Contacts of the helix formed by residues 229 - 239 (chain B) in PDB entry 1KNU
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 229 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222B TYR* 4.6 8.5 - - + -
223B ILE* 3.6 31.4 - - + +
226B PHE* 3.7 16.8 - - - +
227B PRO 3.4 6.5 + - - +
228B LEU* 1.3 76.9 - - - +
230B LYS* 1.3 60.5 + - - +
231B ALA* 3.5 4.2 + - - +
232B LYS* 2.9 34.2 + - + +
233B ALA* 2.9 28.7 + - - +
332B SER* 5.4 0.2 - - - -
333B LEU* 5.3 0.9 - - - -
381B ASP* 3.6 15.7 - - - +
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Residues in contact with LYS 230 (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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222B TYR* 4.4 2.2 + - - +
229B THR* 1.3 72.5 - - - +
231B ALA* 1.3 54.8 + - - +
233B ALA* 3.6 2.8 - - - +
234B ARG* 2.7 66.0 + - + +
332B SER* 3.3 38.6 + - - +
374B PHE* 6.0 3.8 - - - -
375B ASN* 4.3 24.8 + - - +
378B GLU* 4.3 5.5 - - - +
379B LEU* 2.6 41.5 + - - +
380B ASP* 4.5 3.8 - - - -
381B ASP* 3.0 20.1 + - - +
384B LEU* 4.0 12.6 - - + +
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Residues in contact with ALA 231 (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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229B THR* 3.9 3.6 - - - +
230B LYS* 1.3 79.0 - - - +
232B LYS* 1.3 62.1 + - + +
234B ARG* 3.6 6.3 + - - +
235B ALA* 3.2 20.3 + - - +
381B ASP* 3.1 19.6 + - - +
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Residues in contact with LYS 232 (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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227B PRO* 3.2 29.1 + - - +
228B LEU* 3.7 12.6 - - + -
229B THR* 2.9 29.9 + - - +
231B ALA* 1.3 76.2 - - + +
233B ALA* 1.3 61.5 + - - +
235B ALA* 2.8 30.0 + - - +
236B ILE* 3.1 13.3 + - + +
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Residues in contact with ALA 233 (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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228B LEU* 3.7 6.6 - - + +
229B THR 2.9 18.4 + - - +
230B LYS* 3.6 4.5 - - - +
232B LYS* 1.3 77.0 - - - +
234B ARG* 1.3 64.0 + - - +
236B ILE* 3.1 6.0 + - - +
237B LEU* 2.9 27.2 + - - +
332B SER 3.6 13.2 - - - +
333B LEU* 3.5 28.0 - - + -
340B LEU* 3.8 15.2 - - + +
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Residues in contact with ARG 234 (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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230B LYS* 2.7 51.4 + - + +
231B ALA* 4.0 6.5 - - - +
233B ALA* 1.3 74.5 - - - +
235B ALA* 1.3 61.7 + - - +
237B LEU* 3.6 17.0 - - - +
238B THR* 3.0 39.1 + - + +
331B ALA 4.2 0.6 + - - -
332B SER* 3.4 20.9 + - - +
334B MET 2.9 28.9 + - - -
335B ASN* 4.3 13.7 - - - +
375B ASN* 4.2 14.1 - - - +
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Residues in contact with ALA 235 (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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231B ALA 3.2 12.2 + - - +
232B LYS* 2.8 16.0 + - - +
234B ARG* 1.3 78.9 - - - +
236B ILE* 1.3 60.3 + - + +
238B THR* 4.3 0.2 - - - -
239B GLY 3.2 18.5 + - - -
240B LYS* 3.2 23.1 + - + -
241B THR* 3.5 27.1 + - - +
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Residues in contact with ILE 236 (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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228B LEU* 4.8 7.9 - - + -
232B LYS* 3.1 14.9 + - + +
233B ALA* 3.5 9.0 - - - +
235B ALA* 1.3 78.6 - - + +
237B LEU* 1.3 61.8 + - - +
238B THR 3.5 0.3 + - - -
239B GLY* 3.5 9.5 + - - -
241B THR* 5.2 12.0 - - + +
244B LYS 4.5 12.8 - - - +
245B SER* 5.7 0.3 - - - -
246B PRO* 3.8 40.3 - - + +
340B LEU* 4.0 20.4 - - + -
343B GLU 5.2 1.6 - - - +
344B GLY* 4.2 25.4 - - - +
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Residues in contact with LEU 237 (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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233B ALA 2.9 20.9 + - - +
234B ARG* 3.4 39.7 + - - +
235B ALA 3.4 0.2 - - - -
236B ILE* 1.3 77.8 - - - +
238B THR* 1.3 62.5 + - + +
246B PRO* 6.1 0.7 - - + -
332B SER 4.4 0.9 - - - +
333B LEU 4.2 19.1 - - - +
334B MET 4.3 5.4 - - - +
335B ASN* 4.0 17.7 + - - +
340B LEU* 3.6 24.2 - - + -
347B PHE* 3.5 33.4 - - + -
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Residues in contact with THR 238 (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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234B ARG* 3.0 28.2 + - + +
237B LEU* 1.3 80.9 - - + +
239B GLY* 1.3 60.4 + - - +
240B LYS* 3.3 25.7 + - - +
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Residues in contact with GLY 239 (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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235B ALA 3.2 6.8 + - - -
236B ILE 3.5 6.5 + - - -
237B LEU 3.4 2.6 - - - -
238B THR* 1.3 79.5 - - - +
240B LYS* 1.3 53.4 + - - +
241B THR* 2.6 23.1 + - - -
242B THR* 3.2 22.9 + - - -
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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