Contacts of the helix formed by residues 218 - 226 (chain C) in PDB entry 4WCX
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 THR 218 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C GLU* 4.0 12.8 + - - +
5C LYS 3.9 24.9 - - - +
6C ALA* 4.0 13.2 - - + -
8C PHE* 4.6 7.2 - - + -
214C ASP 2.7 23.9 + - - +
215C TYR* 3.4 3.6 + - - -
216C HIS 3.3 0.2 - - - -
217C LEU* 1.3 76.1 - - - +
219C ALA* 1.3 62.4 + - - +
220C MET 3.4 2.0 - - - -
221C ASP* 3.1 26.0 + - - +
222C ARG* 2.9 35.6 + - - +
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Residues in contact with ALA 219 (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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172C ALA* 3.7 11.2 - - + -
178C TYR* 3.7 17.2 - - - +
189C TYR* 5.1 0.4 - - + -
191C LEU* 3.4 25.8 - - + -
215C TYR 3.5 2.2 + - - -
216C HIS 3.2 18.1 + - - +
217C LEU 3.3 0.8 - - - -
218C THR* 1.3 77.8 - - - +
220C MET* 1.3 60.4 + - - +
222C ARG* 3.0 16.9 + - - +
223C ALA* 2.9 27.2 + - - +
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Residues in contact with MET 220 (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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189C TYR* 3.7 35.0 - - + +
191C LEU* 3.5 30.3 - - + +
217C LEU 4.5 2.0 + - - -
218C THR 3.4 0.6 - - - -
219C ALA* 1.3 77.0 - - + +
221C ASP* 1.3 57.4 + - - +
223C ALA* 3.7 2.0 - - - +
224C MET* 2.9 32.7 + - - +
231C VAL* 3.7 21.1 - - + -
232C GLY 3.1 29.6 - - - +
233C LEU* 3.7 19.5 - - + -
252C HIS* 4.3 11.2 - - + +
256C LEU* 4.0 24.5 - - + -
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Residues in contact with ASP 221 (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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8C PHE* 4.1 13.2 - - - -
217C LEU 4.8 0.9 - - - +
218C THR* 3.1 20.5 + - + +
220C MET* 1.3 75.3 - - - +
222C ARG* 1.3 58.3 + - + +
225C GLU* 2.9 29.1 + - - +
252C HIS* 5.0 0.2 + - - -
255C HIS* 2.8 39.2 + - - -
256C LEU* 3.7 5.4 - - - +
259C LYS* 2.8 27.8 + - - +
260C PHE* 3.5 20.6 - - + -
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Residues in contact with ARG 222 (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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172C ALA* 4.0 0.4 - - - +
173C THR 2.8 31.0 + - - +
174C THR* 4.7 1.6 - - - +
175C VAL* 3.8 32.2 - - + +
178C TYR* 3.8 9.4 - - + -
215C TYR* 3.1 54.3 + - - -
218C THR* 2.9 36.5 + - - +
219C ALA* 3.0 26.1 + - - +
221C ASP* 1.3 77.6 - - + +
223C ALA* 1.3 58.9 + - - +
225C GLU* 3.4 4.8 + - - +
226C ALA* 3.0 28.9 + - - +
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Residues in contact with ALA 223 (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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178C TYR* 3.6 25.3 - - + -
189C TYR* 4.0 22.9 - - + -
219C ALA 2.9 15.7 + - - +
220C MET* 3.3 9.6 + - - +
222C ARG* 1.3 78.3 - - - +
224C MET* 1.3 59.0 + - - +
226C ALA* 3.3 8.8 + - - +
227C GLY 3.3 0.2 + - - -
228C ILE* 3.0 36.0 + - + +
231C VAL* 4.6 3.6 - - + -
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Residues in contact with MET 224 (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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220C MET 2.9 17.9 + - - +
223C ALA* 1.3 71.9 - - - +
225C GLU* 1.3 68.2 + - - +
226C ALA 3.1 1.6 - - - -
227C GLY* 2.9 13.9 + - - -
228C ILE 3.3 16.3 - - - +
229C ASP* 4.2 18.2 - - - +
231C VAL* 3.8 34.3 - - + -
256C LEU* 4.4 11.9 - - + -
260C PHE* 3.6 52.0 - - + -
262C VAL* 3.6 24.7 - - + +
263C GLY 4.3 5.8 - - - +
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Residues in contact with GLU 225 (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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183A LYS* 5.8 9.2 - - - +
175C VAL* 4.6 11.8 - - + +
179C LYS* 5.3 3.6 + - - -
221C ASP 2.9 20.4 + - - +
222C ARG* 3.4 8.9 + - - +
224C MET* 1.3 75.2 - - - +
226C ALA* 1.3 59.4 + - - +
227C GLY* 3.2 1.7 + - - -
260C PHE* 3.9 10.3 - - + -
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Residues in contact with ALA 226 (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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175C VAL* 3.6 22.2 - - + +
178C TYR* 3.5 24.5 - - + +
179C LYS* 3.7 27.6 + - + +
182C LYS* 4.0 9.4 - - - +
222C ARG 3.0 16.2 + - - +
223C ALA 3.5 7.0 - - - +
224C MET 3.1 0.6 - - - -
225C GLU* 1.3 74.5 - - - +
227C GLY* 1.3 59.8 + - - +
228C ILE 3.5 0.6 + - - +
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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