Contacts of the helix formed by residues 422 - 437 (chain A) in PDB entry 2ES0
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 PHE 422 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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419A ARG 5.1 3.3 + - - -
420A TYR* 3.1 1.6 - - - +
421A THR* 1.3 99.9 - - + +
423A GLU* 1.3 53.5 + - - +
424A ASP 3.5 2.0 - - - -
425A ALA* 4.0 18.6 - - + -
426A GLN* 2.7 41.5 + - + +
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Residues in contact with GLU 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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420A TYR* 3.3 37.9 + - + +
421A THR 3.5 2.2 + - - -
422A PHE* 1.3 76.2 - - - +
424A ASP* 1.3 70.3 + - - +
426A GLN* 4.0 7.9 - - - +
427A GLU* 3.1 23.4 + - + +
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Residues in contact with ASP 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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422A PHE 3.5 0.2 - - - -
423A GLU* 1.3 79.2 - - - +
425A ALA* 1.3 65.7 + - - +
427A GLU* 3.2 7.1 + - - +
428A HIS* 3.0 24.7 + - - +
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Residues in contact with ALA 425 (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 PHE* 3.7 25.1 - - + +
424A ASP* 1.3 78.6 - - - +
426A GLN* 1.3 63.0 + - - +
428A HIS* 3.3 6.8 + - - +
429A ILE* 3.1 31.0 + - + +
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Residues in contact with GLN 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 PHE* 2.7 26.7 + - + +
423A GLU* 4.0 6.8 - - - +
425A ALA* 1.3 73.7 - - - +
427A GLU* 1.3 53.9 + - - +
429A ILE* 3.4 5.6 + - + +
430A TYR* 2.8 36.1 + - + +
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Residues in contact with GLU 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 GLU* 3.1 18.0 + - + +
424A ASP* 3.2 6.9 + - - +
426A GLN* 1.3 74.6 - - - +
428A HIS* 1.3 66.2 + - - +
430A TYR* 3.6 17.2 - - - +
431A LYS* 3.0 68.5 + - - +
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Residues in contact with HIS 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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424A ASP 3.0 12.9 + - - +
425A ALA* 3.6 10.3 - - - +
427A GLU* 1.3 77.5 - - - +
429A ILE* 1.3 73.3 + - + +
431A LYS* 3.3 10.4 + - + +
432A LEU* 2.9 41.6 + - + +
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Residues in contact with ILE 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 ALA* 3.1 19.2 + - + +
426A GLN* 3.9 5.6 - - + +
428A HIS* 1.3 89.6 - - + +
430A TYR* 1.3 65.1 + - - +
432A LEU* 3.5 19.5 - - + +
433A MET* 2.9 43.7 + - + +
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Residues in contact with TYR 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 GLN* 2.8 26.0 + - + +
427A GLU* 3.6 20.9 - - - +
429A ILE* 1.3 73.9 - - - +
431A LYS* 1.3 75.2 + - + +
433A MET* 3.4 17.5 + - + +
434A LYS* 3.0 66.4 + - + +
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Residues in contact with LYS 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 GLU* 3.0 54.4 + - - +
428A HIS* 3.6 9.4 - - + +
430A TYR* 1.3 85.5 - - + +
432A LEU* 1.3 57.9 + - - +
434A LYS* 3.4 7.1 + - + +
435A SER* 2.9 34.1 + - - -
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Residues in contact with LEU 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 HIS* 2.9 29.8 + - + +
429A ILE* 3.5 25.8 - - + +
430A TYR 3.2 0.2 - - - -
431A LYS* 1.3 77.4 - - - +
433A MET* 1.3 55.8 + - + +
435A SER* 3.8 3.4 - - - +
436A ASP* 2.8 68.6 + - + +
437A SER* 4.7 0.4 + - - +
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Residues in contact with MET 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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429A ILE* 2.9 36.7 + - + +
430A TYR* 3.8 19.1 - - + +
432A LEU* 1.3 78.0 - - + +
434A LYS* 1.3 60.8 + - - +
437A SER* 3.0 20.2 + - - +
438A TYR* 2.8 29.5 + - - +
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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
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430A TYR* 3.0 60.5 + - + +
431A LYS* 3.7 7.9 - - + +
433A MET* 1.3 79.0 - - - +
435A SER* 1.3 62.2 + - - +
438A TYR* 3.4 32.6 + - + +
439A ALA* 4.4 3.1 + - - +
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Residues in contact with SER 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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431A LYS 2.9 23.0 + - - -
432A LEU* 3.4 5.7 + - - +
434A LYS* 1.3 80.4 - - - +
436A ASP* 1.3 76.8 + - - +
438A TYR 5.1 0.2 - - - -
439A ALA* 5.2 8.5 - - - +
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Residues in contact with ASP 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 LEU* 2.8 41.5 + - + +
435A SER* 1.3 92.8 + - - +
437A SER* 1.3 61.3 + - - +
439A ALA 5.5 0.4 - - - -
440A ARG* 3.4 25.3 - - - +
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Residues in contact with SER 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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432A LEU* 4.7 0.5 + - - +
433A MET* 3.0 24.4 + - - +
436A ASP* 1.3 81.0 + - - +
438A TYR* 1.3 67.4 + - - +
439A ALA 3.5 1.3 - - - -
440A ARG* 3.3 9.3 + - - +
441A PHE* 3.0 22.6 + - - +
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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