Contacts of the helix formed by residues 395 - 416 (chain A) in PDB entry 2YWB
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 THR 395 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A LEU* 4.2 7.2 - - - -
393A GLU* 3.5 33.6 + - + +
394A VAL* 1.3 78.4 - - - +
396A GLU* 1.3 65.4 + - - +
397A GLU* 3.4 7.6 + - - +
398A ARG* 3.1 35.8 + - - +
399A LEU* 3.1 23.3 + - - +
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Residues in contact with GLU 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A GLY 5.2 1.4 - - - +
275A LEU* 4.0 27.6 - - + +
395A THR* 1.3 74.8 - - - +
397A GLU* 1.3 58.4 + - - +
399A LEU* 3.3 16.0 + - - +
400A GLU* 2.9 28.3 + - + +
403A ARG* 3.1 34.1 + - - -
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Residues in contact with GLU 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A THR* 3.3 7.2 + - - +
396A GLU* 1.3 79.2 - - - +
398A ARG* 1.3 62.4 + - + +
400A GLU* 3.3 8.9 + - + +
401A ILE* 3.1 40.3 + - + +
446A TYR* 4.1 17.0 + - - -
484A GLU* 5.1 5.2 - - - +
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Residues in contact with ARG 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A VAL* 4.0 17.5 - - + +
392A GLY* 4.0 4.0 - - - -
393A GLU* 3.0 46.9 + - - +
395A THR* 3.1 27.8 + - - +
397A GLU* 1.3 72.5 - - + +
399A LEU* 1.3 61.1 + - + +
401A ILE* 3.3 4.5 + - - -
402A LEU* 2.9 32.2 + - - +
429A LEU* 3.5 17.2 - - + +
431A PRO* 3.3 38.8 - - - +
446A TYR* 3.9 24.7 + - + +
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Residues in contact with LEU 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A GLY 3.8 12.6 - - - +
245A LEU* 3.8 24.0 - - + -
275A LEU* 4.6 6.1 - - + -
386A LEU* 3.8 37.7 - - + +
390A VAL* 4.5 6.7 - - + -
394A VAL* 3.8 23.1 - - + -
395A THR 3.1 22.2 + - - +
396A GLU* 3.7 19.5 - - - +
397A GLU 3.3 0.2 - - - -
398A ARG* 1.3 76.2 - - - +
400A GLU* 1.3 57.5 + - - +
402A LEU* 4.0 3.9 - - - +
403A ARG* 2.9 49.2 + - - +
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Residues in contact with GLU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A GLU* 2.9 18.7 + - + +
397A GLU* 3.5 10.7 - - - +
398A ARG 3.2 0.2 - - - -
399A LEU* 1.3 75.9 - - - +
401A ILE* 1.3 69.7 + - - +
403A ARG* 3.6 22.9 - - - +
404A ARG* 2.8 63.9 + - - +
484A GLU* 4.4 1.9 - - - +
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Residues in contact with ILE 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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397A GLU* 3.1 32.1 + - + +
398A ARG* 3.3 6.3 + - - +
400A GLU* 1.3 77.4 - - - +
402A LEU* 1.3 68.3 + - - +
404A ARG* 3.1 24.7 + - - +
405A ALA* 3.1 19.1 + - - +
429A LEU* 4.3 7.0 - - + -
446A TYR* 3.6 32.3 - - + -
482A VAL* 3.8 14.0 - - + +
484A GLU* 3.8 19.7 - - + +
485A ILE* 3.7 30.3 - - + -
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Residues in contact with LEU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386A LEU* 4.0 25.4 - - + -
389A ARG* 3.6 33.9 - - + +
390A VAL* 3.7 16.6 - - + -
398A ARG 2.9 17.2 + - - +
399A LEU 4.0 3.8 - - - +
401A ILE* 1.3 79.6 - - - +
403A ARG* 1.3 56.8 + - - +
405A ALA* 3.1 4.1 + - - -
406A ASP* 2.8 34.8 + - + +
427A ALA* 3.5 24.9 - - + +
429A LEU* 4.1 14.1 - - + +
448A LEU* 3.8 24.0 - - + -
