Contacts of the helix formed by residues 240 - 244 (chain B) 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 GLY 240 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205B PRO* 3.8 13.6 - - - +
238B GLU* 2.5 20.3 + - - -
239B GLY* 1.3 71.7 - - - +
241B PHE* 1.3 51.9 + - - +
242B TRP 3.3 0.9 - - - -
243B ALA* 2.7 36.2 + - - +
244B CYS* 3.9 3.1 + - - -
164C ALA* 5.9 0.4 - - - -
229C MET 4.2 0.8 + - - -
231C THR* 3.3 30.4 + - - +
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Residues in contact with PHE 241 (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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244A CYS* 4.6 2.0 - - - -
137B GLN* 3.2 51.6 - - + +
141B ARG* 4.0 22.6 + - + -
142B ALA 6.2 0.4 - - - -
143B VAL* 6.1 4.5 - - + -
200B MET* 4.0 15.7 - - + -
203B ARG* 3.3 77.2 + - + +
204B ILE* 4.2 8.5 - - + -
205B PRO* 4.1 1.0 - - - +
238B GLU* 2.7 16.2 + - + +
239B GLY 3.5 1.6 + - - -
240B GLY* 1.3 71.5 - - - +
242B TRP* 1.3 67.0 + + - +
243B ALA 3.1 1.4 + - - -
244B CYS* 3.5 18.9 + - - +
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Residues in contact with TRP 242 (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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140A GLN 4.7 1.7 - - - +
141A ARG* 3.8 4.9 + - - -
136B SER 3.4 21.3 - - - -
137B GLN* 2.9 36.6 + - + +
140B GLN* 3.5 43.7 - - + -
141B ARG* 2.7 51.5 + - + +
178B ASN* 3.3 27.8 - - + -
234B THR* 3.9 19.3 - - - -
236B PRO* 4.0 11.9 - - + -
238B GLU* 3.6 21.8 + - + +
240B GLY 3.3 1.0 - - - -
241B PHE* 1.3 84.0 - + - +
243B ALA* 1.3 60.6 + - - +
244B CYS 3.3 1.7 + - - -
161C LYS* 5.0 4.9 + - - +
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Residues in contact with ALA 243 (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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140A GLN 5.1 0.2 - - - -
141A ARG* 3.4 6.7 - - - -
142A ALA* 2.7 24.3 + - - +
205B PRO* 5.7 2.0 - - + -
240B GLY* 2.7 25.0 + - - +
242B TRP* 1.3 75.3 - - - +
244B CYS* 1.3 58.0 + - + +
161C LYS* 3.8 38.3 - - + +
164C ALA* 5.1 2.2 - - + -
165C LEU* 5.9 0.9 - - + +
231C THR 4.8 0.2 - - - +
232C GLY* 4.1 22.7 - - - +
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Residues in contact with CYS 244 (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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141A ARG* 3.4 21.6 - - - +
142A ALA* 3.3 30.0 - - + +
203A ARG* 2.8 48.3 + - - -
241A PHE* 4.3 3.8 - - - -
141B ARG* 4.8 1.7 + - - -
203B ARG* 3.9 26.5 + - - -
205B PRO* 4.5 6.5 - - - -
240B GLY 4.2 6.5 - - - -
241B PHE 3.5 15.0 + - - +
242B TRP 3.3 0.4 - - - -
243B ALA* 1.3 80.8 - - - +
165C LEU* 4.0 29.4 - - + -
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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