Contacts of the helix formed by residues 459 - 472 (chain A) in PDB entry 2WKP
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 459 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457A GLU 3.3 5.1 + - - +
458A THR* 1.3 73.2 - - - +
460A ARG* 1.3 62.5 + - - +
461A ALA* 2.9 24.8 + - - +
462A THR* 3.1 32.4 + - - +
463A VAL* 3.2 12.8 + - - +
480A LEU* 5.3 3.3 - - + +
481A ILE* 5.2 3.2 - - - +
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Residues in contact with ARG 460 (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 ARG* 6.4 0.2 - - - +
454A GLN* 2.9 32.7 + - - +
455A GLY 5.5 3.2 + - - -
458A THR* 3.2 14.9 + - - +
459A ASP* 1.3 74.4 + - - +
461A ALA* 1.3 58.2 + - - +
463A VAL* 3.2 32.2 + - - +
464A ARG* 2.9 49.1 + - + +
1725A FMN 4.6 10.9 + - - -
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Residues in contact with ALA 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A ASP* 2.9 14.0 + - - +
460A ARG* 1.3 77.4 - - - +
462A THR* 1.3 62.9 + - - +
464A ARG* 3.2 31.0 + - - +
465A LYS* 3.1 28.1 + - - +
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Residues in contact with THR 462 (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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459A ASP* 3.1 28.3 + - - +
461A ALA* 1.3 74.9 - - - +
463A VAL* 1.3 66.0 + - - +
465A LYS* 3.1 22.7 + - + +
466A ILE* 3.3 13.6 + - - +
478A VAL* 3.6 36.6 - - + -
479A GLN 3.7 18.6 + - - +
480A LEU* 4.1 11.7 - - + -
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Residues in contact with VAL 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A GLN* 3.8 15.0 - - - +
458A THR* 3.6 30.7 - - + -
459A ASP 3.2 4.7 + - - +
460A ARG* 3.2 37.1 + - - +
462A THR* 1.3 77.5 - - - +
464A ARG* 1.3 63.0 + - + +
466A ILE* 3.1 11.6 + - + +
467A ARG* 3.0 19.9 + - - +
480A LEU* 3.9 8.5 - - + -
1725A FMN 3.4 34.9 - - - +
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Residues in contact with ARG 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A ARG* 2.9 38.1 + - + +
461A ALA* 3.2 32.3 + - - +
463A VAL* 1.3 78.0 - - + +
465A LYS* 1.3 54.8 + - - +
467A ARG* 3.3 38.7 + - - +
468A ASP* 2.9 40.4 + - - +
1725A FMN 6.1 0.2 - - - -
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Residues in contact with LYS 465 (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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461A ALA* 3.1 22.0 + - - +
462A THR* 3.1 16.8 + - + +
464A ARG* 1.3 76.3 - - - +
466A ILE* 1.3 63.1 + - - +
468A ASP* 3.5 8.7 + - - +
469A ALA* 3.1 23.0 + - - +
476A VAL* 4.4 10.2 - - + +
478A VAL* 4.4 22.1 - - + +
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Residues in contact with ILE 466 (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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462A THR 3.6 13.0 - - - +
463A VAL* 3.1 11.2 + - + +
465A LYS* 1.3 75.3 - - - +
467A ARG* 1.3 65.5 + - - +
469A ALA* 3.1 3.1 + - - +
470A ILE* 3.0 35.3 + - + +
476A VAL* 4.3 11.0 - - + -
478A VAL* 3.9 28.7 - - + -
480A LEU* 4.1 20.9 - - + -
494A PHE* 3.9 25.4 - - + -
496A LEU* 4.6 3.4 - - + -
1725A FMN 3.6 36.3 - - - +
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Residues in contact with ARG 467 (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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463A VAL 3.0 7.9 + - - +
464A ARG* 3.6 43.5 - - - +
466A ILE* 1.3 78.4 - - - +
468A ASP* 1.3 74.8 + - - +
470A ILE* 3.3 8.5 + - - +
471A ASP* 2.9 46.3 + - - +
1725A FMN 3.7 42.1 + - - +
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Residues in contact with ASP 468 (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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464A ARG* 2.9 25.8 + - - +
465A LYS* 3.7 8.8 - - - +
466A ILE 3.2 0.2 - - - -
467A ARG* 1.3 93.5 + - - +
469A ALA* 1.3 57.4 + - - +
471A ASP* 3.4 6.9 + - - +
472A ASN* 2.9 40.6 + - - +
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Residues in contact with ALA 469 (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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465A LYS 3.1 17.5 + - - +
466A ILE 3.1 4.5 + - - +
468A ASP* 1.3 77.1 - - - +
470A ILE* 1.3 58.7 + - - +
472A ASN* 3.3 1.3 + - - -
473A GLN 2.9 23.4 + - - -
474A THR* 3.0 40.2 + - - +
475A GLU 4.3 0.2 - - - +
476A VAL* 3.6 28.3 - - + -
496A LEU* 4.5 2.2 - - + -
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Residues in contact with ILE 470 (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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420A PRO* 5.7 1.1 - - + -
425A ASN* 3.9 13.2 - - + +
466A ILE* 3.0 28.6 + - + +
467A ARG* 3.3 7.8 + - - +
469A ALA* 1.3 76.4 - - - +
471A ASP* 1.3 68.4 + - - +
473A GLN* 3.0 13.3 + - - +
496A LEU* 3.7 19.7 - - + -
509A PHE* 3.6 34.7 - - + -
1725A FMN 3.1 48.0 - - + +
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Residues in contact with ASP 471 (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 ARG* 2.9 42.3 + - - +
468A ASP* 3.7 9.3 - - - +
470A ILE* 1.3 81.4 - - - +
472A ASN* 1.3 65.9 + - - +
473A GLN* 3.6 5.5 + - - +
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Residues in contact with ASN 472 (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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468A ASP* 2.9 30.8 + - - +
469A ALA 4.1 2.0 - - - +
471A ASP* 1.3 82.0 + - - +
473A GLN* 1.3 71.6 + - - +
474A THR* 3.2 21.0 - - + +
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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