Contacts of the helix formed by residues 418 - 438 (chain A) in PDB entry 1U0E
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 418 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A PRO* 3.6 17.5 + - - +
415A ILE 2.9 9.6 + - - -
417A LYS* 1.3 76.9 - - - +
419A LEU* 1.3 57.8 + - - +
420A HIS 3.4 2.5 - - - -
421A HIS* 3.3 4.6 + - - -
422A LYS* 2.9 28.0 + - - +
1211A BME 3.2 25.5 - - - -
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Residues in contact with LEU 419 (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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415A ILE 3.5 1.6 + - - -
416A ARG* 3.1 58.8 + - + +
417A LYS 3.4 1.0 + - - -
418A GLY* 1.3 77.0 - - - +
420A HIS* 1.3 64.2 + - - +
422A LYS* 3.4 29.0 + - - +
423A ILE* 3.2 46.2 + - + +
219B THR* 4.0 14.1 - - + +
525B GLU* 4.6 4.0 - - - +
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Residues in contact with HIS 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A HIS 5.8 0.9 - - - +
415A ILE* 3.6 20.8 + - + +
416A ARG* 3.7 15.7 - - + -
418A GLY 3.4 0.4 - - - -
419A LEU* 1.3 79.9 - - + +
421A HIS* 1.3 58.2 + - - +
423A ILE* 3.3 4.0 + - - +
424A LEU* 2.9 27.1 + - - +
186B ILE* 2.8 39.5 + - + +
188B GLY* 3.6 20.8 - - - +
191B ILE* 3.9 12.6 - - + -
219B THR* 3.8 20.8 - - + +
220B ASN* 3.2 26.4 + - - -
223B THR* 2.7 26.8 + - - -
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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
----------------------------------------------------------
341A ASP* 6.1 0.2 - - - -
407A ILE* 4.4 8.1 - - + -
408A PRO* 2.9 32.8 + - + -
409A VAL 2.9 21.4 + - - -
411A THR* 3.6 44.3 + - + -
413A HIS 5.9 0.2 - - - +
418A GLY* 3.3 4.2 + - - +
420A HIS* 1.3 76.8 - - - +
422A LYS* 1.3 61.2 + - - +
424A LEU* 3.6 29.1 - - + +
425A LEU* 2.8 52.3 + - + +
1211A BME 3.8 17.3 - - - -
187B ASP* 5.0 2.5 + - - -
188B GLY 5.1 1.5 + - - +
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Residues in contact with LYS 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A GLY 2.9 17.9 + - - +
419A LEU* 3.6 26.3 - - - +
420A HIS 3.3 0.2 - - - -
421A HIS* 1.3 76.6 - - - +
423A ILE* 1.3 55.7 + - - +
425A LEU* 4.5 0.2 - - - -
426A ALA* 3.0 25.6 + - - +
1211A BME 3.9 20.3 - - + -
525B GLU* 3.6 50.3 + - + +
528B LEU* 3.4 21.2 - - + +
529B GLU* 4.2 30.3 + - + +
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Residues in contact with ILE 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 LEU* 3.2 34.2 + - + +
420A HIS 3.6 6.1 - - - +
422A LYS* 1.3 73.9 - - - +
424A LEU* 1.3 61.6 + - - +
426A ALA* 3.2 7.0 + - + +
427A ASN* 2.8 46.0 + - - +
186B ILE* 3.7 22.9 - - + -
215B GLN* 3.7 33.0 - - + +
216B GLU* 5.2 3.4 - - + -
219B THR* 4.0 23.8 - - + +
525B GLU* 3.9 21.8 - - + +
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Residues in contact with LEU 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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340A TYR* 3.3 42.6 - - + +
383A GLY 3.9 7.2 - - - +
384A THR* 4.0 2.9 - - + -
407A ILE* 3.9 8.5 - - + -
420A HIS 2.9 17.8 + - - +
421A HIS* 3.3 30.9 + - + +
423A ILE* 1.3 75.0 - - - +
425A LEU* 1.3 62.4 + - - +
427A ASN* 3.3 5.6 + - - +
428A PHE* 2.9 22.3 + - - +
185B ASN* 3.8 22.0 - - - +
186B ILE* 3.9 16.3 - - + +
187B ASP* 3.8 23.6 - - + -
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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
----------------------------------------------------------
407A ILE* 3.7 33.4 - - + -
408A PRO 4.4 7.2 - - - +
