Contacts of the helix formed by residues 457 - 466 (chain A) in PDB entry 4Z1H
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 GLU 457 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456A THR* 1.3 86.7 + - - +
458A GLN* 1.3 68.5 + - + +
459A GLU* 3.5 33.3 - - - +
460A VAL* 3.1 29.0 + - + +
461A LYS* 3.3 11.4 + - - +
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Residues in contact with GLN 458 (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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456A THR 3.6 2.6 + - - -
457A GLU* 1.3 74.4 - - + +
459A GLU* 1.3 57.3 + - - +
461A LYS* 3.1 22.9 + - - +
462A GLU* 2.9 53.4 + - - +
538A HIS 5.4 0.7 - - - +
539A LEU* 3.2 17.1 + - - +
540A ARG* 4.4 12.8 + - - -
541A GLU* 2.3 53.2 + - + +
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Residues in contact with GLU 459 (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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457A GLU* 3.3 23.1 - - - +
458A GLN* 1.3 75.0 - - - +
460A VAL* 1.3 59.7 + - - +
462A GLU* 3.8 13.0 - - + +
463A ASP* 2.8 48.4 + - - +
466A LYS* 5.1 6.3 + - - +
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Residues in contact with VAL 460 (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 GLN* 4.4 22.2 - - - +
455A ALA* 3.7 21.3 - - + -
456A THR* 5.1 3.1 - - - +
457A GLU* 3.1 31.0 + - + +
459A GLU* 1.3 74.7 - - - +
461A LYS* 1.3 66.4 + - - +
463A ASP* 3.0 12.0 + - + +
464A ILE* 2.9 34.7 + - + +
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Residues in contact with LYS 461 (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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452A ILE* 3.2 29.8 + - + +
453A VAL 3.9 1.0 + - - -
455A ALA* 2.9 36.9 + - + +
456A THR* 3.3 21.5 - - - +
457A GLU 3.5 9.6 - - - +
458A GLN* 3.1 25.0 + - - +
460A VAL* 1.3 77.3 - - - +
462A GLU* 1.3 56.9 + - - +
464A ILE* 3.7 1.0 + - - -
465A ALA* 2.9 27.2 + - - +
538A HIS* 3.1 38.2 + - + +
539A LEU* 3.7 18.9 - - + +
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Residues in contact with GLU 462 (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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458A GLN* 2.9 54.9 + - - +
459A GLU* 4.0 11.7 - - + +
461A LYS* 1.3 76.7 - - - +
463A ASP* 1.3 58.5 + - - +
465A ALA* 3.7 6.5 - - - -
466A LYS* 2.9 38.8 + - - +
539A LEU* 4.6 1.8 - - + -
541A GLU* 3.2 4.4 - - - +
542A PHE* 3.2 22.3 - - + -
543A ASP* 2.5 41.7 + - - +
544A LYS 4.2 4.2 + - - -
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Residues in contact with ASP 463 (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 GLN* 6.4 0.2 - - - +
420A GLN* 6.6 0.2 - - - -
423A ILE* 3.5 31.2 - - + +
424A LYS* 3.4 18.3 + - - -
459A GLU* 2.8 37.5 + - - +
460A VAL* 3.2 13.1 - - + +
462A GLU* 1.3 76.2 - - - +
464A ILE* 1.3 62.5 + - - +
466A LYS* 2.8 50.7 + - - +
467A LEU 4.2 0.7 + - - -
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Residues in contact with ILE 464 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383A TRP* 3.5 53.6 - - + +
419A GLN* 4.3 1.6 - - - +
423A ILE* 4.2 9.2 - - + -
448A MET* 3.6 28.6 - - + +
451A GLY 3.8 24.7 - - - +
452A ILE* 3.7 11.4 - - + +
455A ALA* 4.9 0.4 - - + -
460A VAL* 2.9 31.6 + - + +
463A ASP* 1.3 75.4 - - - +
465A ALA* 1.3 57.7 + - - +
467A LEU* 2.8 33.2 + - + +
468A LEU* 4.0 2.1 + - - +
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Residues in contact with ALA 465 (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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452A ILE* 3.6 15.2 - - + +
461A LYS 2.9 20.2 + - - +
462A GLU* 3.2 12.3 + - - +
464A ILE* 1.3 71.7 - - - +
466A LYS* 1.3 56.9 + - - +
467A LEU 3.0 5.8 - - - -
468A LEU* 3.1 27.8 + - + +
482A SER* 5.0 1.0 - - - -
483A LEU* 3.8 30.4 - - + +
539A LEU* 3.9 14.4 - - + -
542A PHE* 4.0 1.8 - - + -
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Residues in contact with LYS 466 (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 LYS* 4.5 6.6 - - - +
427A ILE* 3.8 29.8 - - + +
459A GLU* 5.1 8.9 + - - +
462A GLU* 2.9 31.0 + - - +
463A ASP* 2.8 39.3 + - - +
464A ILE 3.1 0.6 - - - -
465A ALA* 1.3 76.3 - - - +
467A LEU* 1.3 60.7 + - - +
468A LEU 3.4 0.4 - - - -
469A ARG* 3.3 19.9 + - - -
482A SER* 4.1 10.2 + - - +
483A LEU 6.0 0.4 - - - +
484A SER* 5.0 8.1 - - - -
542A PHE* 3.9 23.1 - - + -
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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