Contacts of the helix formed by residues 226 - 233 (chain C) in PDB entry 3OX4
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 ASN 226 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222C MET* 2.8 31.3 + - - +
223C ILE 3.3 0.2 + - - -
224C ALA 3.5 0.4 - - - -
225C LYS* 1.3 94.8 + - - +
227C LEU* 1.3 67.6 + - - +
228C LYS 3.3 2.4 - - - +
229C THR* 3.3 10.9 + - - +
230C ALA* 2.9 23.6 + - - +
238C PRO 4.5 1.2 - - - +
239C ALA* 4.0 18.5 + - - +
242C ALA* 3.2 34.3 - - + +
243C MET* 4.1 6.5 - - - -
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Residues in contact with LEU 227 (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 THR* 3.8 12.3 - - - +
189C ALA* 4.2 1.3 - - - -
192C GLY* 3.8 23.6 - - - -
193C MET* 4.0 17.9 - - - +
223C ILE* 3.0 31.0 + - + +
226C ASN* 1.3 75.0 - - - +
228C LYS* 1.3 64.1 + - - +
230C ALA* 3.2 6.7 + - + +
231C CYS* 3.0 34.8 + - - -
243C MET* 3.6 27.5 - - + -
330C LEU* 4.1 12.6 - - + -
334C ILE* 3.9 27.1 - - + -
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Residues in contact with LYS 228 (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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223C ILE 4.8 0.2 + - - -
224C ALA 5.9 1.4 + - - +
226C ASN 3.3 0.6 - - - +
227C LEU* 1.3 76.2 - - - +
229C THR* 1.3 59.0 + - - +
231C CYS* 2.8 6.4 + - - +
232C ASP* 2.8 57.9 + - - +
330C LEU* 3.8 17.7 - - + +
333C SER* 3.1 53.1 + - - +
334C ILE* 4.2 9.9 - - + -
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Residues in contact with THR 229 (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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225C LYS 4.8 6.3 + - - -
226C ASN* 3.3 14.1 + - - +
228C LYS* 1.3 78.6 - - - +
230C ALA* 1.3 57.2 + - - +
232C ASP* 3.2 7.3 + - - +
233C ASN* 3.0 31.2 + - + +
236C ASP* 3.0 34.3 - - + +
239C ALA* 3.7 4.5 - - + -
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Residues in contact with ALA 230 (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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185C LYS* 5.8 0.2 - - - -
188C THR* 4.3 6.4 + - - +
226C ASN 2.9 17.5 + - - +
227C LEU* 3.4 8.5 - - + +
229C THR* 1.3 76.5 - - - +
231C CYS* 1.3 60.8 + - - +
233C ASN 4.3 4.3 - - - -
234C GLY* 3.5 22.5 + - - -
239C ALA* 3.9 19.0 - - + +
240C ARG* 4.1 24.1 + - - +
243C MET* 4.2 18.4 - - + -
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Residues in contact with CYS 231 (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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185C LYS* 3.1 38.8 - - + +
188C THR* 3.2 24.7 - - - +
189C ALA* 3.5 29.4 - - - -
227C LEU* 3.0 20.6 + - - +
228C LYS 2.8 8.8 + - - +
230C ALA* 1.3 77.8 - - - +
232C ASP* 1.3 65.2 + - - +
233C ASN 3.2 2.8 + - - -
234C GLY 4.8 1.4 + - - -
334C ILE* 3.6 22.0 - - + -
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Residues in contact with ASP 232 (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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344B GLY* 5.7 3.9 - - - -
346B LYS* 4.4 22.6 + - - +
185C LYS* 3.7 16.9 - - - +
228C LYS* 2.8 46.5 + - - +
229C THR* 3.2 5.9 + - - +
231C CYS* 1.3 79.8 - - - +
233C ASN* 1.3 64.0 + - - +
333C SER 5.0 1.7 - - - +
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Residues in contact with ASN 233 (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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346B LYS* 5.4 9.5 - - - +
229C THR* 3.0 13.7 + - + +
230C ALA* 3.7 5.9 - - - +
231C CYS 3.2 1.0 + - - -
232C ASP* 1.3 83.1 + - - +
234C GLY* 1.3 54.8 + - - +
235C LYS* 2.7 43.3 + - - +
236C ASP* 2.8 34.4 + - + +
240C ARG* 5.0 0.3 + - - +
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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