Contacts of the helix formed by residues 419 - 439 (chain A) in PDB entry 1JIQ
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 GLY 419 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A THR* 6.0 0.4 - - - -
415A PRO* 3.5 19.0 + - - +
416A ILE 2.9 9.1 + - - -
418A LYS* 1.3 75.9 - - - +
420A LEU* 1.3 59.4 + - - +
421A HIS 3.4 2.0 - - - -
422A HIS* 3.5 8.7 + - - +
423A LYS* 2.9 30.9 + - - +
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Residues in contact with LEU 420 (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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416A ILE 3.6 1.0 + - - -
417A ARG* 3.1 52.1 + - + +
418A LYS 3.3 1.2 + - - -
419A GLY* 1.3 74.5 - - - +
421A HIS* 1.3 66.6 + - - +
423A LYS* 3.4 22.0 + - + +
424A ILE* 3.2 38.2 + - + +
220B THR* 4.1 15.5 - - + -
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Residues in contact with HIS 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A HIS 5.7 0.9 - - - +
416A ILE* 3.5 24.3 + - + +
417A ARG* 3.6 16.4 - - + +
419A GLY 3.4 0.6 - - - -
420A LEU* 1.3 79.9 - - - +
422A HIS* 1.3 59.0 + - - +
424A ILE* 3.2 4.5 + - - +
425A LEU* 3.0 26.2 + - - +
187B ILE* 2.8 39.0 + - + +
189B GLY* 3.7 17.2 - - - +
192B ILE* 3.9 11.2 - - + -
220B THR* 3.7 20.4 - - + +
221B ASN* 3.2 27.3 + - - -
224B THR* 2.8 26.3 + - - -
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Residues in contact with HIS 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A TYR 5.2 0.2 - - - -
408A ILE* 4.3 9.6 - - + -
409A PRO* 2.9 33.3 + - + -
410A VAL 3.0 21.3 + - - -
411A GLN* 4.7 0.2 - - - -
412A THR* 3.6 43.7 + - + -
414A HIS 5.8 0.4 - - - +
415A PRO* 5.9 0.2 - - + -
419A GLY* 3.5 10.3 + - - +
420A LEU 3.3 0.4 - - - -
421A HIS* 1.3 75.5 - - - +
423A LYS* 1.3 61.3 + - - +
425A LEU* 3.5 28.3 - - + +
426A LEU* 2.8 54.2 + - + +
188B ASP* 4.9 3.4 + - - -
189B GLY 5.7 1.6 - - - +
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Residues in contact with LYS 423 (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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419A GLY 2.9 20.0 + - - +
420A LEU* 3.5 23.8 - - + +
421A HIS 3.2 0.2 - - - -
422A HIS* 1.3 77.5 - - - +
424A ILE* 1.3 58.2 + - + +
426A LEU* 4.6 4.2 - - - +
427A ALA* 3.0 25.6 + - - +
526B GLU* 3.8 32.6 + - + +
527B PRO* 4.7 1.6 - - - +
529B LEU* 3.5 28.9 - - + +
530B ASP* 2.7 41.1 + - - +
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Residues in contact with ILE 424 (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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420A LEU* 3.2 34.6 + - + +
421A HIS 3.2 5.1 + - - +
423A LYS* 1.3 74.9 - - + +
425A LEU* 1.3 65.8 + - - +
427A ALA* 3.3 6.5 + - - +
428A ASN* 2.8 45.0 + - - +
187B ILE* 3.8 28.0 - - + -
216B GLN* 3.9 35.0 - - + +
217B GLU* 4.7 3.6 - - + -
220B THR* 4.0 21.5 - - + +
526B GLU* 4.3 11.7 - - + +
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Residues in contact with LEU 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A TYR* 3.4 41.4 - - + +
384A GLY 4.0 6.7 - - - +
385A THR* 4.2 3.1 - - + -
408A ILE* 4.0 8.1 - - + -
421A HIS 3.0 13.7 + - - +
422A HIS* 3.5 32.3 - - + +
424A ILE* 1.3 77.1 - - - +
426A LEU* 1.3 62.6 + - - +
428A ASN* 3.2 5.7 + - - +
429A PHE* 2.9 22.2 + - - +
186B ASN* 3.8 22.0 - - - +
187B ILE* 3.9 16.3 - - + +
188B ASP* 3.8 26.0 - - + +
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Residues in contact with LEU 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ILE* 3.7 33.4 - - + -
