Contacts of the helix formed by residues 482 - 493 (chain A) in PDB entry 4OWW
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 482 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431A ALA* 6.1 0.8 - - - +
480A LYS 3.7 2.4 + - - -
481A LEU* 1.3 75.4 - - - +
483A LYS* 1.3 65.0 + - - +
484A GLU* 4.1 16.3 + - - +
485A LEU* 3.0 7.2 + - + +
486A ARG* 2.9 23.7 + - - +
89C ALA* 6.0 0.5 - - - +
90C PHE* 3.5 38.8 - - + -
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Residues in contact with LYS 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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481A LEU 3.3 3.2 + - - -
482A ASP* 1.3 76.7 - - - +
484A GLU* 1.3 61.1 + - + +
486A ARG* 3.2 21.5 + - - +
487A ALA* 2.8 30.0 + - - +
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Residues in contact with GLU 484 (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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435A ASP* 5.6 0.3 - - - +
439A ARG* 4.7 10.6 + - - -
482A ASP* 3.2 15.8 + - - +
483A LYS* 1.3 82.5 - - + +
485A LEU* 1.3 56.7 - - - +
487A ALA* 3.2 7.3 + - - +
488A MET* 3.0 31.2 + - + +
87C ASP 5.2 1.9 - - - +
89C ALA* 4.2 20.0 + - - +
90C PHE* 3.8 19.9 - - - -
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Residues in contact with LEU 485 (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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431A ALA* 3.6 41.1 - - + +
434A LEU* 4.2 11.9 - - + +
435A ASP* 3.9 29.8 - - + +
481A LEU* 3.9 17.9 - - + -
482A ASP* 3.0 12.2 + - + +
484A GLU* 1.3 80.7 - - - +
486A ARG* 1.3 57.9 + - - +
488A MET* 3.3 18.9 + - - +
489A LEU* 3.0 41.6 + - + +
90C PHE* 3.8 25.1 - - + -
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Residues in contact with ARG 486 (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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476A PHE 3.9 20.5 - - - +
477A ASP* 3.3 33.7 + - - +
478A ASN 3.4 13.9 + - - +
479A PRO* 4.0 23.2 + - - +
481A LEU* 3.3 34.7 + - + -
482A ASP 2.9 11.6 + - - +
483A LYS* 3.2 19.7 + - - +
485A LEU* 1.3 76.5 - - - +
487A ALA* 1.3 57.6 + - - +
489A LEU* 3.8 2.6 - - - +
490A ARG* 3.0 45.6 + - - +
497A CYS* 5.4 0.2 - - - -
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Residues in contact with ALA 487 (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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483A LYS 2.8 15.7 + - - +
484A GLU* 3.5 8.1 - - - +
486A ARG* 1.3 74.8 - - - +
488A MET* 1.3 59.1 + - - +
490A ARG* 3.9 16.9 - - - +
491A GLU* 2.9 32.8 + - - +
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Residues in contact with MET 488 (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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435A ASP* 3.9 15.5 - - - +
438A CYS* 3.9 30.1 - - + +
439A ARG* 3.8 41.7 - - + +
484A GLU* 3.0 17.5 + - + +
485A LEU* 3.4 19.7 - - - +
487A ALA* 1.3 76.7 - - - +
489A LEU* 1.3 57.3 + - - +
491A GLU* 3.7 6.9 - - - +
492A LYS* 3.0 42.9 + - + +
90C PHE* 6.2 0.7 - - - -
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Residues in contact with LEU 489 (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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434A LEU* 4.0 26.5 - - + +
437A MET* 3.9 21.1 - - + -
438A CYS* 3.5 26.0 - - - -
476A PHE* 3.6 49.8 - - + +
481A LEU* 4.1 5.8 - - + -
485A LEU* 3.0 24.4 + - + +
486A ARG 3.8 4.3 - - - +
488A MET* 1.3 77.6 - - - +
490A ARG* 1.3 54.7 + - - +
493A PHE* 2.7 46.4 + - + +
497A CYS* 3.9 2.6 - - - -
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Residues in contact with ARG 490 (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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477A ASP* 2.7 29.7 + - - -
486A ARG* 3.0 28.0 + - - +
487A ALA* 3.9 20.8 - - - +
489A LEU* 1.3 76.3 - - - +
491A GLU* 1.3 61.5 + - - +
494A PRO* 3.4 26.8 - - + +
497A CYS* 3.6 26.8 - - + +
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Residues in contact with GLU 491 (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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487A ALA 2.9 18.6 + - - +
488A MET* 3.7 7.1 - - - +
490A ARG* 1.3 79.0 - - - +
492A LYS* 1.3 69.5 + - + +
494A PRO* 3.8 10.5 - - - +
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Residues in contact with LYS 492 (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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438A CYS* 3.3 47.4 + - + +
441A ILE* 4.3 13.0 - - - -
442A PRO* 3.7 16.6 - - - +
449A GLU* 5.1 0.2 + - - -
453A ARG* 3.6 38.4 + - - +
488A MET* 3.0 25.8 + - + +
491A GLU* 1.3 89.1 - - + +
493A PHE* 1.3 77.4 + - + +
494A PRO* 3.4 8.6 - - - +
495A GLU* 4.5 0.7 - - - +
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Residues in contact with PHE 493 (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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437A MET* 3.7 20.4 - - + -
438A CYS* 4.2 12.8 - - - -
441A ILE* 3.5 31.2 - - + -
453A ARG* 5.1 7.4 - - + -
456A VAL* 3.6 16.8 - - + -
457A PHE* 4.5 16.6 - + + -
460A LEU* 3.9 21.1 - - + -
476A PHE* 4.4 9.2 - + + -
489A LEU* 2.7 31.3 + - + +
492A LYS* 1.3 88.2 - - + +
494A PRO* 1.3 64.7 - - - +
495A GLU* 3.2 6.5 - - - -
496A PHE* 3.2 29.6 + + + -
497A CYS* 3.3 13.9 - - - -
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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