Contacts of the helix formed by residues 189 - 202 (chain C) in PDB entry 1A4O
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 CYS 189 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188C ALA* 1.3 77.7 - - - +
190C SER* 1.3 58.0 + - - +
193C LYS* 3.3 27.7 + - - +
225C LEU* 3.8 15.5 - - + +
228C TRP* 3.4 50.2 - - + +
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Residues in contact with SER 190 (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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188C ALA* 3.4 19.2 + - - +
189C CYS* 1.3 77.9 - - - +
191C LEU* 1.3 59.9 + - - +
193C LYS* 3.7 1.7 + - - +
194C THR* 2.8 35.4 + - - -
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Residues in contact with LEU 191 (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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153C PHE* 3.6 39.7 - - + -
171C ALA* 4.5 6.1 - - + +
174C PHE* 4.3 9.9 - - + -
175C SER* 4.0 27.6 - - - +
178C TYR* 4.0 19.1 - - + +
188C ALA 2.9 14.4 + - - +
190C SER* 1.3 80.7 + - - +
192C ALA* 1.3 59.0 + - - +
194C THR* 3.9 10.6 - - + -
195C ALA* 3.0 32.2 + - + +
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Residues in contact with ALA 192 (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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171C ALA 5.3 0.2 - - - -
172C LEU* 5.6 0.9 - - + -
175C SER* 3.4 21.3 + - - +
188C ALA 3.0 8.4 + - - +
191C LEU* 1.3 74.8 - - - +
193C LYS* 1.3 68.3 + - - +
196C PHE* 3.3 21.5 + - - +
221C LEU* 3.6 33.1 - - + +
225C LEU* 3.8 21.9 - - + +
228C TRP* 4.2 6.3 - - + -
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Residues in contact with LYS 193 (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 CYS 3.3 21.7 + - - +
190C SER* 4.0 2.5 - - - +
191C LEU 3.4 0.2 - - - -
192C ALA* 1.3 78.2 - - - +
194C THR* 1.3 58.2 + - - +
196C PHE* 3.0 17.6 + - + +
197C ASP* 2.9 27.5 + - + +
225C LEU* 4.0 18.9 - - + +
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Residues in contact with THR 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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190C SER* 2.8 21.7 + - - -
191C LEU* 3.9 12.1 - - + +
193C LYS* 1.3 80.3 - - - +
195C ALA* 1.3 59.8 + - + +
197C ASP* 3.0 29.1 - - + +
198C GLU* 3.3 26.1 - - - +
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Residues in contact with ALA 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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153C PHE* 6.5 0.4 - - + -
168C LEU* 4.2 7.1 - - + +
171C ALA* 3.5 28.3 - - + -
191C LEU* 3.0 21.0 + - + +
192C ALA 4.3 2.7 - - - +
194C THR* 1.3 78.4 - - + +
196C PHE* 1.3 57.7 + - - +
198C GLU* 3.5 14.0 + - - +
199C ALA* 3.0 25.2 + - - +
221C LEU* 4.3 4.7 - - + -
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Residues in contact with PHE 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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168C LEU* 4.7 1.5 - - - +
192C ALA 3.3 17.2 + - - +
193C LYS* 3.7 22.7 - - + -
195C ALA* 1.3 76.5 - - - +
197C ASP* 1.3 65.7 + - - +
199C ALA* 3.5 8.3 - - - -
200C ILE* 2.9 67.6 + - + +
218C MET* 4.0 26.2 - - + -
219C GLN* 6.0 0.4 - - - -
221C LEU* 4.1 13.7 - - + -
222C ARG* 4.1 26.2 - - + -
225C LEU* 4.7 9.2 - - + -
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Residues in contact with ASP 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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193C LYS* 2.9 13.3 + - + +
194C THR* 3.0 21.0 - - - +
196C PHE* 1.3 79.7 - - - +
198C GLU* 1.3 71.3 + - - +
200C ILE* 3.3 12.4 + - - +
201C ALA* 3.6 9.7 + - - +
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Residues in contact with GLU 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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167C ARG* 4.2 18.1 + - - +
194C THR* 3.3 33.3 + - - +
195C ALA* 3.8 12.4 - - - +
197C ASP* 1.3 86.1 - - - +
199C ALA* 1.3 58.5 + - - +
200C ILE 3.2 0.2 - - - -
201C ALA* 3.1 29.6 + - + +
202C GLU* 4.0 2.3 + - - +
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Residues in contact with ALA 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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168C LEU* 3.7 20.9 - - + -
195C ALA 3.0 19.0 + - - +
196C PHE* 3.1 15.0 + - - +
198C GLU* 1.3 79.3 - - - +
200C ILE* 1.3 57.8 + - - +
201C ALA 3.2 1.3 + - - -
202C GLU* 3.8 14.5 + - - +
203C LEU* 4.7 3.3 + - - +
218C MET* 3.6 27.2 - - + +
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Residues in contact with ILE 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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196C PHE* 2.9 50.5 + - + +
197C ASP* 3.3 6.5 + - - +
198C GLU 3.2 0.4 - - - -
199C ALA* 1.3 76.2 - - - +
201C ALA* 1.3 56.6 + - - +
202C GLU 3.1 5.4 - - - -
203C LEU* 3.1 46.6 - - + +
218C MET* 3.8 15.3 - - + -
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Residues in contact with ALA 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 ASP* 3.6 5.6 + - - +
198C GLU* 3.1 24.3 + - + +
200C ILE* 1.3 78.7 - - - +
202C GLU* 1.3 55.3 + - - +
203C LEU 3.3 4.0 - - - -
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Residues in contact with GLU 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 GLU 4.0 2.6 + - - +
199C ALA* 3.8 11.3 + - - +
200C ILE 3.1 1.0 - - - -
201C ALA* 1.3 78.7 - - - +
203C LEU* 1.3 69.3 + - - +
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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