409A PRO 4.4 7.6 - - - +
410A VAL* 4.3 6.7 - - - +
422A HIS* 2.8 45.9 + - + +
423A LYS* 3.7 8.1 - - - +
425A LEU* 1.3 73.1 - - - +
427A ALA* 1.3 63.4 + - - +
429A PHE* 3.2 3.3 + - + +
430A LEU* 2.9 33.9 + - + +
529B LEU* 3.9 12.6 - - + -
549B ILE* 3.7 42.8 - - + -
553B ARG* 6.1 1.6 - - - +
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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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423A LYS 3.0 17.4 + - - +
424A ILE 3.6 5.4 - - - +
425A LEU 3.2 0.2 - - - -
426A LEU* 1.3 75.9 - - - +
428A ASN* 1.3 57.6 + - - +
430A LEU* 3.7 1.7 - - - +
431A ALA* 2.8 32.1 + - - +
522B ALA* 3.9 16.7 - - + +
525B ILE* 4.0 14.7 - - + +
526B GLU* 3.6 35.2 - - + +
529B LEU* 4.0 2.0 - - + +
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Residues in contact with ASN 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A TYR* 4.1 2.7 - - + -
385A THR* 4.1 14.2 - - + +
388A GLN* 2.8 35.9 + - - +
424A ILE* 2.8 44.4 + - - +
425A LEU 3.7 3.8 - - - +
427A ALA* 1.3 75.6 - - - +
429A PHE* 1.3 65.9 + - - +
431A ALA* 4.4 0.9 - - - -
432A GLN* 3.0 32.0 + - - +
216B GLN* 4.8 6.1 - - - +
217B GLU* 4.3 7.6 + - - +
518B GLY 5.0 1.9 - - - +
519B LYS* 5.6 2.1 - - - +
522B ALA* 4.0 21.6 - - - +
526B GLU* 5.0 0.4 + - - -
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Residues in contact with PHE 429 (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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341A TYR* 3.7 28.6 - + + -
406A PHE* 3.5 43.1 - - + -
407A LEU 3.6 15.7 - - - -
408A ILE* 3.6 33.2 - - + -
425A LEU 2.9 13.2 + - - +
426A LEU* 3.2 10.7 + - + +
428A ASN* 1.3 76.7 - - - +
430A LEU* 1.3 83.6 + - + +
433A THR* 3.8 22.2 + - - +
476A SER* 3.9 20.4 - - - -
477A ILE 4.4 0.2 - - - -
478A VAL* 3.8 27.1 - - + -
545B LEU* 4.9 0.9 - - + -
549B ILE* 5.3 1.1 - - + -
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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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57A LYS* 4.1 1.6 + - - -
426A LEU 2.9 21.4 + - - +
427A ALA 3.7 2.9 - - - +
429A PHE* 1.3 89.8 - - + +
431A ALA* 1.3 64.8 + - - +
433A THR* 3.3 8.3 + - - -
434A GLU* 3.1 22.7 + - - +
525B ILE* 3.8 26.2 - - + -
529B LEU* 3.9 12.1 - - + -
542B THR* 4.7 7.6 + - + +
545B LEU* 3.6 37.2 - - + -
546B ILE* 3.6 27.6 - - + +
549B ILE* 4.0 15.7 - - + -
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Residues in contact with ALA 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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427A ALA 2.8 22.1 + - - +
428A ASN* 3.3 2.7 + - - +
430A LEU* 1.3 74.8 - - - +
432A GLN* 1.3 59.8 + - + +
434A GLU* 3.6 4.9 - - - +
435A ALA* 2.8 31.9 + - - +
518B GLY* 3.7 10.0 - - - +
521B LEU* 3.6 8.6 - - + +
522B ALA* 3.2 34.1 - - + +
525B ILE* 3.8 8.7 - - + +
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Residues in contact with GLN 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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341A TYR* 3.7 4.5 - - - +
388A GLN* 3.5 37.2 - - - +
392A TYR* 3.2 17.2 - - + +
396A HIS* 2.8 30.1 + - - -
406A PHE* 3.7 22.2 - - + -
428A ASN* 3.0 21.9 + - - +
429A PHE 4.2 0.2 - - - +
431A ALA* 1.3 76.8 - - + +
433A THR* 1.3 58.0 + - - +
435A ALA* 3.3 2.6 + - - +
436A LEU* 2.9 35.4 + - + +
515B VAL 5.3 2.4 + - - -
518B GLY* 3.6 26.4 + - - -
519B LYS* 4.7 0.8 - - - +
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Residues in contact with THR 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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57A LYS* 2.6 31.2 + - - +
