.0 - - + +
390B TYR* 3.5 1.3 + - - -
391B PHE* 2.9 61.3 + - + -
437B MET* 4.1 5.6 + - - -
438B LEU* 3.5 35.5 + - + +
441B GLU* 3.7 17.6 - - - +
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Residues in contact with PRO 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B GLN 3.5 14.8 - - - +
385B VAL 3.4 15.7 - - - +
386B TYR 3.2 4.9 - - - -
387B ARG* 1.3 94.3 - - + +
389B VAL* 1.3 65.1 + - + +
391B PHE* 3.4 10.9 + - + +
392B GLN* 3.2 21.8 + - - +
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Residues in contact with VAL 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B LEU* 4.4 10.1 - - + -
337B VAL* 4.1 22.7 - - + -
338B ASN* 4.8 11.4 - - - +
341B MET* 3.3 25.0 - - + +
364B TRP* 4.4 7.0 - - + -
385B VAL 3.4 22.0 - - - +
386B TYR* 3.2 25.5 + - + +
388B PRO* 1.3 80.9 - - + +
390B TYR* 1.3 57.3 + - + +
392B GLN* 3.3 9.7 + - - +
393B LEU 3.1 20.8 + - - -
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Residues in contact with TYR 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B TRP* 2.6 37.4 + + - -
367B LEU* 3.4 31.0 - - + +
368B GLN* 2.8 31.4 + - + -
371B ILE* 5.2 0.2 - - + -
386B TYR* 2.9 34.8 + - + +
389B VAL* 1.3 78.1 - - + +
391B PHE* 1.3 61.9 + - - +
393B LEU* 3.3 15.4 + - + +
394B VAL* 2.9 29.9 + - - +
433B TYR* 6.5 0.2 - - + -
434B VAL* 4.1 32.0 - - + +
437B MET* 3.9 20.2 - - + -
438B LEU* 3.9 22.2 - - + -
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Residues in contact with PHE 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B ARG* 2.9 61.7 + - + -
388B PRO* 3.4 10.1 + - + +
389B VAL 3.3 0.2 - - - -
390B TYR* 1.3 76.5 - - - +
392B GLN* 1.3 65.9 + - - +
394B VAL* 3.1 16.3 + - + +
395B ASP* 3.2 19.2 + - - +
438B LEU* 3.7 27.6 - - + -
441B GLU* 3.9 29.4 - - + -
442B LEU* 4.5 0.9 - - + -
445B ASN* 4.3 25.6 - - + -
449B LYS* 5.0 0.5 + - - -
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Residues in contact with GLN 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B ASN* 4.6 9.7 + - - +
341B MET* 4.1 28.1 - - + +
388B PRO 3.2 9.8 + - - +
389B VAL* 3.4 14.4 - - - +
390B TYR 3.2 0.2 - - - -
391B PHE* 1.3 81.0 - - - +
393B LEU* 1.3 61.4 + - - +
395B ASP* 3.1 14.4 + - + +
396B VAL* 3.0 25.5 + - + +
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Residues in contact with LEU 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B MET* 3.8 18.3 - - + +
344B THR* 4.1 10.8 - - + -
364B TRP* 3.6 60.1 - - + +
389B VAL 3.1 13.6 + - - +
390B TYR* 3.5 16.2 - - + +
391B PHE 3.1 0.4 - - - -
392B GLN* 1.3 73.6 - - - +
394B VAL* 1.3 57.0 + - - +
396B VAL* 2.9 4.9 + - + +
397B LEU* 2.7 54.9 + - + +
434B VAL* 4.0 22.2 - - + -
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Residues in contact with VAL 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B TYR 2.9 18.7 + - - +
391B PHE* 3.3 9.4 - - + +
393B LEU* 1.3 76.1 - - - +
395B ASP* 1.3 64.9 + - - +
397B LEU* 4.0 5.5 - - - +
398B LEU* 3.2 36.5 + - + +
431B LEU* 4.6 11.2 - - + -
434B VAL* 3.5 23.8 - - + -
438B LEU* 3.8 12.3 - - + -
442B LEU* 3.9 22.7 - - + -
445B ASN* 4.4 5.4 - - - +
446B LEU* 5.0 2.7 - - + -
449B LYS* 4.1 14.1 - - - +
