Contacts of the helix formed by residues 470 - 476 (chain E) in PDB entry 5ZR1
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 ILE 470 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333E ILE* 3.8 27.4 - - + +
336E TYR* 4.3 7.4 - - + -
337E ILE* 4.6 7.0 - - + -
456E TRP* 3.7 21.1 - - + -
459E ILE* 3.8 24.5 - - + +
460E LYS* 4.8 7.2 - - + -
463E SER* 3.3 30.5 - - - +
468E PHE* 3.4 15.5 + - + -
469E ASN* 1.3 72.9 + - - +
471E SER* 1.3 66.8 + - - +
472E ASP 3.2 0.2 - - - -
473E TYR* 3.2 14.3 + - + +
474E PHE* 3.3 33.6 - - + -
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Residues in contact with SER 471 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456E TRP* 4.2 18.7 - - - -
460E LYS* 4.9 13.2 - - - +
469E ASN* 3.2 11.5 - - - -
470E ILE* 1.3 81.5 - - - +
472E ASP* 1.3 51.5 + - - +
474E PHE* 3.2 2.8 + - - +
475E SER* 2.5 47.2 + - - -
479E GLU* 3.5 16.4 + - - +
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Residues in contact with ASP 472 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469E ASN* 2.5 42.4 + - - +
470E ILE 3.2 1.0 - - - -
471E SER* 1.3 79.1 - - - +
473E TYR* 1.3 65.3 + - + +
474E PHE 3.2 0.4 + - - -
475E SER* 3.7 15.8 + - - -
476E ASP* 3.7 22.6 + - - +
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Residues in contact with TYR 473 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337E ILE* 4.8 9.4 - - + -
341E LEU* 4.0 17.2 - - + +
349E ILE* 3.6 31.4 + - + +
350E PHE* 3.5 40.3 - + - -
393E ILE* 4.4 2.8 - - - +
468E PHE* 3.5 33.9 - + - -
469E ASN 3.6 15.9 - - - -
470E ILE* 3.2 16.0 + - + +
472E ASP* 1.3 81.0 - - + +
474E PHE* 1.3 68.4 + - + +
476E ASP* 4.6 3.7 + - - +
477E ILE* 3.9 16.6 - - - +
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Residues in contact with PHE 474 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336E TYR* 3.8 42.8 - + - -
337E ILE* 4.6 3.6 - - + -
340E TYR* 3.7 18.6 - - + -
341E LEU* 3.6 25.4 - - + -
374E ARG* 3.3 34.1 + - + +
456E TRP* 4.0 10.1 - + + -
470E ILE* 3.3 34.8 - - + -
471E SER* 3.2 6.7 + - - +
473E TYR* 1.3 81.2 - - + +
475E SER* 1.3 61.7 + - - +
476E ASP 3.3 1.3 - - - -
477E ILE* 3.3 37.5 - - + +
479E GLU* 3.3 19.9 + - - +
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Residues in contact with SER 475 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368E LYS* 4.4 5.2 - - - -
471E SER* 2.5 37.9 + - - -
472E ASP* 3.7 14.9 + - - -
473E TYR 3.6 0.4 - - - -
474E PHE* 1.3 75.2 - - - +
476E ASP* 1.3 65.6 + - - +
477E ILE 3.4 0.5 + - - -
478E HIS 3.8 1.9 - - - -
479E GLU* 3.1 42.3 + - - +
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Residues in contact with ASP 476 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365E ARG* 3.8 11.7 - - - +
368E LYS* 3.4 27.4 + - - +
472E ASP* 3.7 15.9 + - - +
473E TYR 5.1 3.4 - - - +
474E PHE* 3.3 0.8 - - - +
475E SER* 1.3 83.6 - - - +
477E ILE* 1.3 58.2 + - + +
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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
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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