406A PHE* 3.5 39.0 - - + -
429A PHE* 3.8 9.7 + - - +
430A LEU* 3.3 9.1 + - - -
432A GLN* 1.3 72.0 - - - +
434A GLU* 1.3 66.1 + - - +
436A LEU* 3.8 7.5 - - - +
437A MET* 3.0 25.1 + - - +
472A ARG 5.1 0.2 - - - +
474A THR* 3.4 20.4 + - - +
476A SER* 3.6 19.0 + - - +
545B LEU* 4.7 1.7 - - - +
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Residues in contact with GLU 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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57A LYS* 3.4 6.5 - - - +
430A LEU 3.1 14.1 + - - +
431A ALA 3.6 2.7 - - - +
432A GLN 3.2 0.2 - - - -
433A THR* 1.3 82.1 + - - +
435A ALA* 1.3 55.7 + - - +
437A MET* 3.3 3.9 + - - +
438A ARG* 2.8 46.0 + - + +
521B LEU* 3.6 27.5 - - + +
525B ILE* 3.4 23.0 - - - +
538B HIS* 2.7 35.0 + - - +
539B ASP* 3.8 9.0 + - - +
542B THR* 3.5 19.5 - - + +
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Residues in contact with ALA 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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396A HIS* 3.8 17.0 + - + -
431A ALA 2.8 21.4 + - - +
432A GLN 3.7 3.8 - - - +
434A GLU* 1.3 71.1 - - - +
436A LEU* 1.3 60.8 + - - +
438A ARG* 4.5 0.4 - - - +
439A GLY* 2.8 30.7 + - - +
468A PHE* 5.4 0.5 - - - +
470A GLY* 4.6 0.5 - - - -
517B LEU* 3.6 29.2 - - + +
518B GLY* 4.1 9.9 - - - +
521B LEU* 3.6 11.8 - - + +
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Residues in contact with LEU 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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392A TYR* 5.8 2.0 - - + -
395A ILE* 3.6 32.5 - - + -
396A HIS* 3.5 29.6 - - + +
404A CYS* 5.1 2.0 - - - -
406A PHE* 4.0 20.4 - - + -
432A GLN* 2.9 22.1 + - + +
433A THR* 3.8 4.5 - - - +
435A ALA* 1.3 76.4 - - - +
437A MET* 1.3 61.4 + - - +
470A GLY* 3.3 6.7 - - - -
471A ASN 3.3 4.7 + - - -
472A ARG* 3.0 54.4 + - + +
474A THR* 3.7 22.9 - - + -
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Residues in contact with MET 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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26A LEU* 3.5 41.6 - - + +
27A ARG* 3.9 16.3 + - - +
30A PHE* 4.1 15.0 - - + -
57A LYS* 4.1 17.3 - - + -
433A THR 3.0 17.7 + - - +
434A GLU* 3.6 2.2 - - - +
436A LEU* 1.3 77.6 - - - +
438A ARG* 1.3 91.7 + - + +
471A ASN* 3.1 21.7 + - - -
472A ARG 3.9 6.0 + - - +
539B ASP* 3.5 35.2 - - + +
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Residues in contact with ARG 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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27A ARG* 3.0 69.5 + - - +
31A ASP* 4.5 13.3 + - - -
434A GLU* 2.8 38.3 + - + +
435A ALA* 4.5 2.0 - - - +
437A MET* 1.3 101.9 - - + +
439A GLY* 1.3 69.8 + - - +
440A LYS 3.8 0.2 + - - -
444A GLU* 4.4 5.7 + - - -
468A PHE 4.9 0.2 - - - +
469A GLU 5.1 1.7 - - - +
470A GLY* 4.4 2.2 - - - -
521B LEU* 5.3 4.3 - - + -
539B ASP* 4.9 8.1 - - - +
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Residues in contact with GLY 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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27A ARG* 3.2 7.3 + - - -
435A ALA 2.8 23.4 + - - -
437A MET 3.6 1.0 - - - -
438A ARG* 1.3 83.0 - - - +
440A LYS* 1.3 62.7 + - - +
444A GLU* 4.3 0.2 - - - +
468A PHE* 3.4 21.5 - - - -
470A GLY* 3.8 9.8 - - - -
517B LEU* 3.6 13.2 - - - +
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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