409A VAL* 4.2 6.1 - - - +
421A HIS* 2.8 43.4 + - + +
422A LYS 3.7 3.6 - - - +
424A LEU* 1.3 72.4 - - - +
426A ALA* 1.3 58.7 + - - +
428A PHE* 3.2 3.2 + - + +
429A LEU* 2.9 39.4 + - + +
1211A BME 3.7 27.6 - - - +
528B LEU* 3.9 9.6 - - + -
548B ILE* 3.7 35.9 - - + -
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Residues in contact with ALA 426 (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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422A LYS 3.0 14.5 + - - +
423A ILE* 3.2 9.8 + - - +
425A LEU* 1.3 76.9 - - - +
427A ASN* 1.3 58.6 + - - +
429A LEU* 3.8 1.6 - - - +
430A ALA* 2.8 31.7 + - - +
521B ALA* 3.8 25.7 - - + +
524B ILE* 3.9 14.8 - - + +
525B GLU* 3.9 22.2 - - + +
528B LEU* 3.9 1.3 - - + +
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Residues in contact with ASN 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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340A TYR* 4.0 2.5 - - - -
384A THR* 4.0 15.3 - - + +
387A GLN* 2.9 34.7 - - - +
423A ILE* 2.8 42.6 + - - +
424A LEU 3.6 6.5 - - - +
426A ALA* 1.3 76.0 - - - +
428A PHE* 1.3 65.4 + - - +
430A ALA* 4.4 0.7 - - - +
431A GLN* 3.0 33.7 + - - +
186B ILE* 5.1 0.2 - - - +
215B GLN* 4.9 4.2 + - - -
216B GLU* 4.5 7.3 + - - +
517B GLY 5.0 1.4 - - - +
518B LYS* 5.6 1.9 - - - +
521B ALA* 3.8 21.5 - - - +
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Residues in contact with PHE 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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340A TYR* 3.7 27.4 - + + -
405A PHE* 3.4 47.3 - - + -
406A LEU 3.5 14.6 - - - -
407A ILE* 3.6 28.3 - - + -
424A LEU 2.9 13.6 + - - +
425A LEU* 3.4 9.4 - - + +
427A ASN* 1.3 76.6 - - - +
429A LEU* 1.3 84.0 + - + +
431A GLN 3.8 3.8 + - - -
432A THR* 3.8 18.1 + - - +
475A SER* 3.9 18.4 - - - -
476A ILE 4.2 0.4 - - - -
477A VAL* 3.6 32.5 - - + -
544B LEU* 4.8 1.8 - - + -
548B ILE* 5.4 1.3 - - + -
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Residues in contact with LEU 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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425A LEU 2.9 22.6 + - - +
426A ALA 3.8 0.7 - - - +
428A PHE* 1.3 85.1 - - + +
430A ALA* 1.3 64.3 + - - +
432A THR* 3.3 19.0 + - - -
433A GLU* 3.3 11.1 + - - +
524B ILE* 3.8 29.1 - - + +
528B LEU* 4.0 7.4 - - + -
541B THR* 4.4 10.0 + - + +
544B LEU* 3.5 40.6 - - + +
545B ILE* 3.6 27.8 - - + -
548B ILE* 3.8 22.0 - - + -
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Residues in contact with ALA 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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426A ALA 2.8 22.9 + - - +
427A ASN* 3.3 2.2 + - - +
429A LEU* 1.3 73.9 - - - +
431A GLN* 1.3 58.9 + - + +
433A GLU* 3.4 5.0 + - - +
434A ALA* 2.8 32.3 + - - +
517B GLY 3.7 9.2 - - - +
520B LEU* 3.6 10.0 - - + +
521B ALA* 3.2 34.3 - - + +
524B ILE* 3.7 8.3 - - + +
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Residues in contact with GLN 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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340A TYR* 3.8 2.9 - - - +
387A GLN* 3.5 36.1 + - - +
391A TYR* 3.1 16.7 - - + +
395A HIS* 2.8 30.4 + - - -
405A PHE* 3.8 23.1 - - + -
427A ASN* 3.0 23.3 + - - +
429A LEU 3.3 0.4 - - - -
430A ALA* 1.3 76.9 - - + +
432A THR* 1.3 58.4 + - - +
434A ALA* 3.4 3.6 + - - +
435A LEU* 2.9 36.3 + - - +
514B VAL* 5.2 3.4 + - - +
517B GLY* 3.6 26.4 - - - -
518B LYS* 4.6 1.6 - - - +
