Contacts of the helix formed by residues 230 - 241 (chain C) in PDB entry 5UQ9
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 SER 230 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224C ASN* 3.0 25.4 + - - +
228C LEU 2.9 7.8 + - - -
229C ASP* 1.3 76.0 + - - +
231C PHE* 1.3 62.7 + - - +
232C LEU* 3.9 6.0 + - - +
233C ILE* 3.2 32.7 + - - +
234C GLU* 3.5 3.5 + - - +
331C LYS* 3.9 15.1 + - - -
368C ILE 5.6 0.7 - - - -
369C ARG 3.7 1.8 - - - -
370C SER* 3.5 22.2 - - - +
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Residues in contact with PHE 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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133C GLU* 6.5 1.1 - - + -
230C SER* 1.3 72.2 - - - +
232C LEU* 1.3 60.0 + - - +
234C GLU* 3.2 27.4 + - - +
235C ILE* 2.8 64.5 + - + +
366C CYS 4.4 0.7 - - - -
367C ILE* 4.0 17.3 - - + +
369C ARG* 3.1 68.8 + - + +
449D TYR* 4.7 11.2 - + - -
450D PHE* 4.6 11.4 - - + -
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Residues in contact with LEU 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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191C GLU* 5.4 0.4 - - + -
194C ASP* 3.9 24.9 - - + +
195C MET* 3.9 28.3 - - + +
198C ILE* 3.7 15.9 - - + -
230C SER* 3.4 5.7 + - - +
231C PHE* 1.3 79.7 - - - +
233C ILE* 1.3 52.8 + - - +
235C ILE* 3.3 10.4 + - + +
236C THR* 2.7 39.8 + - - -
331C LYS* 6.3 0.2 - - - +
367C ILE* 3.7 38.3 + - + +
368C ILE* 4.8 11.0 - - + -
446D GLN* 4.7 9.9 - - + +
450D PHE* 4.0 15.3 - - + -
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Residues in contact with ILE 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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198C ILE* 4.2 15.5 - - + -
220C PHE* 3.2 44.4 - - + +
223C TRP* 4.7 4.3 - - + -
224C ASN* 3.9 14.1 - - + +
228C LEU* 3.3 47.6 - - + +
230C SER* 3.2 13.5 + - - +
231C PHE 3.2 0.8 - - - -
232C LEU* 1.3 73.3 - - - +
234C GLU* 1.3 61.2 + - - +
236C THR* 3.8 6.6 - - - -
237C ALA* 3.0 28.4 + - - +
327C LEU* 4.5 10.8 - - + -
331C LYS* 6.0 1.1 - - - +
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Residues in contact with GLU 234 (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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221C GLU* 6.2 1.1 - - - +
224C ASN* 3.1 24.2 + - - +
230C SER 3.5 3.5 + - - +
231C PHE* 3.2 32.2 + - + +
233C ILE* 1.3 76.4 - - - +
235C ILE* 1.3 61.0 + - - +
237C ALA* 3.3 5.7 + - - +
238C ASN* 3.1 41.9 + - - +
449D TYR* 5.5 1.0 + - - +
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Residues in contact with ILE 235 (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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231C PHE* 2.8 66.5 + - + +
232C LEU* 3.5 12.1 - - + +
234C GLU* 1.3 72.7 - - + +
236C THR* 1.3 63.6 + - - +
238C ASN* 3.2 4.0 + - - +
239C ILE* 3.0 38.8 + - + +
446D GLN* 4.5 11.4 - - + +
449D TYR* 3.5 44.4 - - + -
450D PHE* 3.8 22.4 - - + -
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Residues in contact with THR 236 (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 ILE* 3.6 24.9 - - + +
220C PHE* 4.3 9.2 - - + -
232C LEU 2.7 24.9 + - - -
233C ILE* 3.8 6.5 - - - -
235C ILE* 1.3 73.9 - - - +
237C ALA* 1.3 58.3 + - - +
239C ILE* 3.2 8.3 + - - +
240C LEU* 2.9 48.6 + - + +
442D LEU* 3.8 22.4 - - + -
446D GLN* 2.6 26.5 + - - +
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Residues in contact with ALA 237 (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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217C ALA* 3.4 20.9 - - - +
220C PHE* 4.1 9.2 - - + +
221C GLU* 3.5 33.7 - - + +
233C ILE 3.0 16.8 + - - +
234C GLU* 3.7 6.5 - - - +
235C ILE 3.2 0.2 - - - -
236C THR* 1.3 76.9 - - - +
238C ASN* 1.3 63.2 + - - +
240C LEU* 3.3 9.0 + - - -
241C LYS* 3.4 19.5 + - - +
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Residues in contact with ASN 238 (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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221C GLU* 4.6 1.7 - - - +
234C GLU* 3.1 35.8 + - - +
235C ILE 3.8 5.6 - - - +
237C ALA* 1.3 76.7 - - - +
239C ILE* 1.3 62.6 + - - +
241C LYS* 3.8 22.0 + - - +
242C PHE* 3.2 26.0 + - + +
449D TYR* 3.5 30.1 + - + +
469D TRP* 5.1 4.7 - - - +
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Residues in contact with ILE 239 (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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235C ILE* 3.0 39.5 + - + +
236C THR* 3.6 5.8 - - - +
237C ALA 3.2 0.2 - - - -
238C ASN* 1.3 76.7 - - - +
240C LEU* 1.3 63.9 + - - +
242C PHE* 3.4 13.5 + - - +
250C LEU* 6.0 0.3 - - - +
251C LEU* 4.6 17.4 + - + +
254C ILE* 6.0 0.2 - - + -
442D LEU* 4.1 12.3 - - + -
445D ALA* 3.2 51.6 - - + +
446D GLN* 3.6 10.1 - - + +
449D TYR* 3.7 18.2 - - + -
469D TRP* 3.9 20.3 + - + +
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Residues in contact with LEU 240 (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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202C TYR* 3.5 30.1 - - + -
213C GLN* 3.7 23.1 - - - +
216C MET* 3.7 22.0 - - + +
217C ALA* 3.7 15.7 - - + +
220C PHE* 3.5 38.1 - - + -
236C THR* 2.9 25.8 + - + +
237C ALA 3.3 0.2 + - - -
239C ILE* 1.3 79.2 - - - +
241C LYS* 1.3 58.7 + - - +
242C PHE 3.4 3.1 + - - +
249C HIS* 3.4 18.4 + - - +
251C LEU* 3.7 21.6 - - + +
442D LEU* 4.6 5.8 - - + -
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Residues in contact with LYS 241 (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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213C GLN 5.0 0.7 - - - -
214C ASP* 3.6 24.3 - - + +
217C ALA* 3.7 15.6 - - + +
221C GLU* 2.1 38.6 + - - -
237C ALA 3.4 17.5 + - - +
238C ASN* 3.9 20.0 + - - +
240C LEU* 1.3 76.7 - - - +
242C PHE* 1.3 63.0 + - - +
243C GLN* 3.5 11.6 + - - +
249C HIS* 4.3 2.9 - - - -
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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