Contacts of the helix formed by residues 393 - 414 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317H HIS 4.8 0.2 - - - -
328H ALA* 3.4 29.8 - - + -
329H ILE 3.6 6.7 - - - -
330H ALA* 3.6 28.3 - - + -
356H VAL* 3.8 28.7 - - + -
357H ARG 4.3 0.4 - - - -
358H HIS* 3.6 50.0 - + + +
365H ILE* 3.3 21.1 - - + +
391H LYS 4.1 0.4 + - - -
392H HIS* 1.3 71.4 - - - +
394H GLU* 1.3 64.5 + - + +
396H PHE* 2.9 27.6 + + - +
397H LYS* 3.5 31.9 + - + -
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Residues in contact with GLU 394 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392H HIS* 3.2 5.7 + - + -
393H PHE* 1.3 79.2 - - + +
395H SER* 1.3 63.7 + - - +
397H LYS* 2.6 48.0 + - - +
398H ARG* 2.9 58.1 + - - +
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Residues in contact with SER 395 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382H GLU* 4.6 2.6 - - - +
388H ILE* 3.6 24.0 - - - +
389H ASN* 3.1 28.1 + - - +
392H HIS* 2.9 20.4 + - - +
394H GLU* 1.3 78.7 - - - +
396H PHE* 1.3 61.9 + - - +
398H ARG* 3.5 15.8 + - - +
399H ALA* 3.1 22.3 + - - +
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Residues in contact with PHE 396 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330H ALA* 3.3 21.4 - - + +
332H ARG* 3.6 38.6 - - + +
356H VAL* 4.0 12.6 - - + -
365H ILE* 4.0 17.0 - - + -
367H ILE* 4.0 15.3 - - + -
388H ILE* 4.6 10.5 - - + -
389H ASN 5.1 0.2 - - - -
390H MET* 3.8 53.4 - - + -
392H HIS 4.0 6.1 - - - -
393H PHE* 2.9 20.6 + + + +
395H SER* 1.3 77.2 - - - +
397H LYS* 1.3 66.3 + - - +
399H ALA* 3.2 8.2 + - + +
400H ASP* 3.1 24.9 + - - +
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Residues in contact with LYS 397 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317H HIS* 3.5 60.4 + - + +
328H ALA* 5.1 0.7 - - - -
330H ALA* 4.5 0.6 - - + +
393H PHE* 3.5 30.9 + - + +
394H GLU* 2.6 42.3 + - - +
396H PHE* 1.3 77.1 - - - +
398H ARG* 1.3 63.5 + - + +
400H ASP* 3.0 5.7 + - - +
401H ILE* 3.0 27.4 + - + +
484H THR* 5.7 2.4 + - - -
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Residues in contact with ARG 398 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382H GLU* 4.9 1.1 - - - +
394H GLU* 2.9 50.5 + - - +
395H SER* 3.7 13.9 + - - +
397H LYS* 1.3 77.8 - - + +
399H ALA* 1.3 62.6 + - - +
401H ILE* 3.4 11.7 + - + +
402H TYR 3.2 13.9 + - - -
479H GLY* 3.1 32.3 + - - +
480H ALA* 3.6 30.9 + - - +
482H ARG* 2.8 26.3 + - + +
483H LEU 6.1 0.7 - - - +
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Residues in contact with ALA 399 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332H ARG* 6.5 0.7 - - - -
378H TYR 5.0 0.3 - - - +
380H ALA* 4.0 26.5 + - + +
382H GLU* 4.3 4.0 + - - +
383H VAL* 4.5 14.4 - - + -
388H ILE* 4.6 2.9 - - + -
395H SER 3.1 14.7 + - - +
396H PHE* 3.6 12.3 - - + +
397H LYS 3.2 0.2 - - - -
398H ARG* 1.3 76.3 - - - +
400H ASP* 1.3 65.2 + - - +
402H TYR* 3.3 6.1 + - - +
403H ALA* 3.3 18.7 + - - +
482H ARG* 3.9 2.0 - - - +
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Residues in contact with ASP 400 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313H LEU* 3.9 10.5 - - + +
317H HIS* 2.7 30.6 + - + +
330H ALA* 3.5 4.0 - - - -
331H HIS* 2.9 29.7 + - - +
332H ARG* 2.9 28.3 + - - -
333H ASP 4.6 0.3 + - - -
334H LEU* 3.9 8.7 + - + +
396H PHE 3.1 13.4 + - - +
397H LYS 3.0 9.3 + - - +
399H ALA* 1.3 74.3 - - - +
401H ILE* 1.3 55.1 + - - +
403H ALA* 2.9 10.1 + - - +
404H MET* 2.7 33.6 + - - +
