Contacts of the helix formed by residues 697 - 708 (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 ALA 697 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612B THR* 3.6 22.7 - - + +
615B ALA* 3.5 10.5 - - + +
616B ASN 4.1 1.3 - - - -
617B GLY 3.4 32.2 - - - +
693B LEU 2.8 17.6 + - - +
694B VAL* 3.3 4.5 + - - +
696B GLY* 1.3 75.9 - - - +
698B MET* 1.3 53.3 + - - +
700B ALA* 3.5 0.9 + - - +
701B THR* 2.6 37.2 + - - -
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Residues in contact with MET 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B LEU* 4.5 6.3 - - + -
538B PRO* 3.5 24.0 - - + -
602B ILE* 3.7 34.1 - - + +
603B LEU* 4.7 2.2 - - + -
606B THR* 3.3 35.0 - - + +
612B THR* 4.0 13.2 - - + +
694B VAL 3.0 17.1 + - - +
695B LYS* 3.6 6.3 - - - +
697B ALA* 1.3 76.2 - - - +
699B ALA* 1.3 65.4 + - - +
701B THR* 3.2 5.5 + - - -
702B TYR* 3.2 34.7 + - + -
1714B PEG 3.6 31.4 - - - +
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Residues in contact with ALA 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695B LYS 2.9 16.7 + - - +
696B GLY* 3.8 6.7 - - - +
698B MET* 1.3 77.4 - - - +
700B ALA* 1.3 56.4 + - - +
702B TYR* 3.2 5.8 + - - +
703B SER* 2.9 29.8 + - - -
1714B PEG 4.4 11.8 - - - -
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Residues in contact with ALA 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617B GLY 4.1 7.2 - - - +
618B PRO 3.9 17.9 - - - +
620B ASP 4.0 9.6 - - - +
622B PRO 5.8 0.2 - - - -
625B ILE* 3.5 22.7 - - + +
696B GLY 3.0 17.3 + - - +
697B ALA 3.8 4.9 - - - +
699B ALA* 1.3 76.2 - - - +
701B THR* 1.3 57.1 + - - +
703B SER* 3.7 6.9 - - - -
704B ALA* 3.0 23.9 + - - +
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Residues in contact with THR 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B TRP* 4.5 8.1 - - + -
602B ILE* 4.8 9.9 - - + -
614B PHE* 4.8 1.1 - - + -
615B ALA* 3.4 8.7 - - - +
625B ILE* 4.1 18.9 - - + +
629B ILE* 4.4 7.0 - - + -
697B ALA 2.6 22.8 + - - -
698B MET* 3.5 9.4 - - - -
699B ALA 3.1 0.2 - - - -
700B ALA* 1.3 78.3 - - - +
702B TYR* 1.3 60.1 + - + +
704B ALA* 3.5 3.5 + - - +
705B LEU* 3.2 38.9 + - + +
1711B NA 2.8 27.4 - - - -
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Residues in contact with TYR 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B ASP* 4.8 9.4 - - - -
536B LEU 3.6 5.1 + - - -
537B LYS* 3.6 46.8 - - + +
538B PRO* 4.1 1.9 - - + +
598B TRP* 4.4 3.9 - + - -
599B SER* 2.9 34.6 + - - -
602B ILE* 3.3 36.3 - - + +
698B MET* 3.2 34.6 + - + +
699B ALA* 3.2 4.9 + - - +
701B THR* 1.3 78.9 - - + +
703B SER* 1.3 61.0 + - - +
705B LEU* 3.8 17.9 - - + +
706B ASN* 2.9 29.6 + - - +
1714B PEG 4.6 0.9 - - - -
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Residues in contact with SER 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622B PRO* 6.0 0.4 - - - -
699B ALA 2.9 17.3 + - - -
700B ALA* 3.7 9.0 - - - -
702B TYR* 1.3 74.7 - - - +
704B ALA* 1.3 65.1 + - - +
706B ASN* 3.4 5.8 + - - +
707B SER* 3.0 26.9 + - - -
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Residues in contact with ALA 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622B PRO* 3.8 31.1 - - + +
625B ILE* 3.9 18.4 - - + -
626B LEU* 3.9 16.2 - - + +
700B ALA 3.0 17.8 + - - +
701B THR 3.6 6.1 - - - +
703B SER* 1.3 76.3 - - - +
705B LEU* 1.3 60.9 + - - +
707B SER* 3.2 21.8 - - - -
708B SER* 3.4 9.0 + - - -
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Residues in contact with LEU 705 (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* 3.4 39.0 - - + -
626B LEU* 4.2 11.0 - - + -
629B ILE* 4.0 26.2 - - + -
701B THR* 3.2 21.4 + - + +
702B TYR* 3.9 17.9 - - + +
703B SER 3.2 0.2 - - - -
704B ALA* 1.3 74.6 - - - +
706B ASN* 1.3 65.6 + - - +
707B SER 3.3 0.2 + - - -
708B SER* 3.4 17.6 + - - +
709B LYS* 3.5 12.4 - - - +
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Residues in contact with ASN 706 (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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560B PHE* 5.2 10.9 - - - -
702B TYR 2.9 18.6 + - - +
703B SER* 3.8 5.8 - - - +
705B LEU* 1.3 75.7 - - - +
707B SER* 1.3 65.3 + - - +
709B LYS* 2.9 27.8 + - - +
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Residues in contact with SER 707 (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* 5.0 12.4 - - - +
626B LEU* 5.3 2.5 - - - -
703B SER 3.0 15.4 + - - -
704B ALA* 3.2 15.1 - - - -
706B ASN* 1.3 78.0 - - - +
708B SER* 1.3 58.3 + - - +
709B LYS 3.0 11.4 + - - +
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Residues in contact with SER 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626B LEU* 3.9 24.7 - - - +
704B ALA 3.4 7.8 + - - -
705B LEU* 3.4 13.1 + - - +
706B ASN 3.3 0.6 - - - -
707B SER* 1.3 76.2 - - - +
709B LYS* 1.3 57.4 + - - +
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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