Contacts of the helix formed by residues 404 - 426 (chain T) in PDB entry 4UJ3
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 SER 404 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379T CYS* 3.6 20.9 - - - -
382T THR* 4.4 4.4 + - - -
384T GLN* 6.2 2.2 - - - -
386T LYS* 4.9 13.9 - - - -
388T CYS* 3.5 9.8 - - - -
390T HIS* 6.0 0.2 - - - -
403T ILE* 1.3 87.1 - - - +
405T PRO* 1.3 77.8 - - - +
406T PHE* 3.6 10.3 + - - +
407T CYS* 3.0 35.2 + - - -
408T ARG* 3.2 3.2 + - - +
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Residues in contact with PRO 405 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386T LYS* 4.9 13.5 - - + -
387T SER* 3.6 21.8 - - - +
388T CYS* 5.0 0.2 - - - -
389T LYS* 5.6 6.0 - - + +
390T HIS* 5.4 7.4 - - + +
403T ILE 4.5 0.2 - - - +
404T SER* 1.3 90.0 - - - +
406T PHE* 1.3 62.2 + - + +
408T ARG* 3.4 9.2 + - + +
409T TYR* 3.4 17.5 + - - +
456T PHE* 4.0 16.6 - - + -
457T LYS 5.0 2.1 - - - +
458T GLU* 3.8 40.1 - - + +
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Residues in contact with PHE 406 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335T PHE* 4.8 1.8 - + - -
382T THR* 5.4 8.7 - - + -
386T LYS* 6.3 2.5 - - + -
404T SER* 3.1 10.3 - - - +
405T PRO* 1.3 83.0 - - + +
407T CYS* 1.3 68.8 + - - +
408T ARG 3.4 0.2 + - - -
409T TYR* 3.4 5.0 + - - +
410T ARG* 3.1 65.8 + - + +
451T ALA 3.9 7.6 - - - -
452T LYS 5.5 0.7 - - - -
453T LEU 5.5 0.2 - - - -
454T GLY* 3.4 33.2 - - - -
456T PHE* 3.8 36.7 - + + -
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Residues in contact with CYS 407 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335T PHE* 3.4 32.8 - - - -
379T CYS* 3.6 22.9 - - - -
381T LEU* 3.7 17.9 - - + -
382T THR* 4.2 5.8 - - - -
403T ILE* 3.1 23.6 - - + -
404T SER* 3.0 15.5 + - - +
406T PHE* 1.3 80.6 - - - +
408T ARG* 1.3 56.1 + - - +
410T ARG* 3.1 2.8 + - - +
411T ILE* 2.8 34.3 + - - +
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Residues in contact with ARG 408 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130S HIS 3.8 19.2 + - - -
131S LEU* 4.7 15.0 + - - +
132S ARG 5.7 1.4 + - - -
355T ILE* 4.1 14.0 - - + +
390T HIS* 3.4 51.2 + - + +
392T ILE* 5.7 0.4 - - + -
403T ILE* 3.7 8.9 - - + +
404T SER 3.2 8.8 + - - +
405T PRO* 3.8 10.5 + - + +
406T PHE 3.3 0.2 - - - -
407T CYS* 1.3 78.8 - - - +
409T TYR* 1.3 59.9 + - - +
411T ILE* 4.5 4.5 - - - -
412T THR* 2.7 62.9 + - + +
457T LYS 5.7 4.2 + - - -
459T GLU* 3.7 30.0 + - - +
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Residues in contact with TYR 409 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405T PRO 3.4 8.7 + - - +
406T PHE 3.8 4.7 - - - +
407T CYS 3.3 0.6 - - - -
408T ARG* 1.3 84.7 - - - +
410T ARG* 1.3 57.6 + - - +
412T THR* 3.5 8.0 + - - -
413T SER* 2.5 45.4 + - - -
447T GLU* 2.3 41.8 + - - +
450T LEU* 5.2 5.6 - - + +
451T ALA* 3.7 22.9 - - + -
455T TYR 3.4 8.3 - - - -
456T PHE* 3.0 46.4 - - + -
457T LYS* 3.7 31.6 - - + +
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Residues in contact with ARG 410 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331T PRO 2.7 29.7 + - - -
332T CYS* 3.1 32.3 + - - +
333T LEU* 5.0 0.4 - - - -
334T THR* 3.7 18.4 + - - -
335T PHE* 3.7 17.8 - - + -
382T THR* 5.4 1.0 - - - +
406T PHE* 3.1 53.3 + - + +
407T CYS 3.1 7.5 + - - +
409T TYR* 1.3 79.0 - - + +
411T ILE* 1.3 59.9 + - - +
413T SER* 3.6 1.9 - - - -
414T VAL* 3.0 30.7 + - - +
451T ALA* 3.9 30.8 + - + +
452T LYS 3.9 15.2 + - - -