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Residues in contact with ILE 401 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313H LEU* 4.2 10.5 - - + -
317H HIS* 4.4 3.6 - - + +
397H LYS* 3.0 18.4 + - + +
398H ARG* 3.5 11.9 - - + +
400H ASP* 1.3 75.3 - - - +
402H TYR* 1.3 63.7 + - - +
404H MET* 3.1 5.7 + - - +
405H GLY 2.9 19.8 + - - -
474H CYS* 3.4 33.8 - - + +
482H ARG* 4.2 7.6 - - + -
483H LEU 3.3 24.7 - - - +
484H THR* 4.1 1.6 - - - -
485H ALA* 3.5 39.9 - - + +
488H ILE* 4.4 6.1 - - + -
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Residues in contact with TYR 402 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377H ARG 4.9 0.2 - - - -
378H TYR 3.6 9.9 - - - -
379H MET 3.3 20.4 + - - -
380H ALA* 3.5 15.9 - - + -
381H PRO* 3.8 21.8 - - + -
398H ARG 3.2 3.4 + - - +
399H ALA 3.6 7.9 - - - +
400H ASP 3.2 0.8 - - - -
401H ILE* 1.3 80.2 - - - +
403H ALA* 1.3 65.3 + - - +
405H GLY* 3.3 2.4 + - - -
406H LEU* 3.3 39.1 + - + +
428H TYR* 2.4 38.2 + - - -
445H VAL* 3.9 9.1 - - + +
451H ARG* 4.2 13.7 - - - -
474H CYS 3.4 23.8 + - - +
475H TRP* 3.7 24.1 + + - -
482H ARG* 3.9 17.3 - - - +
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Residues in contact with ALA 403 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334H LEU* 3.9 30.3 - - + +
378H TYR* 3.8 20.4 - - + +
399H ALA 3.3 7.8 + - - +
400H ASP* 2.9 10.4 + - - +
402H TYR* 1.3 83.7 - - - +
404H MET* 1.3 65.2 + - - +
406H LEU* 3.0 17.8 + - - +
407H VAL* 3.0 17.9 + - - +
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Residues in contact with MET 404 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309H THR* 3.1 43.3 - - + +
310H ALA* 3.1 19.7 - - - -
313H LEU* 3.2 32.8 - - + -
334H LEU* 4.0 12.3 - - + +
400H ASP 2.7 17.0 + - - +
401H ILE* 3.1 11.0 + - - +
403H ALA* 1.3 71.8 - - - +
405H GLY* 1.3 58.3 + - - +
407H VAL* 2.9 11.1 + - + +
408H PHE* 2.8 61.0 + - + -
474H CYS* 5.4 1.3 - - - -
485H ALA* 5.3 2.0 - - + -
488H ILE* 4.4 15.0 - - + -
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Residues in contact with GLY 405 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401H ILE 2.9 13.0 + - - -
402H TYR 3.6 4.5 - - - -
403H ALA 3.1 0.4 - - - -
404H MET* 1.3 78.4 - - - +
406H LEU* 1.3 61.0 + - - +
408H PHE* 3.1 10.9 + - - +
409H TRP 3.0 17.7 + - - -
471H MET* 4.0 4.9 - - - +
474H CYS* 3.8 16.9 - - - -
475H TRP* 3.5 21.5 - - - -
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Residues in contact with LEU 406 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377H ARG 3.6 20.4 - - - +
378H TYR* 3.8 19.1 - - + +
402H TYR* 3.3 38.7 + - + +
403H ALA* 3.0 7.3 + - - +
405H GLY* 1.3 76.3 - - - +
407H VAL* 1.3 63.2 + - - +
409H TRP* 3.0 6.4 + - - +
410H GLU* 3.0 23.4 + - - +
427H PRO* 3.6 21.3 - - + +
428H TYR* 4.1 9.4 - - + +
452H PRO* 3.6 31.0 - - + -
475H TRP* 3.4 21.3 - - + +
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Residues in contact with VAL 407 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288H LEU* 3.7 28.5 - - + -
309H THR* 4.9 4.0 - - + -
334H LEU* 4.8 2.2 - - + -
335H LYS* 4.0 30.7 - - - +
336H SER* 4.0 6.1 - - - +
339H ILE* 3.9 14.6 - - + -
378H TYR* 4.0 6.3 - - + -
403H ALA 3.0 17.5 + - - +
404H MET* 2.9 15.3 + - + +
406H LEU* 1.3 77.6 - - - +
408H PHE* 1.3 65.8 + - + +
410H GLU* 3.0 21.4 + - + +
411H ILE* 3.0 18.7 + - + +
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Residues in contact with PHE 408 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306H ALA* 3.5 39.9 - - + -
309H THR* 4.3 9.2 - - + -
404H MET* 2.8 51.4 + - + -
