Contacts of the helix formed by residues 393 - 414 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D HIS 4.8 0.2 - - - -
328D ALA* 3.4 30.1 - - + -
329D ILE 3.6 7.2 - - - -
330D ALA* 3.6 27.8 - - + -
356D VAL* 3.8 28.3 - - + -
357D ARG 4.3 0.7 - - - -
358D HIS* 3.6 49.1 + + + +
365D ILE* 3.3 21.3 - - + +
392D HIS* 1.3 70.1 - - - +
394D GLU* 1.3 65.3 + - + +
396D PHE* 2.8 28.0 + + - +
397D LYS* 3.4 30.9 + - + -
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Residues in contact with GLU 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392D HIS* 3.2 5.5 + - + +
393D PHE* 1.3 78.5 - - + +
395D SER* 1.3 62.8 + - - +
397D LYS* 2.6 47.6 + - - +
398D ARG* 2.9 58.1 + - - +
484D THR* 5.6 2.1 + - - -
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Residues in contact with SER 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382D GLU* 4.6 3.2 - - - +
388D ILE* 3.6 23.5 - - - +
389D ASN* 3.1 28.5 + - - +
392D HIS* 2.9 19.1 + - - +
394D GLU* 1.3 79.7 - - - +
396D PHE* 1.3 63.1 + - - +
398D ARG* 3.5 15.9 + - - +
399D ALA* 3.1 22.9 + - - +
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Residues in contact with PHE 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D ALA* 3.3 21.3 - - + +
332D ARG* 3.6 40.4 - - + +
356D VAL* 4.0 12.1 - - + -
365D ILE* 4.0 15.9 - - + -
367D ILE* 4.0 14.4 - - + -
388D ILE* 4.7 11.2 - - + -
389D ASN 5.1 0.4 - - - -
390D MET* 3.8 53.4 - - + -
392D HIS 4.0 5.4 - - - -
393D PHE* 2.8 21.6 + + + +
395D SER* 1.3 76.3 - - - +
397D LYS* 1.3 65.1 + - - +
399D ALA* 3.2 8.0 + - + +
400D ASP* 3.1 25.1 + - - +
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Residues in contact with LYS 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317D HIS* 3.5 59.7 + - + +
328D ALA* 5.1 0.9 - - - -
330D ALA* 5.0 0.2 - - - -
393D PHE* 3.4 32.3 + - + +
394D GLU* 2.6 43.4 + - - +
396D PHE* 1.3 76.6 - - - +
398D ARG* 1.3 64.1 + - + +
400D ASP* 3.0 6.1 + - - +
401D ILE* 3.0 27.3 + - + +
484D THR* 5.7 2.8 + - - +
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Residues in contact with ARG 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382D GLU* 4.9 1.6 - - - +
394D GLU* 2.9 48.9 + - - +
395D SER* 3.7 13.5 + - - +
397D LYS* 1.3 77.0 - - + +
399D ALA* 1.3 61.9 + - - +
401D ILE* 3.4 12.3 + - + +
402D TYR 3.2 13.5 + - - -
479D GLY* 3.1 31.4 + - - +
480D ALA* 3.6 31.7 + - - +
482D ARG* 2.8 27.7 + - + +
483D LEU 6.1 0.4 - - - +
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Residues in contact with ALA 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332D ARG* 6.5 0.7 - - - -
378D TYR 5.0 0.3 - - - +
380D ALA* 4.0 27.2 + - + +
382D GLU* 4.3 3.6 + - - +
383D VAL* 4.5 15.0 - - + -
388D ILE* 4.6 2.7 - - + -
395D SER 3.1 14.6 + - - +
396D PHE* 3.6 11.0 - - + +
397D LYS 3.2 0.2 - - - -
398D ARG* 1.3 76.4 - - - +
400D ASP* 1.3 65.9 + - - +
402D TYR* 3.3 6.6 + - - +
403D ALA* 3.3 18.0 + - - +
482D ARG* 3.9 1.5 - - - +
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Residues in contact with ASP 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D LEU* 4.1 9.6 - - + -
317D HIS* 2.7 30.7 + - + +
330D ALA* 3.5 4.0 - - - -
331D HIS* 2.9 30.2 + - - +
332D ARG* 2.9 28.3 + - - -
333D ASP 4.6 0.3 + - - -
334D LEU* 3.9 8.2 - - + +
396D PHE 3.1 13.4 + - - +
397D LYS 3.0 8.4 + - - +
399D ALA* 1.3 75.6 - - - +
401D ILE* 1.3 53.7 + - - +
403D ALA* 2.9 9.7 + - - +
404D MET* 2.7 34.7 + - - +
