Contacts of the helix formed by residues 602 - 609 (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 ILE 602 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538B PRO* 5.2 1.3 - - + -
598B TRP* 3.0 35.4 + - + +
599B SER* 3.3 12.3 - - - +
601B GLY* 1.3 75.2 - - - +
603B LEU* 1.3 64.6 + - + +
605B TYR* 3.4 7.6 - - - +
606B THR* 2.8 33.5 + - - -
613B PRO* 4.0 21.7 - - + +
614B PHE* 4.1 3.1 - - + -
656B LEU* 3.6 19.7 - - + -
698B MET* 3.7 17.0 - - + -
701B THR* 4.8 7.4 - - + -
702B TYR* 3.3 40.2 - - + +
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Residues in contact with LEU 603 (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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497B LEU* 3.6 35.0 - - + -
498B LEU* 4.3 12.3 - - + -
515B VAL* 4.8 10.1 - - + -
516B LEU* 6.2 3.8 - - + -
519B ILE* 5.4 3.8 - - + -
536B LEU 5.9 1.1 - - - +
538B PRO* 4.1 25.4 - - + -
541B ILE* 4.1 20.6 - - + -
599B SER 3.2 8.2 + - - +
600B LEU* 3.5 15.9 - - + +
602B ILE* 1.3 80.5 - - - +
604B LEU* 1.3 66.2 + - - +
606B THR* 3.2 7.0 + - - -
607B MET* 3.0 41.7 + - + +
698B MET* 4.7 2.2 - - - -
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Residues in contact with LEU 604 (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 8.9 - - + +
600B LEU 2.9 17.0 + - - +
601B GLY* 3.5 5.4 - - - +
603B LEU* 1.3 76.0 - - - +
605B TYR* 1.3 62.3 + - - +
607B MET* 3.2 19.9 + - + +
608B LEU* 3.1 37.9 + - + +
648B ALA* 4.9 0.7 - - - +
651B LEU* 3.7 20.6 - - + -
652B VAL* 3.4 26.9 - - + -
655B MET* 3.6 25.4 - - - -
674B TRP* 3.6 33.7 - - + -
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Residues in contact with TYR 605 (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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601B GLY 2.9 20.1 + - - +
602B ILE* 3.4 6.5 - - - +
603B LEU 3.3 0.2 - - - -
604B LEU* 1.3 73.0 - - - +
606B THR* 1.3 57.4 + - - +
608B LEU* 3.4 2.1 + - - +
609B ALA* 2.9 36.8 + - + +
611B TYR* 3.3 36.2 - + - -
613B PRO* 3.5 45.3 + - + +
634B PHE* 4.2 7.9 - + + -
635B THR* 2.6 40.8 + - - -
636B LEU* 4.1 4.3 - - + -
641B TRP* 3.4 27.2 + + - -
652B VAL* 3.9 21.7 - - + +
656B LEU* 4.2 4.7 - - + -
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Residues in contact with THR 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B LEU* 4.6 13.2 - - + -
502B LEU* 5.4 5.7 - - + +
602B ILE 2.8 21.3 + - - -
603B LEU* 3.2 6.5 + - - -
605B TYR* 1.3 74.3 - - - +
607B MET* 1.3 59.9 + - - +
610B GLY* 2.7 31.0 + - - -
611B TYR 3.4 14.8 - - - +
612B THR* 3.7 13.5 - - - -
613B PRO* 4.3 0.2 - - - +
694B VAL* 3.6 31.0 - - + -
698B MET* 3.3 22.5 - - + +
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Residues in contact with MET 607 (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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497B LEU* 5.0 0.2 - - - -
498B LEU* 5.2 0.4 - - + -
501B ILE* 3.6 23.3 - - + -
502B LEU* 5.6 1.3 - - - -
507B PHE* 3.7 31.1 - - + -
512B ALA* 4.0 22.7 - - + +
515B VAL* 3.8 27.1 - - + -
516B LEU* 4.7 7.9 - - + +
603B LEU* 3.0 30.0 + - + +
604B LEU* 3.7 34.5 - - + +
606B THR* 1.3 74.6 - - - +
608B LEU* 1.3 62.1 + - + +
686B LEU* 3.5 13.9 - - - +
1712B CL 3.4 20.9 - - - +
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Residues in contact with LEU 608 (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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509B GLU* 4.3 17.3 - - + -
512B ALA* 4.7 6.3 - - + -
604B LEU* 3.1 26.3 + - + +
605B TYR 3.8 2.7 - - - +
607B MET* 1.3 80.4 - - - +
609B ALA* 1.3 57.9 + - - +
640B ASN* 3.0 25.5 + - - +
641B TRP* 3.6 21.3 - - + -
644B VAL* 3.9 13.5 - - + +
648B ALA* 3.8 20.9 - - + -
652B VAL* 3.5 31.4 - - + -
674B TRP* 3.9 26.2 - - + -
686B LEU* 4.0 9.6 - - + +
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Residues in contact with ALA 609 (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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605B TYR* 2.9 33.4 + - + +
608B LEU* 1.3 75.5 - - - +
610B GLY* 1.3 62.2 + - - +
611B TYR* 3.4 25.8 - - + +
640B ASN* 3.1 26.2 + - - +
641B TRP* 3.4 28.3 - - + +
687B SER 3.8 0.9 - - - +
688B HIS* 4.9 0.2 - - - -
689B GLN* 5.8 0.2 - - - +
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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