Contacts of the helix formed by residues 393 - 414 (chain F) in PDB entry 1B6C
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 393 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317F HIS 4.8 0.2 - - - -
328F ALA* 3.4 29.8 - - + -
329F ILE 3.6 6.7 - - - -
330F ALA* 3.6 27.8 - - + -
356F VAL* 3.8 28.7 - - + -
357F ARG 4.3 0.4 - - - -
358F HIS* 3.6 50.5 - + + +
365F ILE* 3.3 22.6 - - + +
391F LYS 4.1 0.4 + - - -
392F HIS* 1.3 71.2 - - - +
394F GLU* 1.3 64.9 + - + +
396F PHE* 2.8 27.6 + + - +
397F LYS* 3.4 31.0 + - + -
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Residues in contact with GLU 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392F HIS* 3.2 5.9 + - + -
393F PHE* 1.3 79.8 - - + +
395F SER* 1.3 64.8 + - - +
397F LYS* 2.6 48.4 + - - +
398F ARG* 2.9 57.6 + - - +
484F THR* 5.6 1.7 + - - -
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Residues in contact with SER 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382F GLU* 4.6 2.1 - - - +
388F ILE* 3.6 24.7 - - - +
389F ASN* 3.1 28.8 + - - +
392F HIS* 2.9 19.9 + - - +
394F GLU* 1.3 79.3 - - - +
396F PHE* 1.3 61.7 + - - +
398F ARG* 3.5 15.8 + - - +
399F ALA* 3.1 22.3 + - - +
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Residues in contact with PHE 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330F ALA* 3.3 21.3 - - + +
332F ARG* 3.6 40.8 - - + +
356F VAL* 4.0 13.0 - - + -
365F ILE* 4.0 15.9 - - + -
367F ILE* 4.0 15.0 - - + -
388F ILE* 4.7 10.5 - - + -
389F ASN 5.1 0.2 - - - -
390F MET* 3.8 53.2 - - + -
392F HIS 4.0 6.1 - - - -
393F PHE* 2.8 21.8 + + + +
395F SER* 1.3 75.9 - - - +
397F LYS* 1.3 65.5 + - - +
399F ALA* 3.2 8.0 + - + +
400F ASP* 3.1 24.1 + - - +
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Residues in contact with LYS 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317F HIS* 3.5 60.8 + - + +
328F ALA* 5.1 0.9 - - - -
330F ALA* 4.5 0.9 - - + +
393F PHE* 3.4 32.0 + - + +
394F GLU* 2.6 43.7 + - - +
396F PHE* 1.3 77.9 - - - +
398F ARG* 1.3 64.4 + - + +
400F ASP* 3.0 5.5 + - - +
401F ILE* 3.0 27.0 + - + +
484F THR* 5.7 2.2 + - - -
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Residues in contact with ARG 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382F GLU* 4.9 1.1 - - - +
394F GLU* 2.9 51.2 + - - +
395F SER* 3.7 13.0 + - - +
397F LYS* 1.3 76.6 - - + +
399F ALA* 1.3 62.2 + - - +
401F ILE* 3.4 12.3 + - + +
402F TYR 3.2 13.2 + - - -
479F GLY* 3.1 30.8 + - - +
480F ALA* 3.6 31.5 + - - +
482F ARG* 2.8 26.4 + - + +
483F LEU 6.1 0.7 - - - +
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Residues in contact with ALA 399 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332F ARG* 6.5 0.7 - - - -
378F TYR 5.0 0.3 - - - +
380F ALA* 4.0 26.5 + - + +
382F GLU* 4.2 3.8 + - - +
383F VAL* 4.5 14.4 - - + -
388F ILE* 4.6 3.1 - - + -
395F SER 3.1 14.9 + - - +
396F PHE* 3.6 12.1 - - + +
397F LYS 3.2 0.4 - - - -
398F ARG* 1.3 74.4 - - - +
400F ASP* 1.3 64.6 + - - +
402F TYR* 3.3 5.4 + - - +
403F ALA* 3.3 19.1 + - - +
482F ARG* 3.9 1.5 - - - +
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Residues in contact with ASP 400 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313F LEU* 4.1 10.5 - - + -
317F HIS* 2.7 29.9 + - + +
330F ALA* 3.5 4.2 - - - -
331F HIS* 2.9 31.8 + - - +
332F ARG* 2.9 29.0 + - - -
333F ASP 4.6 0.2 + - - -
334F LEU* 3.9 7.9 + - + +
396F PHE 3.1 13.1 + - - +
397F LYS 3.0 9.3 + - - +
399F ALA* 1.3 76.5 - - - +
401F ILE* 1.3 54.4 + - - +
403F ALA* 2.9 9.1 + - - +