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Residues in contact with ILE 411 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333T LEU* 4.4 18.4 - - + -
335T PHE* 4.6 3.8 - - + -
344T VAL* 4.2 19.1 - - + -
348T VAL* 4.9 2.0 - - + -
353T LEU* 3.5 31.4 - - + -
355T ILE* 4.1 10.1 - - + -
381T LEU* 3.5 32.1 - - + -
392T ILE* 4.4 19.5 - - + -
403T ILE* 5.1 0.2 - - + -
407T CYS* 2.8 22.9 + - + +
408T ARG* 3.9 4.0 - - - +
410T ARG* 1.3 75.3 - - - +
412T THR* 1.3 60.9 + - - +
414T VAL* 3.1 5.0 + - - +
415T CYS* 2.9 28.5 + - - -
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Residues in contact with THR 412 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130S HIS* 3.7 22.4 - - + +
131S LEU* 4.6 7.0 - - + -
355T ILE* 3.5 24.9 - - + -
408T ARG* 2.7 53.2 + - + +
409T TYR* 3.5 13.3 + - - -
411T ILE* 1.3 72.5 - - - +
413T SER* 1.3 53.7 + - - +
415T CYS* 3.2 9.8 + - - +
416T ASN* 2.8 43.4 + - - +
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Residues in contact with SER 413 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409T TYR* 2.5 52.0 + - - -
410T ARG* 3.6 7.2 - - - -
412T THR* 1.3 79.7 + - - +
414T VAL* 1.3 59.5 + - - +
416T ASN* 3.6 12.2 + - - +
417T PHE* 3.4 14.7 + - - +
444T LEU* 4.7 4.5 - - - +
447T GLU* 4.3 10.4 + - - +
448T MET* 3.8 33.5 - - - +
451T ALA* 4.3 1.0 - - - +
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Residues in contact with VAL 414 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329T ILE* 3.7 30.7 - - + +
332T CYS* 3.6 30.1 - - + -
333T LEU* 4.1 16.4 - - + -
348T VAL* 4.3 9.2 - - + -
410T ARG 3.0 17.0 - - - +
411T ILE 3.1 7.1 + - - +
413T SER* 1.3 75.2 - - - +
415T CYS* 1.3 65.2 + - - +
417T PHE* 3.1 12.0 + - - +
418T PHE* 3.2 28.4 + - + -
448T MET* 4.0 12.1 - - + -
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Residues in contact with CYS 415 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130S HIS* 3.4 40.0 - - + +
348T VAL* 3.8 23.8 - - - -
353T LEU* 3.7 31.2 - - - -
411T ILE* 2.9 23.3 + - - +
412T THR 3.5 2.7 - - - +
414T VAL* 1.3 77.4 - - - +
416T ASN* 1.3 55.5 + - - +
418T PHE* 3.4 2.3 + - - +
419T THR* 2.8 30.3 + - - -
422T ARG* 5.0 0.9 + - - -
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Residues in contact with ASN 416 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130S HIS* 2.9 21.7 + - - -
131S LEU* 4.1 15.1 - - - +
412T THR* 2.8 27.6 + - - +
413T SER* 3.6 10.8 - - - +
414T VAL 3.2 0.2 - - - -
415T CYS* 1.3 74.3 - - - +
417T PHE* 1.3 65.6 + - - +
419T THR* 3.0 26.4 - - + +
420T TYR* 3.1 5.9 + - - +
444T LEU* 3.6 21.3 - - + +
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Residues in contact with PHE 417 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321T LEU* 3.9 16.4 - - + -
324T ILE* 3.3 44.0 - - + -
329T ILE* 4.2 13.7 - - + -
413T SER 3.4 3.9 + - - +
414T VAL 3.1 8.3 + - - +
416T ASN* 1.3 78.2 - - - +
418T PHE* 1.3 78.2 + + - +
420T TYR* 3.2 4.4 + - + +
421T ILE* 2.9 64.6 + - + +
441T VAL* 4.2 11.4 - - + -
444T LEU* 3.6 24.6 - - + +
445T ARG* 4.9 1.6 - - + -
448T MET* 4.0 29.2 - - + -
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Residues in contact with PHE 418 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314T MET* 3.8 29.2 - - + -
316T ARG* 5.6 0.2 - - - -
321T LEU* 5.5 3.4 - - + -
325T TYR* 3.0 40.8 - + - -
329T ILE* 3.4 26.5 - - + -
348T VAL* 3.6 36.1 - - + +
349T GLU* 4.1 16.6 - - + -
414T VAL* 3.2 23.7 + - + +
415T CYS 3.8 5.6 - - - +
417T PHE* 1.3 86.0 - + - +
419T THR* 1.3 61.7 + - - +
421T ILE* 3.5 5.0 - - + +
422T ARG* 2.8 42.7 + - + +
