Contacts of the helix formed by residues 226 - 237 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198C PRO* 3.4 30.8 - - - +
222C VAL* 3.8 7.3 - - + +
223C HIS* 3.2 24.0 + - + +
225C ASP* 1.3 74.8 - - - +
227C LEU* 1.3 57.4 + - - +
228C ALA 4.0 0.2 + - - -
229C GLY* 3.0 18.9 + - - -
230C LEU* 3.0 25.7 + - - +
260G ARG* 3.0 28.1 + - - +
288G CYS 5.9 2.5 - - - +
289G GLY* 6.5 0.9 - - - -
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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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224C LYS 3.4 21.1 - - - +
225C ASP* 3.2 9.4 + - - +
226C ASP* 1.3 71.3 - - - +
228C ALA* 1.3 62.2 + - - +
230C LEU* 3.3 8.8 + - + +
231C LYS* 2.8 27.7 + - - +
246C SER* 3.5 24.0 - - - +
252C GLN 5.5 0.4 - - - +
255C GLU* 4.4 23.8 - - + -
256C VAL* 4.0 26.7 - - + +
259C THR* 4.9 6.5 - - + +
261C SER* 3.6 16.0 - - - +
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Residues in contact with ALA 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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226C ASP 3.3 0.8 - - - -
227C LEU* 1.3 76.7 - - - +
229C GLY* 1.3 59.6 + - - +
231C LYS* 3.3 11.0 + - + +
232C LYS* 2.9 28.8 + - - +
260G ARG* 3.5 36.1 - - - +
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Residues in contact with GLY 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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198C PRO* 3.8 15.8 - - - +
222C VAL* 4.2 5.8 - - - -
226C ASP* 3.0 29.8 + - - -
228C ALA* 1.3 75.7 - - - +
230C LEU* 1.3 63.5 + - - +
232C LYS* 3.1 18.7 + - - +
233C VAL* 3.2 18.9 + - - +
260G ARG* 5.2 0.2 - - - +
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Residues in contact with LEU 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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220C GLN* 4.2 11.7 - - - +
221C PRO* 3.7 30.7 - - + -
222C VAL* 3.6 15.8 - - + +
226C ASP 3.0 13.8 + - - +
227C LEU* 3.3 12.5 + - + +
229C GLY* 1.3 75.2 - - - +
231C LYS* 1.3 62.4 + - - +
233C VAL* 3.4 5.7 + - - +
234C THR* 3.1 26.3 + - - -
241C ILE* 3.8 12.6 - - + -
242C MET 5.0 1.6 - - - +
243C ALA* 4.1 21.1 - - + -
246C SER* 4.0 19.5 - - - +
256C VAL* 5.0 1.8 - - + -
261C SER* 3.4 23.3 - - - +
262C ALA* 4.3 3.4 - - + -
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Residues in contact with LYS 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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227C LEU 2.8 15.4 + - - +
228C ALA* 3.3 13.5 - - - +
230C LEU* 1.3 74.7 - - - +
232C LYS* 1.3 64.9 + - - +
234C THR* 3.3 2.3 + - - -
235C ASP* 2.9 47.3 + - - +
259C THR* 3.2 29.8 + - - +
260C ARG* 3.5 21.6 + - - +
261C SER* 3.7 15.9 + - - +
232E LYS* 5.6 5.1 - - - +
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Residues in contact with LYS 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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198C PRO* 4.7 16.6 - - + +
199C LYS* 4.3 26.0 - - + +
202C VAL* 4.9 10.5 - - + -
228C ALA 2.9 15.3 + - - +
229C GLY* 3.1 13.9 + - - +
231C LYS* 1.3 75.7 - - - +
233C VAL* 1.3 61.9 + - - +
235C ASP* 3.3 5.9 + - - +
236C ALA* 3.0 27.8 + - + +
234G THR* 4.4 5.7 - - - +
235G ASP* 4.0 31.6 + - + +
237G THR 5.3 2.7 - - - +
263G ASP* 4.5 11.5 + - - -
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Residues in contact with VAL 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 PRO* 3.7 28.9 - - + +
201C ALA* 3.9 11.9 - - + -
202C VAL* 4.0 9.0 - - + -
205C ILE* 3.5 31.6 - - + -
221C PRO* 4.1 10.3 - - + -
222C VAL* 4.2 8.3 - - + -
229C GLY 3.2 13.9 + - - +
230C LEU 3.8 5.4 - - - +
231C LYS 3.3 0.2 - - - -
232C LYS* 1.3 72.3 - - - +
234C THR* 1.3 68.2 + - - +
236C ALA 3.2 7.8 + - - -
237C THR* 3.1 26.3 + - + +
241C ILE* 3.6 15.5 - - + -
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Residues in contact with THR 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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230C LEU 3.1 8.1 + - - -
231C LYS 3.5 8.3 - - - -
233C VAL* 1.3 78.1 - - - +
235C ASP* 1.3 69.4 + - - +
237C THR 3.9 0.2 - - - +
241C ILE* 3.1 28.0 - - - +
260C ARG 4.4 5.2 - - - +
261C SER 2.9 20.0 + - - -
262C ALA* 3.4 16.3 - - - +
263C ASP* 3.7 25.1 - - - +
199E LYS* 2.8 32.5 + - + +
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Residues in contact with ASP 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 LYS* 2.9 52.2 + - - +
232C LYS* 3.9 4.9 - - - +
234C THR* 1.3 86.9 - - - +
236C ALA* 1.3 59.9 + - - +
237C THR 3.6 3.1 - - - +
260C ARG 4.7 1.0 - - - +
199E LYS* 5.5 0.8 - - - +
232E LYS* 4.5 18.0 - - - +
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Residues in contact with ALA 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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202C VAL* 3.7 32.5 - - + -
206C ARG* 3.1 28.2 + - - +
232C LYS* 3.0 19.6 + - + +
233C VAL 3.2 0.8 + - - +
235C ASP* 1.3 78.6 - - - +
237C THR* 1.3 61.3 + - - +
238C ASP* 5.5 0.2 - - - +
238G ASP* 5.2 2.9 - - - +
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Residues in contact with THR 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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202C VAL* 4.2 20.0 - - + +
205C ILE* 3.6 33.7 - - + -
206C ARG* 4.9 5.6 - - - +
209C GLU* 3.7 13.7 - - - -
233C VAL* 3.1 18.2 + - + +
234C THR 3.9 1.2 - - - +
235C ASP 4.3 2.9 - - - +
236C ALA* 1.3 82.0 - - + +
238C ASP* 1.3 64.2 + - - +
239C THR* 3.2 20.6 + - - -
241C ILE* 4.2 4.5 - - - +
199E LYS* 3.1 19.6 + - - +
203E THR* 5.1 0.2 + - - -
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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