405H GLY* 3.1 10.5 + - - +
407H VAL* 1.3 77.3 - - + +
409H TRP* 1.3 57.5 + - - +
411H ILE* 3.4 6.1 + - + +
412H ALA* 2.9 31.5 + - - +
467H MET* 3.7 25.1 - - + +
470H ILE* 3.8 20.6 - - + -
471H MET* 4.2 11.2 - - + -
474H CYS* 5.8 0.4 - - - -
488H ILE* 3.6 28.7 - - + -
492H LEU* 3.9 9.9 - - + -
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Residues in contact with TRP 409 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405H GLY 3.0 8.2 + - - +
406H LEU* 3.0 11.1 + - - +
408H PHE* 1.3 77.0 - - - +
410H GLU* 1.3 82.7 + - + +
412H ALA* 3.9 1.6 - - - +
413H ARG* 3.0 59.5 + - - +
425H GLN* 3.5 14.8 - - + -
426H LEU 3.5 17.3 - - - -
427H PRO* 3.7 15.5 - - + -
428H TYR 4.9 0.2 - - - -
429H TYR* 3.7 29.2 - + - -
452H PRO* 3.5 24.8 - - + +
453H ASN* 2.8 33.2 + - + -
458H TRP* 4.0 11.6 - + - -
471H MET* 3.0 37.2 - - + +
475H TRP* 3.9 6.1 - + + -
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Residues in contact with GLU 410 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292H LEU* 4.3 9.2 - - + +
336H SER* 2.2 26.1 + - - +
378H TYR* 2.4 35.8 + - - -
406H LEU 3.0 15.5 + - - +
407H VAL* 3.0 14.4 + - + +
409H TRP* 1.3 81.9 - - + +
411H ILE* 1.3 62.4 + - - +
413H ARG* 3.5 12.9 - - - +
414H ARG* 3.6 13.5 - - - +
424H TYR* 2.3 36.0 + - + -
425H GLN 3.8 14.8 - - - +
427H PRO* 3.8 13.2 - - + -
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Residues in contact with ILE 411 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288H LEU* 3.7 32.1 - - + -
292H LEU* 4.0 14.4 - - + -
297H VAL* 4.0 5.9 - - + +
302H MET* 3.7 34.8 - - + +
305H LEU* 4.0 27.8 - - + +
306H ALA* 4.3 13.7 - - + +
309H THR* 5.1 1.1 - - - +
407H VAL* 3.0 19.4 + - + +
408H PHE* 3.7 12.6 - - + +
409H TRP 3.2 0.2 - - - -
410H GLU* 1.3 74.5 - - - +
412H ALA* 1.3 56.9 + - - +
414H ARG* 2.7 31.2 + - - +
415H CYS 3.4 3.6 + - - -
467H MET* 5.1 1.1 - - + -
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Residues in contact with ALA 412 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302H MET* 3.9 17.7 - - - -
408H PHE 2.9 18.1 + - - +
409H TRP* 4.6 0.2 - - - -
411H ILE* 1.3 76.8 - - - +
413H ARG* 1.3 62.1 + - - +
415H CYS* 2.9 20.7 + - - +
457H ARG* 5.3 0.9 + - - -
458H TRP* 3.5 36.8 + - + -
464H LEU* 4.0 14.8 - - + +
467H MET* 4.8 7.0 - - + -
471H MET* 4.8 2.9 - - - -
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Residues in contact with ARG 413 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B PRO* 6.1 0.8 - - - +
434B SER 5.8 0.6 - - - +
409H TRP* 3.0 57.5 + - + +
410H GLU 3.5 7.6 - - - +
411H ILE 3.1 0.2 - - - -
412H ALA* 1.3 77.2 - - - +
414H ARG* 1.3 59.1 + - + +
415H CYS 3.8 0.9 + - - +
421H HIS* 4.1 1.6 - - - +
422H GLU* 2.9 63.2 + - + +
423H ASP* 2.2 38.7 + - - +
425H GLN* 3.5 23.6 - - - +
429H TYR* 3.1 24.8 + - - -
457H ARG* 5.0 2.9 + - - +
458H TRP* 3.7 13.6 - - + +
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Residues in contact with ARG 414 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292H LEU* 2.7 55.5 + - + -
293H ASN* 3.9 11.1 + - - +
294H ARG 4.5 0.8 + - - -
295H TYR 3.0 27.3 + - - +
296H THR* 3.5 26.0 - - - +
297H VAL* 2.7 33.0 + - + -
410H GLU 3.6 14.6 - - - +
411H ILE 2.7 11.7 + - - +
413H ARG* 1.3 80.1 - - + +
415H CYS* 1.3 63.2 + - - +
416H SER 3.2 0.5 + - - -
421H HIS* 3.7 11.1 + - - -
422H GLU 3.1 25.9 + - - -
423H ASP* 4.1 8.5 + - - +
424H TYR* 3.8 22.8 - - + +
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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