Contacts of the helix formed by residues 456 - 466 (chain A) in PDB entry 2WNT
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 PRO 456 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449A ILE* 3.9 43.3 - - + -
451A LYS* 5.4 5.2 - - + -
455A ASP* 1.3 87.5 - - - +
457A SER* 1.3 52.5 + - - +
458A GLU 3.4 1.6 - - - -
459A GLU* 3.2 17.1 + - + +
460A ILE* 2.8 51.4 + - + +
485A VAL* 4.1 25.1 - - + -
487A LEU* 5.2 0.2 - - + -
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Residues in contact with SER 457 (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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455A ASP* 2.9 13.9 - - - -
456A PRO* 1.3 78.5 - - - +
458A GLU* 1.3 58.5 + - - +
460A ILE* 3.3 6.7 + - - +
461A GLU* 3.0 43.6 + - - +
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Residues in contact with GLU 458 (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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455A ASP 4.5 2.6 + - - +
457A SER* 1.3 76.4 - - - +
459A GLU* 1.3 63.5 + - - +
461A GLU* 4.0 9.3 - - + +
462A ILE* 3.2 39.6 + - + +
558A PHE 5.2 0.7 - - - -
561A ALA 4.1 17.3 - - - +
562A LYS* 3.5 11.1 - - - +
563A GLN* 2.7 37.6 + - + +
565A ARG* 4.5 18.1 + - - +
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Residues in contact with GLU 459 (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 LYS* 3.3 27.8 + - - +
449A ILE* 4.1 12.8 - - - +
455A ASP 5.4 0.2 + - - -
456A PRO* 3.2 17.6 + - + +
458A GLU* 1.3 78.5 - - - +
460A ILE* 1.3 63.0 + - - +
462A ILE* 3.4 5.1 + - - +
463A LEU* 3.0 37.4 + - + +
487A LEU* 4.4 14.8 - - + +
556A CYS 5.3 0.7 - - - +
557A ASP* 3.7 1.0 - - - +
558A PHE* 3.5 48.5 + - + +
559A GLY* 3.9 10.3 - - - -
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Residues in contact with ILE 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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456A PRO* 2.8 34.3 + - + +
457A SER* 3.7 6.1 - - - +
459A GLU* 1.3 74.8 - - - +
461A GLU* 1.3 67.6 + - + +
463A LEU* 3.4 6.2 + - - +
464A LEU* 3.0 41.4 + - + +
475A LEU* 4.3 8.0 - - + +
478A VAL* 3.9 19.1 - - + -
485A VAL* 4.3 8.7 - - + -
487A LEU* 3.9 32.5 - - + -
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Residues in contact with GLU 461 (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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457A SER* 3.0 30.0 + - - +
458A GLU* 4.1 7.4 + - + +
460A ILE* 1.3 77.4 - - + +
462A ILE* 1.3 63.8 + - + +
464A LEU* 3.3 8.4 + - - +
465A ARG* 3.0 46.8 + - - +
565A ARG* 2.6 36.2 + - - +
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Residues in contact with ILE 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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458A GLU* 3.2 26.5 + - + +
459A GLU* 3.8 5.2 - - - +
460A ILE 3.3 0.2 - - - -
461A GLU* 1.3 78.6 - - + +
463A LEU* 1.3 59.7 + - + +
465A ARG* 4.6 2.2 - - - +
466A TYR* 2.9 47.8 + - + +
467A GLY 3.9 0.2 + - - -
472A ILE* 6.0 0.8 - - + +
526A LEU* 5.2 0.7 - - + -
531A VAL* 4.0 16.2 - - + -
558A PHE* 3.8 29.6 - - + -
561A ALA* 3.7 37.0 - - + +
562A LYS 4.3 1.3 - - - +
563A GLN* 4.4 24.2 - - + +
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Residues in contact with LEU 463 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459A GLU* 3.0 39.4 + - + +
460A ILE* 3.9 4.7 - - - +
461A GLU 3.3 0.2 - - - -
462A ILE* 1.3 75.0 - - + +
464A LEU* 1.3 62.8 + - - +
467A GLY* 2.9 27.9 + - - +
472A ILE* 4.2 9.0 - - + -
473A ILE* 4.0 32.1 - - + +
475A LEU* 3.9 34.1 - - + +
487A LEU* 4.7 11.4 - - + -
489A THR* 5.4 4.7 - - + -
556A CYS 6.1 0.4 - - - +
558A PHE* 4.0 28.3 - - + -
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Residues in contact with LEU 464 (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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460A ILE* 3.0 32.5 + - + +
461A GLU* 3.7 7.2 - - - +
463A LEU* 1.3 79.3 - - - +
465A ARG* 1.3 62.0 + - - +
467A GLY* 4.4 1.2 + - - -
468A GLN* 5.4 1.9 + - - +
475A LEU* 3.7 28.5 - - + +
478A VAL* 5.0 7.0 - - + -
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Residues in contact with ARG 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 GLU* 3.0 49.8 + - - +
462A ILE* 3.9 3.6 - - - +
464A LEU* 1.3 81.2 - - - +
466A TYR* 1.3 94.8 + - + +
467A GLY 3.6 0.4 - - - -
468A GLN* 5.0 3.2 + - - +
563A GLN* 3.5 21.6 - - - +
565A ARG* 5.1 0.6 - - - +
571A LEU* 3.3 31.9 - - - +
465B ARG* 4.3 25.2 - - - +
570B LEU* 4.7 7.3 - - - +
571B LEU* 5.5 14.0 + - + +
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Residues in contact with TYR 466 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462A ILE* 2.9 38.1 + - + +
465A ARG* 1.3 103.9 - - + +
467A GLY* 1.3 56.5 + - - +
468A GLN 2.9 12.5 + - - -
469A HIS* 3.0 22.5 + - - +
472A ILE* 3.6 20.6 - - + +
525A TYR* 3.6 26.2 - + + -
526A LEU* 4.3 9.2 - - + -
529A GLN* 3.5 46.6 + - + +
531A VAL* 3.3 21.3 - - + -
563A GLN* 3.1 24.1 + - - -
571A LEU* 5.1 1.2 - - - +
570B LEU* 4.3 4.7 - - - +
571B LEU* 5.8 2.7 - - + -
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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