Contacts of the helix formed by residues 226 - 237 (chain F) in PDB entry 1TKK
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 ASP 226 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A ARG* 5.2 5.3 + - - +
260B ARG* 3.0 29.2 + - - -
288B CYS 4.9 8.6 - - - +
289B GLY* 6.0 0.5 - - - -
198F PRO* 3.7 14.6 - - - +
222F VAL* 3.7 9.2 - - + +
223F HIS* 3.1 26.7 + - + +
224F LYS 4.7 0.4 - - - -
225F ASP* 1.3 73.5 - - - +
227F LEU* 1.3 58.3 + - - +
228F ALA 3.9 0.5 + - - -
229F GLY* 2.9 26.5 + - - -
230F LEU* 3.1 25.5 + - - +
246F SER* 5.5 0.8 + - - -
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Residues in contact with LEU 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251A ARG* 5.4 2.0 - - - +
224F LYS 3.8 20.2 - - - +
225F ASP* 3.2 12.5 + - - +
226F ASP* 1.3 72.7 - - - +
228F ALA* 1.3 67.1 + - - +
230F LEU* 3.1 8.4 + - + +
231F LYS* 2.9 22.3 + - - +
246F SER* 4.4 17.9 - - - +
255F GLU* 3.8 31.6 - - + -
256F VAL* 4.4 16.4 - - + -
259F THR* 4.5 6.5 - - + +
261F SER* 3.9 20.2 + - - +
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Residues in contact with ALA 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B ARG* 3.4 41.2 + - - +
226F ASP* 3.5 0.8 + - - -
227F LEU* 1.3 77.6 - - - +
229F GLY* 1.3 56.7 + - - +
231F LYS* 3.3 9.7 + - - +
232F LYS* 3.0 28.1 + - - +
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Residues in contact with GLY 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260B ARG* 3.6 8.4 - - - +
198F PRO* 3.8 11.9 - - - +
222F VAL* 4.0 6.3 - - - -
226F ASP* 2.9 30.5 + - - -
228F ALA* 1.3 77.4 - - - +
230F LEU* 1.3 58.6 + - - +
232F LYS* 3.4 8.0 + - - +
233F VAL* 3.3 26.7 + - - +
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Residues in contact with LEU 230 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220F GLN* 4.2 10.8 - - - +
221F PRO* 3.6 35.0 - - + -
222F VAL* 3.6 13.8 - - + +
226F ASP 3.1 14.5 + - - +
227F LEU* 3.1 11.4 + - + +
229F GLY* 1.3 73.8 - - - +
231F LYS* 1.3 64.1 + - - +
233F VAL* 3.4 4.4 + - - +
234F THR* 3.0 26.3 + - - -
241F ILE* 3.8 11.7 - - + -
243F ALA* 4.1 22.9 - - + -
246F SER* 4.0 21.3 - - - +
256F VAL* 5.2 3.6 - - + -
261F SER* 3.2 22.1 - - - +
262F ALA* 4.2 3.1 - - + -
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Residues in contact with LYS 231 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D LYS* 5.8 3.0 - - - +
227F LEU 2.9 13.5 + - - +
228F ALA* 3.6 12.8 - - - +
230F LEU* 1.3 71.9 - - - +
232F LYS* 1.3 60.8 + - - +
234F THR* 3.3 3.3 + - - -
235F ASP* 2.8 49.3 + - - +
259F THR* 2.8 30.5 + - - +
260F ARG* 3.1 23.8 + - - +
261F SER* 3.6 19.4 + - - +
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Residues in contact with LYS 232 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B ASP* 4.4 19.3 - - - +
260B ARG* 3.9 22.0 - - - +
263B ASP* 5.3 7.4 + - - -
198F PRO* 3.1 41.8 - - - +
199F LYS* 4.6 14.8 - - + +
202F VAL* 4.7 8.1 - - + -
228F ALA 3.0 11.3 + - - +
229F GLY* 3.5 9.4 - - - +
230F LEU 3.3 0.2 - - - -
231F LYS* 1.3 76.7 - - - +
233F VAL* 1.3 56.5 + - - +
235F ASP* 3.3 4.9 + - - +
236F ALA* 2.9 38.6 + - + +
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Residues in contact with VAL 233 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198F PRO* 3.6 29.6 - - + +
201F ALA* 3.7 13.2 - - + -
202F VAL* 4.1 7.6 - - + +
205F ILE* 3.9 16.8 - - + -
221F PRO* 3.8 15.9 - - + -
222F VAL* 4.3 7.9 - - + -
229F GLY 3.3 15.2 + - - +
230F LEU 3.8 6.1 - - - +
231F LYS 3.3 0.4 - - - -
232F LYS* 1.3 75.5 - - - +
234F THR* 1.3 62.1 + - - +
237F THR* 2.9 36.4 + - + +
241F ILE* 3.8 23.6 - - + -
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Residues in contact with THR 234 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D LYS* 2.7 37.4 + - + +
230F LEU 3.0 9.4 + - - -
231F LYS 3.4 8.5 - - - -
233F VAL* 1.3 77.2 - - - +
235F ASP* 1.3 68.7 - - - +
237F THR 4.0 0.7 - - - +
241F ILE* 3.2 20.8 - - - +
260F ARG 4.1 9.0 - - - +
261F SER 2.9 23.1 + - - +
262F ALA* 3.4 9.0 - - - -
263F ASP* 3.5 24.5 - - - +
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Residues in contact with ASP 235 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D LYS* 4.2 27.5 - - + +
231F LYS* 2.8 52.7 + - - +
232F LYS* 3.9 4.5 - - - +
234F THR* 1.3 84.9 - - - +
236F ALA* 1.3 61.9 + - - +
237F THR 3.6 4.2 - - - +
260F ARG 4.6 0.9 - - - +
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Residues in contact with ALA 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202F VAL* 3.6 29.2 - - + -
206F ARG* 3.4 27.3 + - - +
232F LYS* 2.9 21.7 + - + +
235F ASP* 1.3 77.3 - - - +
237F THR* 1.3 60.7 + - - +
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Residues in contact with THR 237 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D LYS* 3.4 19.1 + - - +
202F VAL* 4.0 22.7 - - + +
205F ILE* 3.4 42.8 - - + -
206F ARG* 5.0 4.9 - - + -
209F GLU* 3.7 3.8 - - - -
233F VAL* 2.9 23.8 + - + +
234F THR 4.0 1.9 - - - +
235F ASP 4.2 3.6 - - - +
236F ALA* 1.3 81.7 - - - +
238F ASP* 1.3 66.4 + - - +
239F THR 3.3 16.6 + - - -
241F ILE* 4.1 3.8 - - - +
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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