Contacts of the helix formed by residues 472 - 480 (chain A) in PDB entry 5WJ9
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 ASP 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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453A LYS* 2.8 33.3 + - + +
463A CYS* 6.1 0.2 - - - -
466A SER* 5.2 0.7 - - - +
467A LEU* 4.0 1.5 - - + +
471A ASP* 1.3 87.4 - - - +
473A MET* 1.3 60.8 + - - +
474A PHE 3.5 0.9 - - - -
475A VAL* 3.8 17.7 - - + +
476A THR* 3.3 27.5 + - - +
471B ASP* 3.1 14.0 + - - +
474D PHE* 3.3 26.0 - - + +
475D VAL* 4.3 12.8 - - - +
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Residues in contact with MET 473 (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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467A LEU* 4.4 20.4 - - + +
470A GLY* 4.7 10.5 - - - -
471A ASP 3.1 2.4 - - - +
472A ASP* 1.3 78.2 - - - +
474A PHE* 1.3 58.0 + - - +
476A THR* 2.7 20.0 + - - +
477A PHE* 3.1 27.7 - - + -
502A ILE* 3.4 35.0 - - + -
506A ILE* 4.6 4.3 - - - -
465B PHE* 3.4 31.4 - - + +
466B SER* 3.6 15.9 - - - +
469B ASN* 3.4 31.2 - - - +
471B ASP* 2.9 16.4 + - + -
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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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473A MET* 1.3 78.7 - - - +
475A VAL* 1.3 59.2 + - + +
476A THR 3.3 0.4 - - - -
477A PHE* 3.3 5.7 + - - +
478A ALA* 2.8 40.4 + - + -
481A GLN* 6.4 1.1 - - + -
453B LYS* 3.5 39.0 - - + -
459B MET* 3.9 11.9 - - + -
462B GLU* 4.0 15.9 - - + -
463B CYS* 3.6 46.7 - - + -
466B SER* 3.6 17.3 - - - +
471B ASP* 3.4 3.4 + - - +
472B ASP* 3.3 33.2 - - + +
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Residues in contact with VAL 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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453A LYS* 3.7 24.9 - - - +
472A ASP* 3.7 24.1 + - + +
473A MET 3.4 0.8 - - - -
474A PHE* 1.3 77.1 - - + +
476A THR* 1.3 52.7 + - - +
478A ALA* 3.1 10.3 + - + +
479A ALA* 2.8 33.6 + - + +
472B ASP* 4.3 19.5 - - - +
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Residues in contact with THR 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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453A LYS* 3.5 13.4 - - + +
454A PHE* 4.8 8.3 - - + -
463A CYS* 3.5 31.9 - - - -
467A LEU* 3.8 10.7 - - + +
472A ASP 3.3 14.3 + - - +
473A MET* 2.7 27.4 + - - +
475A VAL* 1.3 77.5 - - - +
477A PHE* 1.3 61.0 + - - -
479A ALA* 3.4 19.8 + - - +
480A MET* 3.6 15.6 - - - +
498A LEU* 3.6 22.6 - - - +
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Residues in contact with PHE 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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473A MET* 3.1 47.3 - - + -
474A PHE* 3.3 8.5 + - + +
476A THR* 1.3 81.9 + - - +
478A ALA* 1.3 58.2 + - - +
480A MET* 3.2 24.6 + - - +
481A GLN* 3.4 13.9 + - - -
495A GLN* 3.5 23.6 - - - -
498A LEU* 3.3 42.4 - - + -
499A TYR* 3.9 34.3 - + - -
502A ILE* 5.6 1.1 - - + -
462B GLU* 3.5 40.8 - - + +
465B PHE* 4.3 5.6 - + - -
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Residues in contact with ALA 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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474A PHE* 2.8 38.4 + - + +
475A VAL* 3.1 15.0 + - + +
477A PHE* 1.3 70.8 - - - +
479A ALA* 1.3 64.3 + - - +
480A MET 3.2 0.4 - - - -
481A GLN* 3.4 23.9 + - + +
482A ALA 4.5 0.9 + - - -
462B GLU* 4.5 0.6 + - - -
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Residues in contact with ALA 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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451A HIS* 3.2 36.9 + - + +
452A VAL* 5.3 7.9 - - + +
453A LYS* 6.3 3.6 - - + -
475A VAL* 2.8 12.2 + - + +
476A THR* 3.4 14.4 - - - +
478A ALA* 1.3 78.3 - - - +
480A MET* 1.3 59.4 + - + +
481A GLN 3.4 0.7 + - - -
482A ALA* 3.7 15.2 + - - +
483A GLN* 4.5 0.2 - - - +
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Residues in contact with MET 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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447A LEU* 4.2 10.8 - - + -
451A HIS* 2.9 48.0 - - + +
454A PHE* 5.0 6.7 - - + -
476A THR 3.6 20.9 - - - +
477A PHE* 3.3 16.2 - - - +
478A ALA 3.2 0.8 - - - -
479A ALA* 1.3 73.6 - - - +
481A GLN* 1.3 57.5 + - - +
482A ALA 3.2 0.9 - - - -
483A GLN* 2.8 21.6 + - - +
484A GLN 3.1 10.2 + - - -
490A VAL 5.1 0.4 - - - +
491A TRP* 3.5 25.7 - - + +
494A SER* 2.9 37.7 - - - +
495A GLN* 4.1 8.3 - - - +
498A LEU* 4.3 12.8 - - + -
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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