404F MET* 2.7 34.5 + - - +
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Residues in contact with ILE 401 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313F LEU* 4.2 10.3 - - + -
317F HIS* 4.4 3.6 - - + +
397F LYS* 3.0 18.4 + - + +
398F ARG* 3.5 11.4 - - + +
399F ALA 3.3 0.2 - - - -
400F ASP* 1.3 76.5 - - - +
402F TYR* 1.3 64.3 + - - +
404F MET* 3.1 5.7 + - - +
405F GLY 2.9 18.9 + - - -
474F CYS* 3.4 34.1 - - + +
482F ARG* 4.2 7.0 - - + -
483F LEU 3.3 24.7 - - - +
484F THR* 4.1 1.3 - - - -
485F ALA* 3.5 40.6 - - + +
488F ILE* 4.4 5.4 - - + -
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Residues in contact with TYR 402 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377F ARG 4.7 0.2 + - - -
378F TYR 3.6 9.2 - - - -
379F MET 3.4 20.3 + - - -
380F ALA* 3.5 16.8 - - + -
381F PRO* 3.8 21.3 - - + -
398F ARG 3.2 3.4 + - - -
399F ALA 3.6 8.3 - - - +
400F ASP 3.2 0.6 - - - -
401F ILE* 1.3 79.8 - - - +
403F ALA* 1.3 65.1 - - - +
405F GLY* 3.3 2.4 + - - -
406F LEU* 3.3 38.5 + - + +
428F TYR* 2.4 38.2 + - - -
441F MET* 5.5 0.2 - - - +
445F VAL* 3.9 9.0 - - - +
451F ARG* 4.2 13.0 - - - -
474F CYS 3.4 23.7 + - - +
475F TRP* 3.7 23.4 + + - -
482F ARG* 3.9 17.0 - - - +
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Residues in contact with ALA 403 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334F LEU* 3.9 31.2 - - + +
378F TYR* 3.8 19.8 - - + +
399F ALA 3.3 7.8 + - - +
400F ASP* 2.9 9.9 + - - +
402F TYR* 1.3 82.4 - - - +
404F MET* 1.3 64.8 + - - +
406F LEU* 3.0 17.5 + - - +
407F VAL* 3.0 17.6 + - - +
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Residues in contact with MET 404 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309F THR* 3.1 43.5 - - + +
310F ALA* 3.1 19.7 - - - -
313F LEU* 3.2 32.5 - - + -
334F LEU* 4.0 13.4 - - + +
400F ASP 2.7 16.2 + - - +
401F ILE* 3.1 10.7 + - + +
403F ALA* 1.3 72.7 - - - +
405F GLY* 1.3 59.1 + - - +
407F VAL* 2.9 9.6 + - + +
408F PHE* 2.8 59.7 + - + -
474F CYS* 5.5 1.6 - - - -
485F ALA* 5.3 2.2 - - + -
488F ILE* 4.4 15.5 - - + -
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Residues in contact with GLY 405 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401F ILE 2.9 13.0 + - - -
402F TYR 3.6 5.2 - - - -
403F ALA 3.1 0.4 - - - -
404F MET* 1.3 77.5 - - - +
406F LEU* 1.3 61.9 + - - +
408F PHE* 3.1 10.8 + - - +
409F TRP 3.0 16.6 + - - -
471F MET* 4.0 5.4 - - - +
474F CYS* 3.8 17.4 - - - -
475F TRP* 3.5 21.4 - - - -
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Residues in contact with LEU 406 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377F ARG 3.6 20.9 - - - +
378F TYR* 3.8 18.6 - - + +
402F TYR* 3.3 38.2 + - + +
403F ALA* 3.0 7.2 + - - +
405F GLY* 1.3 75.5 - - - +
407F VAL* 1.3 63.0 + - - +
409F TRP* 3.0 6.4 + - - +
410F GLU* 3.0 23.7 + - - +
427F PRO* 3.6 22.4 - - + +
428F TYR* 4.1 9.0 - - + +
452F PRO* 3.6 31.4 - - + -
475F TRP* 3.4 22.6 - - + +
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Residues in contact with VAL 407 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288F LEU* 3.7 29.2 - - + -
309F THR* 4.9 3.6 - - + -
334F LEU* 4.8 2.0 - - + -
335F LYS* 4.0 31.0 - - - +
336F SER* 4.0 6.3 - - - +
339F ILE* 3.9 14.6 - - + -
378F TYR* 4.0 6.7 - - + -
403F ALA 3.0 17.7 + - - +
404F MET* 2.9 14.0 + - + +
406F LEU* 1.3 76.8 - - - +
408F PHE* 1.3 66.1 + - + +
410F GLU* 3.0 22.1 + - + +
411F ILE* 3.0 19.0 + - + +
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Residues in contact with PHE 408 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306F ALA* 3.5 38.1 - - + -
