Contacts of the helix formed by residues 697 - 708 (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 ALA 697 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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612A THR* 3.7 22.9 - - + +
615A ALA* 3.6 10.0 - - + +
616A ASN 4.1 1.3 - - - -
617A GLY 3.5 32.3 - - - +
618A PRO 3.8 1.2 - - - -
693A LEU 2.9 16.9 + - - +
694A VAL* 3.3 4.5 + - - +
696A GLY* 1.3 75.5 - - - +
698A MET* 1.3 52.8 + - - +
700A ALA* 3.6 0.8 + - - +
701A THR* 2.6 37.3 + - - -
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Residues in contact with MET 698 (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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498A LEU* 4.5 7.0 - - + -
537A LYS* 5.5 0.4 - - + -
538A PRO* 3.5 42.8 - - + -
539A SER 5.9 0.2 - - - +
602A ILE* 3.7 34.5 - - + +
603A LEU* 4.7 2.0 - - + -
606A THR* 3.3 35.7 - - + +
612A THR* 4.0 13.2 - - + +
694A VAL 3.0 17.6 + - - +
695A LYS* 3.6 9.0 - - - +
696A GLY 3.2 0.2 - - - -
697A ALA* 1.3 75.6 - - - +
699A ALA* 1.3 63.7 + - - +
701A THR* 3.3 4.7 + - - -
702A TYR* 3.2 35.6 + - + -
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Residues in contact with ALA 699 (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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537A LYS* 6.4 1.3 - - - -
695A LYS 2.9 17.6 + - - +
696A GLY* 3.8 5.8 - - - +
698A MET* 1.3 77.0 - - - +
700A ALA* 1.3 57.6 + - - +
702A TYR* 3.2 6.2 + - - +
703A SER* 2.9 30.5 + - - -
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Residues in contact with ALA 700 (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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617A GLY 4.2 7.2 - - - +
618A PRO 3.9 18.2 - - - +
620A ASP 4.1 7.4 - - - +
625A ILE* 3.6 19.4 - - + +
696A GLY 3.0 17.6 + - - +
697A ALA 3.9 4.5 - - - +
698A MET 3.3 0.2 - - - -
699A ALA* 1.3 76.0 - - - +
701A THR* 1.3 58.1 + - - +
703A SER* 3.4 7.0 + - - -
704A ALA* 2.9 29.1 + - - +
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Residues in contact with THR 701 (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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598A TRP* 4.6 7.6 - - + -
602A ILE* 4.8 11.7 - - + -
612A THR* 4.4 5.4 + - - -
613A PRO* 6.4 1.1 - - + -
614A PHE* 4.8 8.3 + - + +
615A ALA* 3.6 16.8 + - - +
625A ILE* 4.2 12.2 - - + +
629A ILE* 4.2 22.2 - - + -
697A ALA 2.6 23.1 + - - -
698A MET* 3.5 10.4 - - - -
699A ALA 3.2 0.4 - - - -
700A ALA* 1.3 78.1 - - - +
702A TYR* 1.3 59.9 + - + +
704A ALA* 3.5 3.5 + - - +
705A LEU* 3.2 32.9 + - + +
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Residues in contact with TYR 702 (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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534A ARG 6.0 0.7 - - - -
535A ASP* 4.6 10.3 - - - +
536A LEU 3.5 7.0 + - - -
537A LYS* 3.6 50.6 - - + +
538A PRO* 4.1 0.8 - - + +
598A TRP* 4.5 3.7 - + - -
599A SER* 2.9 36.3 + - - -
602A ILE* 3.3 33.8 - - + +
698A MET* 3.2 30.1 + - + +
699A ALA* 3.2 6.3 + - - +
701A THR* 1.3 79.6 - - + +
703A SER* 1.3 61.5 + - - +
705A LEU* 3.8 18.2 - - + +
706A ASN* 2.9 29.8 + - - +
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Residues in contact with SER 703 (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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622A PRO* 6.0 0.7 - - - -
699A ALA 2.9 18.7 + - - -
700A ALA* 3.7 9.4 - - - -
701A THR 3.3 0.2 - - - -
702A TYR* 1.3 75.9 - - - +
704A ALA* 1.3 64.9 + - - +
706A ASN* 3.4 4.9 + - - +
707A SER* 3.1 26.5 + - - -
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Residues in contact with ALA 704 (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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622A PRO* 3.8 32.5 - - + +
625A ILE* 4.0 17.7 - - + -
626A LEU* 3.8 20.0 - - + +
700A ALA 2.9 17.7 + - - +
701A THR 3.7 5.8 - - - +
703A SER* 1.3 76.0 - - - +
705A LEU* 1.3 60.9 + - - +
707A SER* 3.2 20.7 - - - -
708A SER 3.3 5.9 + - - -
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Residues in contact with LEU 705 (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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598A TRP* 3.4 38.1 - - + -
626A LEU* 4.0 19.1 - - + -
629A ILE* 4.1 19.3 - - + -
701A THR* 3.2 22.6 + - + +
702A TYR* 3.9 18.2 - - + +
703A SER 3.2 0.6 - - - -
704A ALA* 1.3 75.8 - - - +
706A ASN* 1.3 66.0 + - - +
707A SER 3.4 0.2 + - - -
708A SER* 3.4 20.5 + - - +
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Residues in contact with ASN 706 (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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560A PHE* 6.4 1.6 - - + -
702A TYR 2.9 17.6 + - - +
703A SER* 3.9 5.8 - - - +
705A LEU* 1.3 75.2 - - - +
707A SER* 1.3 64.4 + - - +
708A SER 3.1 8.3 - - - +
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Residues in contact with SER 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622A PRO* 5.0 12.8 - - - +
626A LEU* 5.4 2.2 - - - -
703A SER 3.1 15.6 + - - -
704A ALA* 3.2 14.1 - - - -
706A ASN* 1.3 77.2 - - - +
708A SER* 1.3 64.5 + - - +
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Residues in contact with SER 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A LEU* 4.5 20.6 - - - +
704A ALA 3.3 8.6 + - - -
705A LEU* 3.5 17.1 - - - +
706A ASN 3.1 10.2 - - - +
707A SER* 1.3 85.0 - - - +
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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