Contacts of the helix formed by residues 466 - 471 (chain D) in PDB entry 4Z2C
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 SER 466 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464D LYS 4.3 0.2 + - - -
465D ALA* 1.3 73.9 - - - +
467D MET* 1.3 61.4 + - - +
468D ASP* 4.1 8.5 - - - -
469D LYS* 2.9 11.4 + - - +
470D ILE* 2.9 28.3 + - - +
7E A 3.5 50.9 - - - -
8E C 4.7 4.4 + - - -
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Residues in contact with MET 467 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465D ALA 3.9 0.8 + - - -
466D SER* 1.3 73.0 - - - +
468D ASP* 1.3 56.8 + - - +
470D ILE* 3.6 10.5 - - + +
471D LEU* 2.9 73.8 + - + +
487D PHE* 4.0 13.9 - - + -
525D TYR* 3.7 33.9 - - - +
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Residues in contact with ASP 468 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466D SER* 3.1 7.8 - - - -
467D MET* 1.3 80.4 - - - +
469D LYS* 1.3 56.4 + - - +
471D LEU* 4.3 6.4 - - - +
472D ALA* 3.3 23.4 + - - +
7E A 5.5 2.7 - - - +
8E C 4.6 12.8 - - - +
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Residues in contact with LYS 469 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465D ALA* 4.8 13.0 - - + -
466D SER* 2.9 15.3 + - - +
468D ASP* 1.3 78.9 - - - +
470D ILE* 1.3 65.4 + - - +
472D ALA* 3.3 7.8 + - + +
473D ASN* 3.1 22.3 + - + +
8E C 4.1 28.7 - - - +
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Residues in contact with ILE 470 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460D LEU* 6.2 2.5 - - + -
462D VAL* 3.8 27.8 - - + +
465D ALA* 4.0 18.6 - - + +
466D SER 2.9 15.7 + - - +
467D MET* 3.2 16.4 + - - +
469D LYS* 1.3 77.6 - - - +
471D LEU* 1.3 62.3 + - - +
472D ALA 3.2 0.7 + - - -
473D ASN* 3.4 17.7 + - - +
476D ILE* 4.0 26.7 - - + +
487D PHE* 4.4 25.4 - - + -
525D TYR* 3.3 37.9 - - + +
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Residues in contact with LEU 471 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467D MET* 2.9 38.8 + - + +
468D ASP* 4.4 6.1 - - - +
470D ILE* 1.3 75.9 - - - +
472D ALA* 1.3 51.0 + - - +
473D ASN 4.3 1.4 - - - +
477D ARG* 2.6 34.1 + - - +
487D PHE* 3.8 38.6 - - + -
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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