Contacts of the helix formed by residues 428 - 450 (chain A) in PDB entry 2Y4U
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 ASN 428 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426A PHE* 3.8 2.0 - - - +
427A GLN* 1.3 92.8 - - - +
429A GLU* 1.3 69.0 + - - +
430A GLU* 4.7 0.7 - - + +
431A GLU* 2.9 39.1 + - - +
432A LYS* 3.0 26.0 + - - +
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Residues in contact with GLU 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A GLN 3.7 2.9 + - - +
428A ASN* 1.3 82.0 - - - +
430A GLU* 1.3 57.9 + - + +
432A LYS* 2.8 22.0 + - - +
433A LYS* 2.7 36.3 + - - +
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Residues in contact with GLU 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A ASN* 4.7 0.9 - - + +
429A GLU* 1.3 79.2 + - + +
431A GLU* 1.3 71.2 + - - +
433A LYS* 3.8 6.6 + - - +
434A LYS* 3.2 28.4 + - - +
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Residues in contact with GLU 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A PHE* 3.7 21.7 - - + -
428A ASN* 2.9 49.6 + - - +
430A GLU* 1.3 77.5 + - + +
432A LYS* 1.3 66.0 - - - +
434A LYS* 3.0 17.6 + - - +
435A ALA* 3.1 9.9 + - - +
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Residues in contact with LYS 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A PRO* 3.1 45.5 - - + +
426A PHE* 2.9 18.2 - - + +
427A GLN 3.8 19.1 - - - -
428A ASN 3.0 10.0 + - - +
429A GLU* 2.8 23.3 + - - +
431A GLU* 1.3 71.5 - - - +
433A LYS* 1.3 55.8 + - - +
434A LYS 2.9 3.6 - - - -
435A ALA* 2.7 24.9 + - - +
436A GLU* 3.0 20.4 + - - +
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Residues in contact with LYS 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A GLU* 2.7 18.2 + - + +
430A GLU* 4.0 8.3 - - - +
432A LYS* 1.3 72.0 - - - +
434A LYS* 1.3 72.1 + - + +
436A GLU* 3.4 35.4 + - - +
437A LYS* 3.6 15.9 - - + +
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Residues in contact with LYS 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A TRP* 5.8 0.4 - - - -
430A GLU* 3.2 19.9 + - - +
431A GLU* 3.0 12.3 + - - +
432A LYS 2.8 1.4 + - - -
433A LYS* 1.3 90.0 - - - +
435A ALA* 1.3 60.5 + - - +
437A LYS* 3.4 28.2 - - + +
438A LYS* 3.7 9.9 + - - +
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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
----------------------------------------------------------
421A TRP* 3.9 34.0 - - + +
423A PRO* 5.0 1.8 - - + -
426A PHE* 2.8 42.4 - - + -
431A GLU 3.1 4.6 + - - +
432A LYS 2.7 8.6 + - - +
434A LYS* 1.3 69.1 - - - +
436A GLU* 1.3 52.4 + - - +
437A LYS 3.0 2.2 - - - -
438A LYS* 2.8 6.8 + - - +
439A PHE* 2.7 33.6 + - - +
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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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423A PRO* 4.0 19.4 - - + +
432A LYS* 3.0 20.5 + - - +
433A LYS* 3.4 31.5 + - - +
435A ALA* 1.3 75.7 - - - +
437A LYS* 1.3 54.3 + - + +
439A PHE* 3.0 9.1 + - - +
440A ILE* 2.6 50.8 + - + +
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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
----------------------------------------------------------
393A ARG* 6.2 0.2 - - - +
433A LYS* 3.6 18.4 - - + +
434A LYS* 3.4 23.1 - - + +
435A ALA 3.0 0.4 - - - -
436A GLU* 1.3 78.6 - - + +
438A LYS* 1.3 54.9 + - + +
440A ILE* 3.8 24.2 - - + +
441A ASP* 2.6 44.4 + - - +
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Residues in contact with LYS 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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398A ILE* 5.3 4.9 - - + +
421A TRP* 3.7 53.7 - - + +
434A LYS 4.0 11.6 + - - +
435A ALA 2.8 11.3 + - - +
437A LYS* 1.3 74.9 - - + +
439A PHE* 1.3 53.1 + - - +
441A ASP* 3.3 8.4 + - + +
442A ILE* 2.7 42.2 + - + +
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Residues in contact with PHE 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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414A TYR* 6.0 1.1 - - - -
418A ALA* 3.5 26.7 - - + -
421A TRP* 3.1 24.8 + - - +
422A HIS* 3.5 31.4 - + + -
423A PRO* 4.3 5.8 - - + -
435A ALA 2.7 15.4 + - - +
436A GLU* 3.4 12.3 - - - +
438A LYS* 1.3 69.4 - - - +
440A ILE* 1.3 67.9 + - + +
441A ASP 2.9 2.6 + - - -
442A ILE* 3.1 37.9 + - + +
443A ALA* 3.3 14.3 + - + +
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Residues in contact with ILE 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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393A ARG* 5.5 4.0 - - - +