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Residues in contact with ARG 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A GLY 4.0 15.4 + - - -
246A LEU 3.6 16.8 + - - +
247A ARG* 4.5 0.4 - - - +
248A LEU* 3.8 42.3 + - + +
386A LEU* 3.4 22.0 - - + +
396A GLU* 3.1 28.7 + - - -
399A LEU* 2.9 38.9 + - - +
400A GLU* 3.6 24.7 - - - +
401A ILE 3.3 0.2 - - - -
402A LEU* 1.3 75.1 - - - +
404A ARG* 1.3 57.0 + - + +
406A ASP* 3.8 6.4 - - - +
407A ASP* 2.9 31.9 + - - +
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Residues in contact with ARG 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A LEU* 4.6 12.8 - - + -
400A GLU* 2.8 43.9 + - - +
401A ILE* 3.1 12.1 + - - +
403A ARG* 1.3 79.5 - - + +
405A ALA* 1.3 62.2 + - - +
407A ASP* 3.7 5.4 - - - +
408A ILE* 3.1 30.2 + - + +
481A ARG 3.6 21.8 + - - -
482A VAL* 4.0 26.2 - - + +
483A PRO* 4.3 4.2 - - - +
484A GLU* 2.7 41.2 + - - -
118C GLY* 5.8 2.9 - - - -
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Residues in contact with ALA 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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401A ILE 3.1 10.3 + - - +
402A LEU 3.1 7.4 + - - +
404A ARG* 1.3 73.4 - - - +
406A ASP* 1.3 65.7 + - - +
408A ILE* 3.2 7.5 + - - +
409A PHE* 3.0 22.7 + - - +
448A LEU* 3.7 37.2 - - + -
478A ILE* 4.0 19.1 - - + +
482A VAL* 4.3 10.0 - - + +
485A ILE* 4.9 4.9 - - + -
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Residues in contact with ASP 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ARG* 2.3 59.5 + - - +
248A LEU 5.5 0.5 + - - -
386A LEU* 5.0 7.5 - - + +
389A ARG* 4.3 3.1 + - - -
402A LEU* 2.8 26.9 + - + +
403A ARG* 3.8 6.5 - - - +
405A ALA* 1.3 73.1 - - - +
407A ASP* 1.3 60.2 + - - +
409A PHE* 3.1 6.5 + - - +
410A THR* 2.9 30.3 + - - -
426A LEU* 4.5 1.0 - - - -
427A ALA* 4.1 29.5 + - + +
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Residues in contact with ASP 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A LEU* 4.0 27.0 - - + +
403A ARG 2.9 19.9 + - - +
404A ARG* 3.7 5.3 - - - +
406A ASP* 1.3 78.9 + - - +
408A ILE* 1.3 63.4 + - - +
410A THR* 3.7 5.2 + - - +
411A SER* 2.8 31.7 + - - -
117C GLU 3.9 2.4 - - - +
118C GLY* 3.9 0.7 - - - -
119C GLU* 3.2 32.4 + - - +
172C LYS* 2.9 30.2 + - - -
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Residues in contact with ILE 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A ARG* 3.1 17.8 + - + +
405A ALA 3.2 7.4 + - - +
407A ASP* 1.3 76.1 - - - +
409A PHE* 1.3 64.9 + - - +
411A SER* 3.5 4.6 + - - -
412A LEU* 3.0 31.7 + - + +
477A ARG* 3.7 31.0 - - + +
478A ILE* 3.9 17.7 - - + -
481A ARG* 3.5 37.2 - - + -
482A VAL* 4.2 11.4 - - + -
119C GLU* 3.9 26.5 - - + +
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Residues in contact with PHE 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405A ALA 3.0 13.2 + - - +
406A ASP* 3.1 12.1 + - - +
408A ILE* 1.3 78.1 - - - +
410A THR* 1.3 65.2 + - - +
412A LEU* 3.3 6.4 + - - +
413A LEU* 3.0 35.1 + - + +
425A ALA* 3.9 11.9 - - + -
426A LEU* 3.5 41.3 - - - -
427A ALA* 4.7 2.0 - - + -
450A LEU* 3.7 47.6 - - + -
451A ARG 4.3 4.7 - - - -
452A ALA* 4.6 10.8 - - + -
466A LEU* 5.1 3.8 - - + -
470A PHE* 3.9 28.5 - + - -
471A LEU* 5.5 0.9 - - + -
474A ALA* 4.6 3.6 - - + -
478A ILE* 4.7 3.6 - - + -