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Residues in contact with ILE 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D LEU* 4.2 11.0 - - + -
317D HIS* 4.4 3.1 - - + +
397D LYS* 3.0 18.9 + - + +
398D ARG* 3.5 12.1 - - - +
399D ALA 3.3 0.2 - - - -
400D ASP* 1.3 75.1 - - - +
402D TYR* 1.3 64.1 + - - +
404D MET* 3.1 5.6 + - - +
405D GLY 2.9 19.4 + - - -
474D CYS* 3.4 33.2 - - + +
482D ARG* 4.2 7.6 - - + -
483D LEU 3.3 24.9 - - - +
484D THR* 4.1 1.3 - - - -
485D ALA* 3.5 41.1 - - + +
488D ILE* 4.4 5.8 - - + -
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Residues in contact with TYR 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378D TYR 3.6 9.0 - - - -
379D MET 3.3 21.5 + - - -
380D ALA* 3.5 16.2 - - + -
381D PRO* 3.8 20.9 - - + -
398D ARG 3.2 3.2 + - - -
399D ALA 3.6 7.4 - - - +
400D ASP 3.2 0.4 - - - -
401D ILE* 1.3 81.2 - - - +
403D ALA* 1.3 62.7 + - - +
405D GLY* 3.3 2.6 + - - -
406D LEU* 3.3 40.0 + - + +
428D TYR* 2.4 38.5 + - - -
445D VAL* 3.9 9.9 - - + +
451D ARG* 4.2 13.0 - - - -
474D CYS 3.4 23.5 + - - +
475D TRP* 3.7 24.2 + + - -
482D ARG* 4.0 17.3 - - - +
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Residues in contact with ALA 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334D LEU* 3.9 31.2 - - + +
378D TYR* 3.8 21.5 - - + +
399D ALA 3.3 7.6 + - - +
400D ASP* 2.9 10.3 + - - +
402D TYR* 1.3 82.2 - - - +
404D MET* 1.3 66.8 + - - +
406D LEU* 3.0 17.4 + - - +
407D VAL* 3.0 17.7 + - - +
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Residues in contact with MET 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D THR* 3.1 43.3 - - + +
310D ALA* 3.1 19.3 - - - +
313D LEU* 3.2 31.9 - - + -
334D LEU* 4.0 13.4 - - + +
400D ASP 2.7 15.8 + - - +
401D ILE* 3.1 11.4 + - - +
403D ALA* 1.3 71.6 - - - +
405D GLY* 1.3 57.7 + - - +
407D VAL* 2.9 10.1 + - + +
408D PHE* 2.8 61.0 + - + -
474D CYS* 5.4 1.8 - - - -
485D ALA* 5.3 2.2 - - + -
488D ILE* 4.4 14.8 - - + -
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Residues in contact with GLY 405 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401D ILE 2.9 14.1 + - - -
402D TYR 3.6 4.5 - - - -
403D ALA 3.1 0.4 - - - -
404D MET* 1.3 76.9 - - - +
406D LEU* 1.3 61.5 + - - +
408D PHE* 3.1 10.6 + - - +
409D TRP 3.0 17.3 + - - -
471D MET* 4.0 5.2 - - - +
474D CYS* 3.8 17.0 - - - -
475D TRP* 3.5 20.9 - - - -
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Residues in contact with LEU 406 (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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377D ARG 3.6 20.6 - - - +
378D TYR* 3.8 18.8 - - + -
402D TYR* 3.3 37.1 + - + +
403D ALA* 3.0 6.5 + - - +
405D GLY* 1.3 75.1 - - - +
407D VAL* 1.3 63.2 + - - +
409D TRP* 3.0 6.2 + - - +
410D GLU* 3.0 23.9 + - - +
427D PRO* 3.6 22.1 - - + +
428D TYR* 4.1 8.7 - - + +
452D PRO* 3.6 31.2 - - + -
475D TRP* 3.4 21.8 - - + +
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Residues in contact with VAL 407 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D LEU* 3.7 28.9 - - + -
309D THR* 4.9 4.0 - - + -
334D LEU* 4.8 2.5 - - + -
335D LYS* 4.0 29.6 - - - +
336D SER* 4.0 6.1 - - - +
339D ILE* 3.9 15.5 - - + -
378D TYR* 4.0 6.5 - - + -
403D ALA 3.0 17.1 + - - +
404D MET* 2.9 14.7 + - + +
406D LEU* 1.3 77.4 - - - +
408D PHE* 1.3 66.9 + - + +
410D GLU* 3.0 21.8 + - + +
411D ILE* 3.0 18.5 + - + +
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Residues in contact with PHE 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306D ALA* 3.5 38.4 - - + -