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Residues in contact with ASP 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B PHE* 3.2 18.6 + - - +
392B GLN* 3.1 13.0 + - + +
393B LEU 3.1 0.4 - - - -
394B VAL* 1.3 82.7 - - - +
396B VAL* 1.3 61.4 + - + +
398B LEU* 3.5 3.5 + - - +
399B HIS* 2.9 41.0 + - + +
445B ASN* 5.4 1.0 - - - +
449B LYS* 2.5 38.5 + - - +
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Residues in contact with VAL 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B MET* 4.1 18.8 - - + +
344B THR* 3.8 15.0 - - + +
345B GLY* 3.3 38.4 - - - +
392B GLN* 3.0 24.7 + - + +
393B LEU* 2.9 11.5 + - + +
395B ASP* 1.3 76.3 - - + +
397B LEU* 1.3 64.8 + - - +
399B HIS* 3.3 10.0 + - + +
400B LYS* 3.0 22.8 + - + +
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Residues in contact with LEU 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B THR* 4.0 20.2 - - + -
361B LEU* 4.0 24.0 - - + -
393B LEU* 2.7 42.1 + - + +
394B VAL 4.0 3.6 - - - +
395B ASP 3.4 0.2 - - - -
396B VAL* 1.3 74.9 - - + +
398B LEU* 1.3 59.8 + - - +
400B LYS* 3.2 7.7 + - + +
401B ALA* 2.9 29.6 + - - +
427B ILE* 3.9 23.0 - - + +
430B THR* 3.7 25.8 - - + -
431B LEU* 3.9 23.6 - - + -
434B VAL* 4.7 2.7 - - + -
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Residues in contact with LEU 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394B VAL* 3.2 24.7 + - + +
395B ASP* 4.0 4.7 - - - +
397B LEU* 1.3 75.0 - - - +
399B HIS* 1.3 67.9 + - + +
401B ALA* 3.5 7.3 + - + +
402B GLN* 3.4 14.7 + - - +
431B LEU* 3.9 31.2 - - + -
446B LEU* 4.1 23.3 - - + -
449B LYS* 4.9 6.3 - - - +
468B ALA* 3.6 28.3 - - + +
469B LEU* 3.7 35.9 - - + -
471B TYR* 5.4 0.4 - - + -
472B GLY* 4.1 4.5 - - - -
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Residues in contact with HIS 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B HIS* 5.5 2.3 - - - -
395B ASP* 2.9 35.2 + - + +
396B VAL* 3.3 12.0 + - + +
397B LEU 3.2 0.6 - - - -
398B LEU* 1.3 79.3 - - + +
400B LYS* 1.3 63.5 + - + +
402B GLN* 3.1 36.7 + - - +
465B HIS* 4.9 15.9 + + - -
469B LEU* 6.5 0.7 - - + -
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Residues in contact with LYS 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B THR 3.6 23.3 - - - +
345B GLY* 4.3 5.8 - - - +
346B ILE 2.7 29.8 + - - +
348B GLY 2.9 24.1 + - - +
349B HIS* 5.5 1.6 + - - +
350B TYR* 4.8 4.0 + - - +
354B GLU* 3.1 20.5 + - - -
357B SER* 3.9 1.6 - - - -
396B VAL* 3.0 20.3 + - + +
397B LEU* 3.2 7.4 + - + +
399B HIS* 1.3 78.9 - - + +
401B ALA* 1.3 57.6 + - - +
402B GLN 3.0 10.4 + - - +
420B PHE* 3.6 17.7 - - - -
423B TYR* 3.3 36.5 - - + +
427B ILE* 4.4 4.3 - - + -
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Residues in contact with ALA 401 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B LEU 2.9 17.3 + - - +
398B LEU* 3.9 10.5 - - + +
399B HIS 3.3 0.4 - - - -
400B LYS* 1.3 77.5 - - - +
402B GLN* 1.3 59.6 + - - +
403B PHE 3.8 0.5 + - - -
420B PHE* 3.8 3.2 - - - -
424B ARG* 3.0 35.6 + - + +
427B ILE* 4.1 17.5 - - + +
468B ALA* 4.4 4.4 - - + +
471B TYR* 4.0 29.2 - - + -
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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