309F THR* 4.3 9.0 - - + -
310F ALA* 4.4 0.4 - - + -
404F MET* 2.8 49.7 + - + -
405F GLY* 3.5 10.3 - - - +
407F VAL* 1.3 78.5 - - + +
409F TRP* 1.3 61.8 + - - +
411F ILE* 3.4 6.0 + - + +
412F ALA* 2.9 26.7 + - - +
467F MET* 3.7 24.2 - - + +
470F ILE* 3.8 21.1 - - + -
471F MET* 4.2 12.1 - - + -
488F ILE* 3.6 28.0 - - + -
492F LEU* 3.9 9.6 - - + -
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Residues in contact with TRP 409 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405F GLY 3.0 8.0 + - - +
406F LEU* 3.0 11.6 + - - +
408F PHE* 1.3 78.8 - - - +
410F GLU* 1.3 81.2 + - + +
412F ALA* 3.3 1.4 + - - +
413F ARG* 3.0 60.7 + - - +
425F GLN* 3.5 15.5 - - + -
426F LEU 3.5 17.0 - - - -
427F PRO* 3.7 14.8 - - + -
428F TYR 4.9 0.7 - - - -
429F TYR* 3.7 28.0 - + - -
452F PRO* 3.5 25.7 - - + +
453F ASN* 2.8 32.4 + - + -
458F TRP* 4.0 10.4 - + - -
471F MET* 3.0 37.2 - - + +
475F TRP* 3.9 6.7 - + + -
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Residues in contact with GLU 410 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F LEU* 4.3 9.0 - - + +
336F SER* 2.2 26.3 + - - +
378F TYR* 2.4 36.3 + - - -
406F LEU 3.0 15.7 + - - +
407F VAL* 3.0 14.3 + - + +
409F TRP* 1.3 82.8 - - + +
411F ILE* 1.3 63.7 + - - +
413F ARG* 3.5 13.1 - - - +
414F ARG* 3.6 13.2 - - - +
424F TYR* 2.3 36.2 + - + -
425F GLN 3.8 14.3 + - - +
427F PRO* 3.8 13.9 - - + -
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Residues in contact with ILE 411 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288F LEU* 3.7 32.3 - - + -
292F LEU* 4.0 15.3 - - + -
297F VAL* 4.0 5.3 - - + +
302F MET* 3.7 35.0 - - + +
305F LEU* 4.0 28.5 - - + +
306F ALA* 4.3 12.6 - - + +
309F THR* 5.1 1.3 - - - +
407F VAL* 3.0 20.3 + - + +
408F PHE* 3.7 12.1 - - + +
410F GLU* 1.3 74.5 - - - +
412F ALA* 1.3 57.4 + - - +
414F ARG* 2.7 30.8 + - - +
415F CYS 3.4 3.6 + - - -
467F MET* 5.1 1.3 - - + -
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Residues in contact with ALA 412 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302F MET* 3.9 17.0 - - - -
408F PHE 2.9 18.3 + - - +
409F TRP* 4.6 0.2 - - - -
411F ILE* 1.3 76.8 - - - +
413F ARG* 1.3 63.2 + - - +
415F CYS* 2.9 19.9 + - - +
457F ARG* 5.3 1.0 + - - -
458F TRP* 3.5 37.4 + - + -
464F LEU* 4.0 14.2 - - + +
467F MET* 4.8 7.4 - - + -
471F MET* 4.8 2.5 - - - -
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Residues in contact with ARG 413 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409F TRP* 3.0 57.1 + - - +
410F GLU 3.5 8.3 - - - +
412F ALA* 1.3 77.8 - - - +
414F ARG* 1.3 58.9 + - + +
415F CYS 3.8 0.3 + - - +
421F HIS* 4.1 1.7 - - - +
422F GLU* 2.9 63.2 + - + +
423F ASP* 2.2 39.0 + - - +
424F TYR* 6.1 0.2 - - - -
425F GLN* 3.5 24.3 - - - +
429F TYR* 3.1 25.6 + - - -
457F ARG* 5.0 2.7 + - - +
458F TRP* 3.7 14.1 - - + -
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Residues in contact with ARG 414 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292F LEU* 2.7 56.2 + - + -
293F ASN* 3.9 11.7 + - - +
294F ARG 4.5 1.4 + - - -
295F TYR 3.0 26.2 + - - +
296F THR* 3.5 25.4 - - - +
297F VAL* 2.7 33.1 + - + -
410F GLU 3.6 15.0 - - - +
411F ILE 2.7 10.5 + - - +
413F ARG* 1.3 80.1 - - + +
415F CYS* 1.3 61.7 + - - +
416F SER 3.2 1.0 + - - -
421F HIS* 3.7 11.0 + - - -
422F GLU 3.1 26.1 + - - -
423F ASP* 4.1 8.9 + - - +
424F TYR* 3.8 21.5 - - + +
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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