436A GLU* 2.6 37.5 + - + +
437A LYS* 3.8 32.1 - - + +
439A PHE* 1.3 72.7 - - - +
441A ASP* 1.3 66.6 + - - +
443A ALA* 4.5 2.1 - - - +
444A ALA* 3.2 24.7 + - + +
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Residues in contact with ASP 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ARG* 3.3 28.3 + - - -
395A TYR* 6.0 0.2 - - - -
398A ILE* 4.0 26.0 - - + +
437A LYS* 2.6 30.0 + - - +
438A LYS* 3.3 9.6 + - + +
439A PHE 3.0 1.0 - - - -
440A ILE* 1.3 86.6 - - - +
442A ILE* 1.3 66.4 + - - +
443A ALA 3.2 1.8 - - - -
444A ALA* 2.9 18.8 + - - +
445A ALA* 3.0 13.5 + - - +
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Residues in contact with ILE 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ILE* 3.5 29.4 - - + +
399A LEU* 6.2 0.7 - - + -
414A TYR* 3.7 30.3 - - + +
417A LEU* 4.6 14.1 - - + +
418A ALA* 4.0 11.7 - - + -
421A TRP* 4.6 19.5 - - + -
438A LYS* 2.7 26.7 + - + +
439A PHE* 3.1 46.4 - - + +
441A ASP* 1.3 73.1 - - - +
443A ALA* 1.3 74.9 + - + +
445A ALA* 3.3 15.9 - - - +
446A LYS* 3.8 8.8 + - - +
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Residues in contact with ALA 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A TYR* 4.3 9.2 - - - +
439A PHE* 3.3 16.9 + - + +
440A ILE* 4.5 2.5 - - - +
442A ILE* 1.3 85.3 - - + +
444A ALA* 1.3 67.0 + - - +
445A ALA 3.1 2.5 - - - -
446A LYS* 2.9 28.4 + - + +
447A GLU* 3.6 6.1 + - - +
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Residues in contact with ALA 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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393A ARG* 6.3 2.2 - - - +
395A TYR* 5.1 7.4 - - + -
440A ILE* 3.2 18.8 + - + +
441A ASP* 2.9 17.2 + - - +
443A ALA* 1.3 78.7 - - - +
445A ALA* 1.3 60.0 + - - +
447A GLU* 3.7 2.9 + - - +
448A VAL* 3.0 34.7 + - + +
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Residues in contact with ALA 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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395A TYR* 4.5 32.6 - - + +
398A ILE* 4.9 7.0 - - + -
410A ILE* 6.2 0.2 - - + -
441A ASP 3.0 9.8 + - - +
442A ILE* 3.3 14.6 - - - +
444A ALA* 1.3 76.7 - - - +
446A LYS* 1.3 66.0 + - + +
448A VAL 3.2 2.3 + - - -
449A LEU* 2.9 41.9 + - + +
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Residues in contact with LYS 446 (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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410A ILE* 3.4 19.8 - - + +
411A ILE* 3.2 52.0 - - - +
414A TYR* 3.4 55.8 - - + +
442A ILE 3.9 4.5 - - - +
443A ALA* 2.9 15.5 + - + +
445A ALA* 1.3 79.8 - - + +
447A GLU* 1.3 62.5 + - - +
449A LEU* 3.2 12.7 + - - +
450A SER* 3.3 18.5 + - - -
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Residues in contact with GLU 447 (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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443A ALA 3.6 5.5 + - - +
444A ALA* 4.5 5.2 - - - +
445A ALA 3.5 0.4 - - - -
446A LYS* 1.3 79.4 - - + +
448A VAL* 1.3 63.3 + - + +
449A LEU 3.6 0.5 + - - -
450A SER* 3.9 18.0 + - - +
451A ASP* 5.6 0.3 - - - +
453A GLU* 4.5 7.4 - - - +
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Residues in contact with VAL 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A TYR* 3.5 46.3 - - + +
444A ALA* 3.0 23.6 - - + +
445A ALA 3.2 3.0 + - - +
446A LYS 3.2 0.8 - - - -
447A GLU* 1.3 82.2 - - + +
449A LEU* 1.3 58.7 + - - +
453A GLU* 2.9 28.6 - - + +
454A MSE 3.9 5.0 + - - -
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Residues in contact with LEU 449 (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 TYR* 5.3 11.2 - - + +
396A TYR* 6.2 0.9 - - + -
407A LYS* 3.7 19.6 - - + +
410A ILE* 3.8 45.1 - - + -
411A ILE* 5.7 3.1 - - + -
445A ALA* 2.9 37.9 + - + +
446A LYS* 3.7 10.5 - - - +
448A VAL* 1.3 80.0 - - - +
450A SER* 1.3 71.7 + - - +
453A GLU 3.1 18.8 - - - +
454A MSE 3.2 37.7 - - + +
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Residues in contact with SER 450 (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 LYS* 3.6 15.7 - - - +
446A LYS 3.3 17.3 + - - -
447A GLU* 3.9 12.1 + - - +
449A LEU* 1.3 87.1 - - - +
451A ASP* 1.3 84.0 + - - +
453A GLU* 3.3 14.7 + - - +
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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
------------------------------------------------------------
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