Contacts of the helix formed by residues 424 - 445 (chain A) in PDB entry 1U2Z
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 MET 424 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363A HIS* 6.1 2.7 - - + -
365A LYS* 3.8 29.6 - - + +
370A TYR* 3.8 17.9 - - + +
422A GLU* 2.9 14.7 + - - +
423A ILE* 1.3 71.4 - - + +
425A ASP* 1.3 58.2 + - - +
426A ASP 4.7 1.6 - - - +
427A ALA* 3.9 16.6 - - + +
428A SER* 2.7 36.9 + - - -
801A SAH 3.2 23.1 - - - +
201C SER* 3.7 40.8 - - - +
202C HIS* 4.4 1.1 - - - -
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Residues in contact with ASP 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A ILE 3.5 0.6 + - - -
424A MET* 1.3 72.6 - - - +
426A ASP* 1.3 72.4 + - - +
428A SER* 3.2 3.5 + - - -
429A ASP* 3.0 26.9 + - - +
457A LYS* 3.1 36.7 + - - +
198C TYR* 4.8 4.0 + - - -
201C SER 5.8 0.2 + - - -
202C HIS* 2.8 37.0 + - + +
204C ILE 5.6 1.2 - - - +
206C SER* 5.4 3.6 + - - -
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Residues in contact with ASP 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LYS* 3.6 42.8 - - + +
361A LEU* 4.3 2.7 - - - -
363A HIS* 3.7 23.7 + - + -
424A MET* 4.7 1.8 - - - +
425A ASP* 1.3 81.5 - - - +
427A ALA* 1.3 67.6 + - - +
429A ASP* 3.1 15.3 + - - +
430A LEU* 3.0 27.1 + - + +
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Residues in contact with ALA 427 (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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361A LEU* 3.5 27.0 - - + +
372A TYR* 5.4 3.4 - - + -
401A GLY* 3.5 22.7 - - - +
402A VAL* 3.8 4.8 - - - +
422A GLU* 3.9 15.3 - - + -
424A MET* 3.7 16.1 + - + +
425A ASP 3.4 0.4 - - - -
426A ASP* 1.3 76.6 - - - +
428A SER* 1.3 57.8 + - - +
430A LEU 3.4 0.5 + - - -
431A THR* 2.8 30.7 + - - -
801A SAH 5.7 0.7 - - - +
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Residues in contact with SER 428 (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 GLY 5.0 0.7 - - - -
422A GLU* 3.6 9.0 + - - +
424A MET 2.7 22.9 + - - -
425A ASP 3.5 6.1 - - - -
426A ASP 3.1 0.2 - - - -
427A ALA* 1.3 76.5 - - - +
429A ASP* 1.3 65.7 + - - +
431A THR* 3.3 16.2 + - - -
432A ILE* 3.3 17.7 + - - +
456A LEU* 3.5 18.4 - - - +
457A LYS* 3.1 38.2 + - - -
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Residues in contact with ASP 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A ASP* 3.0 19.9 + - - +
426A ASP* 3.1 15.8 + - - +
428A SER* 1.3 75.5 - - - +
430A LEU* 1.3 65.1 + - + +
432A ILE* 3.2 12.7 + - - +
433A LEU* 3.2 28.1 + - + +
457A LYS* 3.1 28.4 + - - -
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Residues in contact with LEU 430 (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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353A SER 3.6 23.3 - - - +
354A ILE* 3.6 20.5 - - + +
357A GLN* 3.9 46.2 - - + +
360A LYS* 5.1 5.4 - - + -
361A LEU* 3.7 39.0 - - + -
402A VAL* 3.8 4.7 - - + -
426A ASP* 3.0 16.6 + - + +
427A ALA 3.8 4.3 - - - +
429A ASP* 1.3 76.7 - - + +
431A THR* 1.3 59.5 + - - +
433A LEU* 3.3 7.7 + - + +
434A GLN* 2.9 32.7 + - - +
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Residues in contact with THR 431 (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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400A SER* 5.6 0.5 + - - -
401A GLY 3.1 16.6 + - - -
402A VAL* 3.2 19.5 + - - +
403A GLY 3.9 0.2 + - - -
427A ALA 2.8 20.2 + - - -
428A SER* 3.4 11.3 - - - -
429A ASP 3.2 0.2 - - - -
430A LEU* 1.3 78.0 - - - +
432A ILE* 1.3 57.6 + - + +
434A GLN* 3.5 1.6 + - - +
435A TYR* 2.9 28.6 + - + +
454A PHE* 3.6 49.6 - - + -