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Residues in contact with THR 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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56A LYS* 3.1 25.4 + - - +
405A PHE* 3.6 35.2 - - + -
428A PHE* 3.8 7.5 + - - +
429A LEU* 3.3 11.3 + - - -
431A GLN* 1.3 74.1 - - - +
433A GLU* 1.3 63.1 + - - +
435A LEU* 3.4 6.7 + - - +
436A MET* 2.9 30.5 + - - +
473A THR* 3.4 25.7 + - - +
475A SER* 3.6 18.9 + - - +
544B LEU* 4.7 1.7 - - - +
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Residues in contact with GLU 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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56A LYS* 3.9 9.2 - - - +
429A LEU 3.3 9.5 + - - +
430A ALA 3.5 6.3 - - - +
432A THR* 1.3 81.4 + - - +
434A ALA* 1.3 51.3 + - - +
436A MET* 3.2 5.0 + - + +
437A LYS* 2.8 51.7 + - + +
520B LEU* 3.4 27.4 - - + +
524B ILE* 3.6 21.7 - - - +
537B HIS* 2.7 35.1 + - - +
538B ASP* 3.7 16.2 + - - +
541B THR* 3.7 10.8 - - - +
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Residues in contact with ALA 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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395A HIS* 3.8 17.8 + - + -
430A ALA 2.8 20.5 + - - +
431A GLN 3.7 4.0 - - - +
433A GLU* 1.3 74.8 - - - +
435A LEU* 1.3 57.8 + - - +
437A LYS* 4.7 0.4 - - - -
438A GLY* 2.9 31.4 + - - +
467A PHE* 5.4 0.5 - - - +
469A GLY* 4.6 0.7 - - - -
516B LEU* 3.7 27.4 - - + +
517B GLY* 4.1 11.0 - - - -
520B LEU* 3.5 12.7 - - + +
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Residues in contact with LEU 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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391A TYR* 5.8 2.0 - - + -
394A ILE* 3.7 37.0 - - + +
395A HIS* 3.5 30.5 - - + +
403A CYS* 5.2 0.9 - - - -
405A PHE* 4.0 19.3 - - + -
431A GLN* 2.9 22.5 + - + +
432A THR* 3.7 4.0 - - - +
433A GLU 3.4 0.2 - - - -
434A ALA* 1.3 75.2 - - - +
436A MET* 1.3 60.9 + - - +
469A GLY* 3.3 6.3 - - - -
470A ASN 3.2 5.0 + - - -
471A ARG* 2.9 51.8 + - + +
473A THR* 3.8 22.4 - - + -
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Residues in contact with MET 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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25A LEU* 3.6 29.8 - - + +
26A ARG* 3.8 30.2 + - + +
29A PHE* 3.8 20.0 - - + -
56A LYS* 3.8 18.8 - - + -
432A THR 2.9 17.6 + - - +
433A GLU* 3.4 5.6 - - + +
435A LEU* 1.3 77.4 - - - +
437A LYS* 1.3 72.5 + - + +
470A ASN* 3.1 21.3 + - - -
471A ARG 3.8 6.9 + - - +
538B ASP* 3.6 41.3 - - + +
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Residues in contact with LYS 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 ARG* 3.4 59.9 + - + +
433A GLU* 2.8 31.0 + - + +
434A ALA* 4.3 1.6 - - - +
436A MET* 1.3 88.9 - - + +
438A GLY* 1.3 72.1 + - - +
443A GLU* 5.2 2.7 + - - -
468A GLU 4.9 2.3 - - - +
469A GLY* 4.3 2.1 - - - -
516B LEU* 5.8 2.7 - - - -
520B LEU* 4.7 23.3 - - + -
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Residues in contact with GLY 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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26A ARG* 4.0 2.9 + - - -
434A ALA 2.9 17.8 + - - -
436A MET 3.7 1.0 - - - -
437A LYS* 1.3 96.1 - - - +
439A LYS* 1.3 61.7 + - - +
440A LEU 4.3 0.4 - - - -
467A PHE* 3.3 21.5 - - - -
469A GLY* 3.7 9.4 - - - -
516B LEU* 3.5 13.8 - - - +
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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
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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