Contacts of the helix formed by residues 476 - 483 (chain A) in PDB entry 2WTJ
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 THR 476 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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404A TYR* 5.9 7.9 - - + -
406A ARG* 6.0 7.6 - - + -
410A CYS* 3.9 7.6 - - - -
466A LEU* 4.9 0.4 - - - +
474A ARG 4.5 4.9 - - - +
475A PHE* 1.3 77.5 - - - +
477A THR* 1.3 64.6 + - - +
478A GLU* 3.4 17.3 + - - +
479A GLU* 3.0 36.4 + - - +
480A ALA* 3.0 22.1 + - - +
482A ARG* 5.3 0.2 + - - -
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Residues in contact with THR 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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332A LEU* 4.2 16.8 - - + +
335A VAL* 3.8 22.4 - - + -
336A GLN* 3.4 44.4 - - - +
339A HIS* 4.3 9.5 + - - +
410A CYS* 3.7 15.4 - - - -
413A LEU* 4.4 1.3 - - + -
476A THR* 1.3 74.1 - - - +
478A GLU* 1.3 67.7 + - - +
480A ALA* 3.2 7.4 + - - +
481A LEU* 2.9 35.4 + - - +
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Residues in contact with GLU 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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336A GLN* 3.2 36.5 - - - +
339A HIS* 6.0 1.6 - - - +
340A GLU* 4.6 9.7 - - - +
476A THR* 3.2 16.3 + - - +
477A THR* 1.3 83.7 + - - +
479A GLU* 1.3 62.9 + - - +
481A LEU* 3.1 6.1 + - - +
482A ARG* 3.1 43.6 + - - +
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Residues in contact with GLU 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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473A ALA 4.9 1.8 - - - +
474A ARG 3.8 4.9 - - - +
475A PHE* 3.2 49.1 - - + -
476A THR* 3.0 38.5 + - - +
478A GLU* 1.3 76.1 - - - +
480A ALA* 1.3 63.4 + - - +
482A ARG* 3.1 36.8 + - - +
483A HIS* 3.1 9.7 + - - -
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Residues in contact with ALA 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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332A LEU* 3.6 27.1 - - + -
462A LEU* 4.0 16.6 - - + -
466A LEU* 4.6 9.4 - - + -
475A PHE* 3.6 11.6 - - + -
476A THR 3.0 14.9 + - - +
477A THR* 3.5 8.3 - - - +
479A GLU* 1.3 75.3 - - - +
481A LEU* 1.3 62.0 + - - +
483A HIS* 3.2 10.9 + - - +
486A LEU* 3.2 22.4 - - - +
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Residues in contact with LEU 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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329A TYR* 3.7 36.1 - - + -
332A LEU* 3.8 26.5 - - + +
333A LEU* 4.1 10.5 - - + -
336A GLN* 3.3 46.4 - - + +
477A THR 2.9 20.4 + - - +
478A GLU* 3.1 5.6 + - - +
480A ALA* 1.3 78.0 - - - +
482A ARG* 1.3 58.3 + - + +
483A HIS 3.3 0.2 - - - -
486A LEU* 4.0 8.0 - - + +
487A GLN* 2.9 17.5 + - - +
492A LYS* 5.0 4.9 + - - -
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Residues in contact with ARG 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 GLU* 3.1 38.0 + - - +
479A GLU* 3.1 27.2 + - - +
481A LEU* 1.3 75.0 - - + +
483A HIS* 1.3 64.4 + - - +
484A PRO* 3.6 3.6 - - - +
487A GLN* 3.3 17.0 + - - +
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Residues in contact with HIS 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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458A LYS* 3.3 29.6 - - + -
461A ASP* 2.7 29.5 + - + -
462A LEU* 3.7 25.4 + - + +
465A LYS* 3.9 8.5 + - + -
475A PHE* 3.9 20.6 - + - -
479A GLU 3.1 9.4 + - - +
480A ALA 3.2 16.0 + - - +
482A ARG* 1.3 77.3 - - - +
484A PRO* 1.3 85.7 - - + +
485A TRP* 3.0 28.2 + - - +
486A LEU* 2.8 15.2 + - + -
487A GLN* 2.9 10.7 + - - -
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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