456A LEU* 4.1 12.5 - - + +
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Residues in contact with ILE 432 (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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428A SER 3.4 13.7 - - - +
429A ASP* 3.2 12.1 + - - +
431A THR* 1.3 76.3 - - + +
433A LEU* 1.3 65.5 + - + +
435A TYR* 3.3 11.8 + - + +
436A GLU* 2.9 40.3 + - + +
454A PHE* 5.7 3.8 - - + -
456A LEU* 3.4 23.3 - - + -
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Residues in contact with LEU 433 (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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210A ILE* 5.9 4.7 - - + +
353A SER* 3.9 17.1 - - - +
357A GLN* 3.6 26.9 - - - +
429A ASP* 3.2 16.2 + - + +
430A LEU* 3.3 20.4 + - + +
432A ILE* 1.3 87.4 - - + +
434A GLN* 1.3 56.6 + - - +
436A GLU* 3.3 7.0 + - + +
437A GLU* 3.0 28.9 + - - +
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Residues in contact with GLN 434 (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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346A LEU* 4.6 3.7 - - - +
349A VAL* 3.6 11.6 - - + +
350A TYR* 3.7 33.3 + - - +
353A SER* 3.2 17.9 + - - +
354A ILE* 3.8 8.6 - - + +
402A VAL* 3.0 29.1 + - - +
403A GLY 4.4 1.8 - - - -
404A ASN* 2.9 29.7 + - - +
407A VAL* 5.1 13.9 - - + +
430A LEU 2.9 17.6 + - - +
431A THR 3.9 2.5 - - - +
433A LEU* 1.3 73.5 - - - +
435A TYR* 1.3 68.4 + - - +
437A GLU 3.3 0.5 + - - -
438A LEU* 2.8 25.0 + - + +
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Residues in contact with TYR 435 (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 VAL* 4.9 4.3 - - + -
431A THR 2.9 20.0 + - - +
432A ILE* 3.6 12.1 - - + +
434A GLN* 1.3 77.9 - - - +
436A GLU* 1.3 71.7 + - - +
438A LEU* 3.2 12.4 + - + +
439A LYS* 3.1 54.4 + - + +
449A LEU* 4.0 17.4 - - + +
450A ASN 5.6 0.3 + - - -
452A VAL* 3.7 48.9 + - + +
454A PHE* 4.6 17.0 - + + -
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Residues in contact with GLU 436 (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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432A ILE* 2.9 30.0 + - + +
433A LEU* 3.6 7.0 - - + +
435A TYR* 1.3 82.5 - - - +
437A GLU* 1.3 63.0 + - - +
439A LYS* 2.8 38.7 + - - +
440A LYS* 3.4 40.7 + - - +
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Residues in contact with GLU 437 (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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208A THR 4.8 0.2 - - - +
209A PRO* 3.6 8.5 - - - +
210A ILE* 3.1 47.0 + - + +
349A VAL* 3.9 28.4 - - + +
352A ARG* 4.1 8.3 - - + +
353A SER* 4.4 6.7 - - - -
433A LEU 3.0 16.1 + - - +
434A GLN 3.8 3.8 - - - +
436A GLU* 1.3 77.1 - - - +
438A LEU* 1.3 62.8 + - - +
440A LYS* 3.2 11.6 + - - +
441A ARG* 2.9 52.4 + - + +
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Residues in contact with LEU 438 (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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345A PHE* 3.7 25.8 - - + -
346A LEU* 4.0 17.5 - - + -
349A VAL* 3.8 16.3 - - + +
407A VAL* 3.5 40.8 - - + -
411A LEU* 4.3 3.6 - - + -
434A GLN* 2.8 19.9 + - + +
435A TYR* 3.2 6.5 + - + +
437A GLU* 1.3 77.0 - - - +
439A LYS* 1.3 58.0 + - - +
441A ARG 3.4 0.7 + - - -
442A CYS* 2.9 34.8 + - - -
449A LEU* 3.8 29.6 - - + -
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Residues in contact with LYS 439 (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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435A TYR* 3.1 49.6 + - + +
436A GLU* 2.8 37.0 + - - +
437A GLU 3.3 0.6 - - - -
438A LEU* 1.3 77.5 - - - +
440A LYS* 1.3 62.9 + - + +