490A TYR* 5.3 0.9 - + - -
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Residues in contact with THR 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ARG* 3.2 29.2 + - - +
406A ASP* 2.9 14.2 + - - -
407A ASP* 3.9 7.0 - - - +
409A PHE* 1.3 77.9 - - - +
411A SER* 1.3 65.1 + - - +
413A LEU* 3.3 15.0 + - - +
414A ARG* 3.1 51.4 + - - +
419A TYR* 4.1 13.1 - - + -
425A ALA* 5.2 2.9 + - - +
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Residues in contact with SER 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A ASP* 2.8 23.0 + - - -
408A ILE* 3.8 6.1 - - - -
410A THR* 1.3 79.6 - - - +
412A LEU* 1.3 62.5 + - - +
414A ARG* 3.2 4.8 + - - +
415A GLU* 2.9 24.8 + - - +
119C GLU* 4.9 9.9 + - - -
171C PRO* 3.4 29.7 - - - +
172C LYS* 3.6 27.0 - - - +
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Residues in contact with LEU 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408A ILE* 3.0 26.0 + - + +
409A PHE* 3.8 3.4 - - - +
411A SER* 1.3 73.1 - - - +
413A LEU* 1.3 66.2 + - - +
415A GLU* 3.3 17.3 + - - +
416A TRP* 2.8 30.8 + - - +
470A PHE* 3.6 16.6 - - + -
473A GLU* 3.7 17.7 - - - +
474A ALA* 3.7 31.9 - - + +
477A ARG* 2.9 53.4 - - - +
119C GLU* 5.7 1.1 - - - +
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Residues in contact with LEU 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409A PHE* 3.0 31.8 + - + +
410A THR* 3.4 13.9 - - - +
411A SER 3.2 0.2 - - - -
412A LEU* 1.3 78.2 - - - +
414A ARG* 1.3 61.7 + - - +
416A TRP 3.4 0.7 + - - -
417A GLY 3.0 3.1 + - - -
418A LEU* 2.8 52.7 + - + +
419A TYR* 3.7 21.3 - - + +
422A VAL* 5.0 4.7 - - + -
425A ALA* 3.5 32.1 - - + -
466A LEU* 4.5 11.4 - - + -
470A PHE* 3.4 30.3 - - + -
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Residues in contact with ARG 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374A THR* 5.3 5.0 + - - +
377A LEU 5.6 1.2 + - - -
378A ARG* 4.0 23.8 - - - +
410A THR* 3.1 32.4 + - - +
411A SER* 3.2 9.4 + - - +
413A LEU* 1.3 78.3 - - - +
415A GLU* 1.3 62.9 + - - +
417A GLY* 2.9 14.4 + - - +
419A TYR* 3.7 56.6 + - + -
420A GLU* 6.1 0.4 - - - +
168C ALA* 4.5 6.5 - - - +
171C PRO* 4.0 25.6 - - + +
172C LYS* 6.3 0.9 - - - -
456C GLU* 5.2 0.2 - - - +
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Residues in contact with GLU 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A SER 2.9 13.6 + - - +
412A LEU* 3.3 29.1 + - - +
414A ARG* 1.3 77.7 - - - +
416A TRP* 1.3 71.6 + - + +
417A GLY 3.5 0.3 + - - -
473A GLU* 4.9 0.3 - - - +
477A ARG* 4.2 1.4 + - - -
102C LYS* 3.2 12.8 + - - -
121C GLN* 2.8 34.5 + - - +
168C ALA* 3.4 37.3 - - - +
169C HIS* 3.1 33.8 + - + +
171C PRO* 4.1 6.0 - - + +
456C GLU* 4.1 5.7 - - - +
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Residues in contact with TRP 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A LEU* 2.8 29.8 + - - +
413A LEU 4.1 0.4 - - - +
415A GLU* 1.3 95.4 + - + +
417A GLY* 1.3 61.8 + - - +
418A LEU* 3.2 24.1 + - + +
421A LYS* 5.5 1.2 + - - -
467A PRO* 6.3 2.5 - - + -
469A GLU* 2.7 33.7 - - - -
470A PHE* 4.1 18.4 - + + -
473A GLU* 2.7 43.3 + - + -
102C LYS* 5.5 3.8 - - - -
456C GLU* 3.0 20.6 - - - +
465C ARG* 5.8 6.7 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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