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Residues in contact with THR 419 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128S LEU* 4.6 9.7 - - + +
130S HIS* 4.1 12.2 - - + -
415T CYS 2.8 16.5 + - - -
416T ASN* 3.0 24.9 - - + +
417T PHE 3.3 0.2 - - - -
418T PHE* 1.3 77.9 - - - +
420T TYR* 1.3 66.3 + - + +
422T ARG* 2.8 28.7 + - - +
423T TYR* 3.2 48.4 + - + +
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Residues in contact with TYR 420 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38S LEU* 5.6 3.1 - - + -
416T ASN 3.1 12.9 + - - +
417T PHE 3.8 2.9 - - - +
419T THR* 1.3 83.3 - - + +
421T ILE* 1.3 68.8 + - + +
423T TYR* 3.1 26.3 + + + +
424T ILE* 3.1 38.7 + - + +
429T VAL* 4.3 13.4 - - + +
432T GLN* 2.7 30.1 + - - -
437T MET* 3.5 24.0 - - - +
440T GLU* 3.3 43.2 - - + +
441T VAL* 4.3 9.2 - - + -
444T LEU* 4.3 13.9 - - + -
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Residues in contact with ILE 421 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308T TRP* 3.7 26.2 - - + -
314T MET* 3.5 28.5 - - + -
320T PHE* 3.6 30.7 - - + -
321T LEU* 4.8 7.2 - - + -
417T PHE* 2.9 50.9 + - + +
418T PHE* 3.5 7.4 - - + +
420T TYR* 1.3 79.0 - - + +
422T ARG* 1.3 61.9 + - - +
424T ILE* 3.2 12.5 + - + +
425T GLN* 3.1 19.6 + - - +
441T VAL* 5.1 6.7 - - + -
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Residues in contact with ARG 422 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127S ASP 5.6 2.2 + - - -
130S HIS* 5.4 3.0 - - - -
314T MET* 4.1 22.9 - - + -
348T VAL 5.6 1.6 + - - -
349T GLU 5.8 3.1 - - - -
351T ASN* 3.6 44.6 + - - +
415T CYS 5.0 0.8 + - - -
418T PHE* 2.8 21.9 + - + +
419T THR* 2.8 40.3 + - - +
421T ILE* 1.3 76.7 - - - +
423T TYR* 1.3 72.0 + - - +
425T GLN* 3.0 10.7 + - - +
426T GLN* 2.8 53.3 + - - +
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Residues in contact with TYR 423 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38S LEU* 4.0 27.6 - - + -
127S ASP* 3.8 6.6 + - - -
128S LEU* 3.8 9.8 - - + +
156S LEU* 3.4 38.8 - - + +
200S GNP 3.6 12.8 + - - -
419T THR* 3.2 29.8 + - + -
420T TYR* 3.1 23.7 + + + +
422T ARG* 1.3 95.2 - - - +
424T ILE* 1.3 59.1 + - - +
426T GLN* 3.7 8.2 + - - +
427T GLY 3.5 1.4 + - - -
428T LEU* 2.9 43.3 + - + +
429T VAL* 3.8 14.1 + - + -
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Residues in contact with ILE 424 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305T PHE* 4.4 14.8 - - + -
308T TRP* 4.0 27.1 - - + -
309T LYS* 4.6 14.4 - - + +
312T PRO* 4.2 13.2 - - + +
420T TYR* 3.1 39.9 + - + +
421T ILE* 3.6 9.4 - - + +
422T ARG 3.1 0.2 - - - -
423T TYR* 1.3 75.7 - - - +
425T GLN* 1.3 67.2 + - - +
427T GLY* 3.1 14.0 + - - -
429T VAL* 4.4 7.0 - - + -
437T MET* 3.2 35.2 - - + -
441T VAL* 5.0 1.3 - - + -
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Residues in contact with GLN 425 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308T TRP* 5.1 1.6 - - + -
312T PRO* 3.7 38.5 + - + +
313T THR* 4.9 1.6 - - - +
314T MET* 4.7 23.0 - - + +
421T ILE 3.1 12.1 + - - +
422T ARG* 3.0 12.1 + - - +
424T ILE* 1.3 78.1 - - - +
426T GLN* 1.3 77.5 + - - +
427T GLY 3.3 2.5 + - - -
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Residues in contact with GLN 426 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156S LEU* 5.5 9.1 - - - +
422T ARG* 2.8 47.9 + - - +
423T TYR* 4.5 9.8 - - - +
424T ILE 3.2 0.4 - - - -
425T GLN* 1.3 92.0 - - - +
427T GLY* 1.3 62.4 + - - +
428T LEU* 3.2 8.5 + - + +
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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