442A CYS* 3.5 6.7 + - - +
443A LYS* 3.2 43.0 + - - +
449A LEU* 4.1 20.6 - - + -
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Residues in contact with LYS 440 (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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205A TYR* 3.1 24.7 + - - +
207A GLY* 5.2 2.5 - - - -
208A THR* 3.0 51.0 + - - +
209A PRO* 3.9 10.8 - - + -
210A ILE* 5.9 2.2 - - - +
436A GLU* 3.4 30.1 - - - +
437A GLU* 3.2 15.5 + - - +
439A LYS* 1.3 75.9 - - + +
441A ARG* 1.3 65.0 + - - +
443A LYS* 3.1 10.6 + - - +
444A LEU 3.0 16.6 + - - -
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Residues in contact with ARG 441 (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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209A PRO* 3.8 16.9 - - + +
210A ILE 2.9 28.3 + - - -
247A TYR* 4.0 3.4 + - - -
249A GLU* 2.9 34.3 + - - -
251A TYR* 5.1 1.6 + - - -
271A LEU* 6.2 1.8 - - - +
345A PHE* 3.5 20.6 - - + -
348A ILE* 4.3 19.6 - - - +
349A VAL* 3.9 15.0 - - + -
352A ARG* 3.6 13.5 - - - +
437A GLU* 2.9 34.3 + - - +
438A LEU 3.9 2.2 - - - +
440A LYS* 1.3 72.3 - - - +
442A CYS* 1.3 66.1 + - - +
444A LEU* 3.1 27.9 + - - +
445A TYR* 3.1 31.5 + - - -
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Residues in contact with CYS 442 (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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345A PHE* 3.8 23.6 - - - -
411A LEU* 4.2 9.9 - - - -
438A LEU* 2.9 32.2 + - - +
439A LYS* 3.7 7.0 - - - +
440A LYS 3.2 0.2 - - - -
441A ARG* 1.3 76.2 - - - +
443A LYS* 1.3 58.1 + - + +
445A TYR* 3.1 3.1 + - - -
446A GLY 3.0 8.8 + - - -
447A MET* 2.9 48.7 + - + +
449A LEU* 4.2 27.4 - - + -
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Residues in contact with LYS 443 (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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198A TYR* 4.0 33.9 - - + +
205A TYR* 4.1 13.1 - - + -
207A GLY* 6.4 1.3 - - - -
244A PHE* 3.7 16.1 - - - -
439A LYS* 3.2 31.9 + - - +
440A LYS* 3.1 13.3 + - - +
442A CYS* 1.3 76.6 - - + +
444A LEU* 1.3 63.9 + - - +
445A TYR 3.0 3.1 + - - -
446A GLY* 3.3 9.4 + - - +
447A MET 5.2 1.6 - - - +
457B LYS* 6.3 4.7 - - - -
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Residues in contact with LEU 444 (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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205A TYR* 3.7 41.7 - - + -
209A PRO* 5.1 1.8 - - + -
241A SER* 4.2 12.7 + - - +
242A ILE* 5.9 0.2 - - - +
243A LEU* 4.0 6.2 - - - +
244A PHE* 3.4 19.6 - - + -
247A TYR* 3.6 45.3 - - + +
440A LYS 3.0 12.1 + - - +
441A ARG* 3.1 29.3 + - - +
443A LYS* 1.3 76.6 - - - +
445A TYR* 1.3 84.3 + - + +
446A GLY 3.6 0.2 - - - -
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Residues in contact with TYR 445 (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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194A PHE* 3.7 13.5 - - - -
199A LEU* 4.7 0.5 - - - +
239A LEU* 5.9 0.2 - - - +
241A SER* 6.1 0.7 - - - -
242A ILE* 4.5 20.0 - - + -
243A LEU* 3.9 15.5 - - - +
271A LEU* 3.9 31.2 - - + +
279A PHE* 3.9 27.9 - + + -
341A PHE* 5.3 3.8 - + - -
345A PHE* 3.5 19.5 - + - -
348A ILE* 5.6 1.7 - - + +
441A ARG* 3.1 30.4 + - - +
442A CYS 3.1 2.0 + - - -
443A LYS 3.0 0.6 - - - -
444A LEU* 1.3 106.2 - - + +
446A GLY* 1.3 60.7 + - - +
447A MET* 3.1 31.0 + - + +
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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
------------------------------------------------------------
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