Contacts of the helix formed by residues 473 - 483 (chain A) in PDB entry 4OE4
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 473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467A TYR* 5.7 0.9 + - - -
469A TYR* 4.1 6.1 - - + +
470A PRO* 2.8 43.6 + - + +
472A THR* 1.3 89.6 + - - +
474A PHE* 1.3 56.9 + - - +
475A ASN 3.4 2.9 - - - -
476A GLU* 3.1 17.1 + - + +
477A ILE* 2.8 30.6 + - + +
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Residues in contact with PHE 474 (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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325A LEU* 3.7 27.8 - - + -
327A HIS* 3.7 31.9 - + + +
328A PRO* 5.1 0.9 - - + -
469A TYR* 3.4 31.1 - + + +
471A ASP 3.4 14.0 + - - +
472A THR 3.3 3.6 + - - +
473A GLU* 1.3 75.9 - - - +
475A ASN* 1.3 79.8 + - - +
477A ILE* 3.2 8.8 + - - +
478A CYS* 3.2 37.6 + - - -
493A ILE* 3.6 26.0 - - + -
500A ALA* 3.7 27.4 - - + -
503A TYR* 4.7 2.2 - + - -
504A ALA* 4.7 0.2 - - + -
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Residues in contact with ASN 475 (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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472A THR 4.8 2.6 + - - +
473A GLU 3.4 0.6 - - - -
474A PHE* 1.3 91.1 - - - +
476A GLU* 1.3 63.3 + - - +
478A CYS* 3.1 13.7 + - - +
479A ASP* 3.3 18.9 + - - +
500A ALA* 5.8 0.3 - - - -
503A TYR* 3.6 44.0 + - - +
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Residues in contact with GLU 476 (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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473A GLU* 3.1 26.0 + - + +
475A ASN* 1.3 76.9 - - - +
477A ILE* 1.3 59.3 + - + +
479A ASP* 3.2 15.1 + - - +
480A ILE* 3.0 37.3 + - + +
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Residues in contact with ILE 477 (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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325A LEU* 3.7 29.4 - - + -
358A TYR* 3.9 20.2 - - + -
450A PRO* 4.6 2.9 - - + -
467A TYR* 3.8 29.4 - - + -
469A TYR* 4.0 21.3 - - + -
473A GLU* 2.8 15.4 + - + +
474A PHE* 3.2 17.2 + - + +
476A GLU* 1.3 76.3 - - + +
478A CYS* 1.3 67.5 + - - +
480A ILE* 3.3 26.0 + - + +
481A ILE* 3.1 29.8 + - + +
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Residues in contact with CYS 478 (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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325A LEU* 3.8 15.9 - - - -
474A PHE* 3.2 42.5 + - - -
475A ASN 3.1 9.3 + - - +
477A ILE* 1.3 80.4 - - - +
479A ASP* 1.3 58.2 + - - +
481A ILE* 3.2 4.3 + - - -
482A ASP* 3.0 25.8 + - - +
503A TYR* 4.1 14.8 - - + -
504A ALA* 4.0 15.0 - - - -
507A LYS* 4.2 11.0 - - + -
508A LEU* 3.3 18.4 - - + +
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Residues in contact with ASP 479 (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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475A ASN* 3.4 13.4 - - - +
476A GLU* 3.4 13.0 - - - +
478A CYS* 1.3 74.5 - - - +
480A ILE* 1.3 57.3 + - + +
482A ASP* 3.7 7.1 - - - +
483A ASN* 2.7 40.8 + - + +
503A TYR* 3.4 11.5 + - - -
507A LYS* 3.2 27.3 - - - +
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Residues in contact with ILE 480 (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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358A TYR* 5.4 4.0 - - + +
450A PRO* 4.1 35.9 - - + +
451A ASP* 5.6 3.1 - - + +
476A GLU* 3.0 23.6 + - + +
477A ILE* 3.6 29.2 - - + +
478A CYS 3.2 0.2 - - - -
479A ASP* 1.3 77.2 - - + +
481A ILE* 1.3 61.3 + - + +
483A ASN* 3.9 2.4 - - - -
484A THR* 3.1 31.2 + - - -
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Residues in contact with ILE 481 (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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323A PHE* 4.0 26.2 - - + -
325A LEU* 4.5 17.5 - - + -
356A ARG* 3.9 21.2 + - - +
358A TYR* 3.9 45.1 - - + +
477A ILE* 3.1 19.6 + - + +
478A CYS* 3.5 9.9 - - - +
479A ASP 3.1 0.4 - - - -
480A ILE* 1.3 77.2 - - + +
482A ASP* 1.3 65.3 + - - +
484A THR 3.2 19.3 + - - +
508A LEU* 3.8 15.5 - - + -
511A SER* 4.0 7.8 + - - -
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Residues in contact with ASP 482 (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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478A CYS 3.0 15.3 + - - +
479A ASP* 3.7 7.2 - - - +
481A ILE* 1.3 79.2 - - - +
483A ASN* 1.3 60.6 + - - +
484A THR 3.2 4.6 + - - +
507A LYS* 3.4 36.0 - - + +
508A LEU* 4.5 0.2 - - + -
510A PHE* 4.6 16.5 - - - +
511A SER* 3.2 16.4 + - - +
202B GLU* 4.7 10.4 - - - +
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Residues in contact with ASN 483 (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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479A ASP* 2.7 21.6 + - + +
480A ILE* 3.9 2.9 - - - +
482A ASP* 1.3 76.9 - - - +
484A THR* 1.3 60.9 + - - +
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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