Contacts of the helix formed by residues 621 - 629 (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 621 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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619B SER 4.5 6.5 - - - +
620B ASP* 1.3 76.4 - - - +
622B PRO* 1.3 72.9 - - + +
623B GLU* 3.0 21.6 + - - +
624B GLU* 3.1 39.9 + - - +
625B ILE* 3.1 14.0 + - - +
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Residues in contact with PRO 622 (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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620B ASP 4.3 2.7 - - - +
621B THR* 1.3 90.0 - - + +
623B GLU* 1.3 64.5 + - - +
625B ILE* 4.8 0.2 - - - -
626B LEU* 2.9 45.1 + - + +
703B SER 6.0 0.4 - - - -
704B ALA* 3.8 30.3 - - + +
707B SER* 5.0 11.4 - - - +
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Residues in contact with GLU 623 (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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621B THR* 3.0 23.2 - - - +
622B PRO* 1.3 83.3 - - - +
624B GLU* 1.3 62.1 + - + +
626B LEU* 4.6 1.5 - - - +
627B THR* 2.7 33.9 + - - +
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Residues in contact with GLU 624 (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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619B SER 4.3 1.9 - - - +
620B ASP* 3.1 23.1 - - - +
621B THR* 3.1 36.0 + - - +
623B GLU* 1.3 78.4 - - + +
625B ILE* 1.3 63.5 + - - +
627B THR* 3.7 4.4 - - - -
628B ARG* 3.2 52.4 + - - +
1713B PEG 4.5 1.6 - - - +
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Residues in contact with ILE 625 (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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614B PHE* 3.6 23.3 - - + +
615B ALA* 3.9 6.3 - - + -
620B ASP* 3.7 31.2 - - + +
621B THR 3.1 17.1 + - - +
624B GLU* 1.3 78.9 - - - +
626B LEU* 1.3 57.9 + - - +
628B ARG* 3.3 4.0 + - - +
629B ILE* 2.9 47.8 + - + +
700B ALA* 3.5 32.8 - - + +
701B THR* 4.2 13.9 - - + -
704B ALA* 3.9 17.5 - - + -
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Residues in contact with LEU 626 (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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622B PRO* 2.9 31.6 + - + +
623B GLU* 4.6 1.8 - - - +
625B ILE* 1.3 73.7 - - - +
627B THR* 1.3 56.7 + - - +
629B ILE* 3.9 10.4 - - + +
630B GLY* 2.8 31.0 + - - -
704B ALA* 3.9 35.9 - - + +
705B LEU* 4.2 15.9 - - + -
707B SER* 5.3 2.0 - - - -
708B SER* 3.9 24.5 - - - +
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Residues in contact with THR 627 (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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623B GLU 2.7 23.9 + - - -
624B GLU* 3.7 5.6 - - - -
626B LEU* 1.3 76.4 - - - +
628B ARG* 1.3 57.5 + - - +
630B GLY* 3.5 1.1 + - - -
631B SER* 3.0 28.8 + - - -
1713B PEG 3.5 24.2 - - - -
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Residues in contact with ARG 628 (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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613B PRO 5.0 2.7 - - - -
614B PHE* 2.9 43.5 + - + +
615B ALA* 3.8 1.4 - - - +
616B ASN* 3.6 21.5 + - - -
620B ASP* 2.8 26.1 + - - -
624B GLU* 3.2 42.6 + - - +
625B ILE 3.3 6.5 + - - +
627B THR* 1.3 72.4 - - - +
629B ILE* 1.3 65.9 + - - +
631B SER* 2.7 19.6 + - - -
632B GLY 3.4 2.4 + - - -
633B LYS 3.8 11.5 + - - +
1713B PEG 3.0 58.8 + - - +
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Residues in contact with ILE 629 (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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598B TRP* 4.1 27.6 - - + +
614B PHE* 3.5 30.6 - - + -
625B ILE* 2.9 38.9 + - + +
626B LEU* 3.9 9.2 - - + +
628B ARG* 1.3 74.6 - - - +
630B GLY* 1.3 64.8 + - - +
632B GLY* 3.0 15.9 + - - -
658B VAL* 4.8 4.0 - - - +
701B THR* 4.4 2.2 - - + -
705B LEU* 4.0 32.8 - - + -
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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