Contacts of the helix formed by residues 665 - 671 (chain B) 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 THR 665 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593B GLU* 5.4 7.9 - - - +
597B ILE* 4.2 4.0 - - - -
663B ARG 5.3 2.0 - - - +
664B LEU* 1.3 78.0 - - - +
666B ALA* 1.3 64.6 + - - +
667B LYS* 3.7 9.2 + - - +
668B GLN* 3.0 39.4 + - - +
669B VAL* 3.1 21.3 + - - +
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Residues in contact with ALA 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B GLY* 4.1 7.4 - - - +
523B VAL* 4.3 6.5 - - + -
524B GLU* 3.8 33.9 - - + +
527B HIS* 4.4 9.6 + - + +
597B ILE* 3.7 23.8 - - + +
600B LEU* 5.9 0.7 - - + -
665B THR* 1.3 73.8 - - - +
667B LYS* 1.3 63.8 + - - +
669B VAL* 3.0 17.3 + - - +
670B LEU* 3.0 18.1 + - - +
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Residues in contact with LYS 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B GLU* 3.2 28.9 + - + +
665B THR* 3.3 9.1 + - - +
666B ALA* 1.3 78.2 - - - +
668B GLN* 1.3 63.5 + - + +
670B LEU* 3.2 6.7 + - - +
671B GLN* 3.1 58.6 + - + +
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Residues in contact with GLN 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B ARG 4.4 1.6 - - - +
664B LEU* 3.4 32.1 - - + +
665B THR* 3.0 40.1 + - - +
667B LYS* 1.3 77.1 - - + +
669B VAL* 1.3 64.6 + - - +
671B GLN* 3.4 18.0 + - - +
672B HIS* 3.3 19.1 + - - +
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Residues in contact with VAL 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B LEU* 4.0 32.3 - - + -
520B GLY* 5.7 3.8 - - - -
597B ILE* 4.5 7.0 - - + -
600B LEU* 6.1 1.8 - - + -
651B LEU* 4.4 5.8 - - + -
655B MET* 4.0 28.5 - - + -
664B LEU* 3.8 24.2 - - + -
665B THR 3.1 15.5 + - - +
666B ALA* 3.0 11.5 + - - +
668B GLN* 1.3 78.3 - - - +
670B LEU* 1.3 64.4 + - + +
671B GLN 3.1 0.2 - - - -
672B HIS* 3.0 23.6 + - - +
675B VAL* 3.7 9.0 - - + +
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Residues in contact with LEU 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B LEU 4.7 0.4 - - - +
517B HIS* 3.7 35.4 + - + +
520B GLY* 3.8 12.8 - - - +
521B LYS* 3.7 34.5 - - + +
524B GLU* 3.1 35.0 - - + +
666B ALA 3.0 9.3 + - - +
667B LYS* 3.2 7.6 + - - +
669B VAL* 1.3 79.3 - - + +
671B GLN* 1.3 60.0 + - + +
672B HIS 3.3 0.2 - - - -
675B VAL* 3.8 13.2 - - + +
676B THR* 3.2 20.3 - - - +
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Residues in contact with GLN 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667B LYS* 3.1 53.1 + - + +
668B GLN* 3.8 18.6 - - - +
669B VAL 3.1 1.4 - - - -
670B LEU* 1.3 78.5 - - + +
672B HIS* 1.3 65.6 + - - +
673B PRO* 3.6 5.0 - - - +
676B THR* 4.0 10.6 + - - +
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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