Contacts of the helix formed by residues 193 - 202 (chain C) in PDB entry 1WNT
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 ASP 193 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189C ALA 5.5 0.8 + - - -
190C THR 5.1 0.2 - - - -
191C TRP 3.4 0.6 - - - -
192C SER* 1.3 77.0 - - - +
194C PRO* 1.3 80.6 - - - +
195C HIS* 3.3 23.5 - - - +
196C LYS* 2.9 49.5 + - + +
197C ALA* 2.8 23.2 + - - +
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Residues in contact with PRO 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C SER 3.1 9.1 - - - +
193C ASP* 1.3 92.3 - - - +
195C HIS* 1.3 57.1 + - - +
197C ALA* 3.6 4.7 + - + +
198C LYS* 3.0 30.5 + - - +
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Residues in contact with HIS 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C ASP* 3.1 18.0 + - - +
194C PRO* 1.3 79.2 - - - +
196C LYS* 1.3 73.2 + - + +
198C LYS* 3.5 17.0 + - - +
199C THR* 2.9 38.6 + - + +
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Residues in contact with LYS 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C ASN* 5.3 8.3 - - - +
190C THR* 4.0 36.7 + - - +
191C TRP* 3.1 25.2 - - + -
193C ASP* 2.9 38.8 + - + +
195C HIS* 1.3 89.3 - - + +
197C ALA* 1.3 61.3 + - - +
199C THR* 3.7 11.1 + - - -
200C MET* 4.1 3.1 + - - +
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Residues in contact with ALA 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C TRP* 3.4 24.7 - - - +
192C SER 5.2 0.4 - - - +
193C ASP 2.8 12.1 + - - +
194C PRO* 4.0 4.7 - - + +
196C LYS* 1.3 77.7 - - - +
198C LYS* 1.3 58.9 + - - +
200C MET* 3.3 5.9 + - - +
201C LEU* 3.0 27.0 + - + +
209C PHE* 3.4 30.4 - - + -
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Residues in contact with LYS 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C PRO 3.0 19.8 + - - +
195C HIS* 3.6 18.0 - - - +
196C LYS 3.4 0.2 - - - -
197C ALA* 1.3 72.8 - - - +
199C THR* 1.3 56.9 + - + +
200C MET 3.0 9.2 + - - -
201C LEU* 3.0 11.7 + - - +
202C ASN* 2.5 43.2 + - - +
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Residues in contact with THR 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C HIS* 2.9 31.7 + - + +
196C LYS* 3.7 9.7 + - - -
197C ALA 3.5 0.2 - - - -
198C LYS* 1.3 80.3 - - + +
200C MET* 1.3 56.7 + - - +
202C ASN* 3.6 17.8 - - + +
203C ARG* 3.7 19.8 - - - +
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Residues in contact with MET 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C GLN* 4.2 11.2 - - - +
143C VAL* 4.6 13.5 - - + -
180C THR* 4.4 2.2 - - - +
181C VAL* 4.5 6.5 - - + -
191C TRP* 3.3 39.0 - - + -
196C LYS 4.1 9.4 + - - +
197C ALA 3.3 10.9 - - - +
198C LYS 3.0 0.2 - - - -
199C THR* 1.3 77.5 + - - +
201C LEU* 1.3 65.2 + - - +
202C ASN 3.0 1.9 + - - -
203C ARG* 3.2 11.7 + - - +
204C ILE* 2.8 25.3 + - + +
209C PHE* 3.3 26.5 - - + -
241C PHE* 3.2 42.8 - - + -
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Residues in contact with LEU 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C ALA* 3.0 13.2 + - + +
198C LYS* 3.0 11.0 + - - +
200C MET* 1.3 76.8 - - - +
202C ASN* 1.3 65.0 - - - +
204C ILE* 3.4 26.3 + - + +
207C GLY* 4.2 14.4 - - - +
208C LYS* 4.2 19.5 - - - -
209C PHE* 3.3 56.3 - - + +
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Residues in contact with ASN 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C LYS* 2.5 42.0 + - - +
199C THR* 3.6 21.7 - - - +
200C MET 3.0 0.2 - - - -
201C LEU* 1.3 85.0 - - - +
203C ARG* 1.3 61.3 + - + +
204C ILE 3.8 2.0 + - - +
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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