309D THR* 4.3 9.6 - - + -
404D MET* 2.8 51.0 + - + -
405D GLY* 3.1 10.7 + - - +
407D VAL* 1.3 77.5 - - + +
409D TRP* 1.3 62.8 + - - +
411D ILE* 3.4 6.6 + - + +
412D ALA* 2.9 26.2 + - - +
467D MET* 3.7 26.3 - - + +
470D ILE* 3.8 21.5 - - + -
471D MET* 4.2 11.4 - - + -
488D ILE* 3.6 26.2 - - + -
492D LEU* 3.9 9.6 - - + -
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Residues in contact with TRP 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405D GLY 3.0 8.8 + - - +
406D LEU* 3.0 10.9 + - - +
408D PHE* 1.3 78.0 - - - +
410D GLU* 1.3 82.7 + - + +
412D ALA* 3.9 1.4 - - - +
413D ARG* 3.0 60.0 + - - +
425D GLN* 3.5 14.6 - - + -
426D LEU 3.5 17.3 - - - -
427D PRO* 3.7 14.6 - - + -
428D TYR 4.9 0.2 - - - -
429D TYR* 3.7 28.3 - + - -
452D PRO* 3.5 24.8 - - + +
453D ASN* 2.8 33.9 + - + -
458D TRP* 4.0 10.4 - + - -
471D MET* 3.0 37.9 - - + +
475D TRP* 3.9 6.5 - + + -
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Residues in contact with GLU 410 (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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292D LEU* 4.3 8.2 - - + +
336D SER* 2.2 25.6 + - - +
378D TYR* 2.4 35.4 + - - -
406D LEU 3.0 14.9 + - - +
407D VAL* 3.0 15.8 + - + +
409D TRP* 1.3 82.7 - - + +
411D ILE* 1.3 64.1 + - - +
413D ARG* 3.5 12.9 - - - +
414D ARG* 3.6 13.7 - - - +
424D TYR* 2.3 35.9 + - + -
425D GLN 3.8 15.0 + - - +
426D LEU* 3.8 0.2 - - - +
427D PRO* 3.8 14.8 - - + -
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Residues in contact with ILE 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288D LEU* 3.7 32.1 - - + -
292D LEU* 4.0 14.4 - - + -
297D VAL* 4.0 6.1 - - + +
302D MET* 3.7 35.7 - - + +
305D LEU* 4.0 26.9 - - + +
306D ALA* 4.3 13.9 - - + +
309D THR* 5.1 0.9 - - - +
407D VAL* 3.0 21.1 + - + +
408D PHE* 3.7 11.9 - - + +
410D GLU* 1.3 74.4 - - - +
412D ALA* 1.3 56.1 + - - +
414D ARG* 2.7 31.2 + - - +
415D CYS 3.4 3.3 + - - -
467D MET* 5.1 1.1 - - + -
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Residues in contact with ALA 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302D MET* 3.9 17.7 - - - -
408D PHE 2.9 18.5 + - - +
411D ILE* 1.3 75.3 - - - +
413D ARG* 1.3 62.9 + - - +
415D CYS* 2.9 20.0 + - - +
457D ARG* 5.3 1.0 + - - -
458D TRP* 3.5 37.9 + - + -
464D LEU* 4.0 14.6 - - + +
467D MET* 4.8 7.0 - - + -
471D MET* 4.8 2.7 - - - -
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Residues in contact with ARG 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409D TRP* 3.0 57.9 + - - +
410D GLU 3.5 8.3 - - - +
412D ALA* 1.3 76.9 - - - +
414D ARG* 1.3 59.3 + - + +
415D CYS 3.4 0.8 + - - -
421D HIS* 4.1 1.4 - - - +
422D GLU* 2.9 62.4 + - + +
423D ASP* 2.2 39.8 + - - +
425D GLN* 3.5 22.6 - - - +
429D TYR* 3.1 25.0 + - - -
457D ARG* 5.0 2.7 + - - +
458D TRP* 3.7 13.6 - - + -
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Residues in contact with ARG 414 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292D LEU* 2.7 55.5 + - + -
293D ASN 3.9 10.9 + - - -
294D ARG 4.5 1.2 + - - -
295D TYR 3.0 25.8 + - - +
296D THR* 3.5 25.3 - - - +
297D VAL* 2.7 33.0 + - + -
410D GLU 3.6 15.5 - - - +
411D ILE 2.7 10.9 + - - +
413D ARG* 1.3 79.4 - - + +
415D CYS* 1.3 62.2 + - - +
416D SER 3.2 1.4 + - - -
421D HIS* 3.7 11.5 + - - -
422D GLU 3.1 26.0 + - - +
423D ASP* 4.1 8.9 + - - +
424D TYR* 3.8 23.3 - - + +
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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