Contacts of the helix formed by residues 223 - 237 (chain C) in PDB entry 1RZR
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 TYR 223 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222C THR* 1.3 72.1 - - - +
224C ASP* 1.3 67.8 + - - +
226C GLY* 3.1 13.9 + - - +
227C ILE* 3.6 24.5 + - + +
249C GLU* 3.3 20.5 + - - +
252C LEU* 4.0 2.0 - - + -
253C GLY* 3.8 13.7 - - - -
256C HIS* 3.1 54.6 + + - +
281G THR* 4.1 20.8 + - - +
282G MSE 3.4 46.9 - - + -
283G VAL 4.8 2.8 + - - -
286G GLN* 4.9 8.0 + - - +
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Residues in contact with ASP 224 (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 ASP* 4.9 2.7 - - - +
222C THR* 3.1 15.4 + - - +
223C TYR* 1.3 80.0 - - - +
225C SER* 1.3 58.7 + - - +
226C GLY 2.9 9.9 + - - -
227C ILE* 3.5 4.4 + - - +
228C GLU* 3.1 27.6 + - - +
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Residues in contact with SER 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C VAL* 4.6 3.8 - - - +
218C GLU 4.9 0.3 - - - +
219C GLY* 3.8 17.5 + - - -
220C ASP* 2.6 36.6 + - - -
222C THR* 3.2 8.6 + - - -
224C ASP* 1.3 77.0 - - - +
226C GLY* 1.3 56.9 + - - +
228C GLU* 3.4 15.5 + - - +
229C ALA* 2.9 28.9 + - - +
250C MSE 3.6 18.6 - - - -
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Residues in contact with GLY 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183C VAL* 6.1 0.2 - - - -
222C THR 3.6 2.0 + - - -
223C TYR 3.1 9.9 + - - -
224C ASP 2.9 4.4 + - - -
225C SER* 1.3 75.2 - - - +
227C ILE* 1.3 57.3 + - - -
228C GLU 2.7 9.4 + - - -
229C ALA* 3.0 5.0 + - - +
230C VAL* 3.0 24.3 + - - +
250C MSE 3.8 9.2 - - - +
253C GLY* 3.5 23.1 - - - -
254C VAL* 3.7 5.3 - - - -
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Residues in contact with ILE 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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223C TYR* 3.6 25.3 + - + +
224C ASP* 3.5 4.8 + - - +
226C GLY* 1.3 72.8 - - - +
228C GLU* 1.3 55.7 + - - +
230C VAL* 4.0 4.7 - - - -
231C GLU* 3.2 14.4 + - - +
253C GLY* 3.1 28.3 - - - +
256C HIS* 3.6 15.0 - - + -
257C GLY* 3.1 21.1 - - - +
260C ASP* 4.1 6.1 - - - +
261C ARG* 3.2 35.6 + - - +
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Residues in contact with GLU 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218C GLU 4.3 5.2 - - - +
219C GLY* 4.2 16.8 - - - -
220C ASP* 4.5 8.5 - - - +
224C ASP* 3.1 25.7 + - - +
225C SER* 3.4 17.6 + - - +
226C GLY 2.7 0.6 + - - -
227C ILE* 1.3 76.2 - - - +
229C ALA* 1.3 66.9 + - - +
230C VAL 3.2 0.9 - - - -
231C GLU* 4.0 3.1 - - - +
232C LYS* 3.1 38.4 + - + +
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Residues in contact with ALA 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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183C VAL* 3.5 36.6 - - + -
217C VAL* 4.1 20.5 - - + +
218C GLU 5.3 2.5 - - - +
225C SER* 2.9 17.6 + - - +
226C GLY* 3.7 4.0 - - - +
228C GLU* 1.3 81.2 - - + +
230C VAL* 1.3 57.5 + - + +
232C LYS* 3.9 1.2 - - - +
233C LEU* 3.0 34.3 + - - +
254C VAL* 5.3 1.1 - - + -
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Residues in contact with VAL 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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183C VAL* 6.3 0.2 - - + -
226C GLY 3.0 13.0 + - - +
227C ILE* 3.9 5.4 - - - +
229C ALA* 1.3 73.3 - - - +
231C GLU* 1.3 71.6 + - - +
232C LYS 3.0 0.9 - - - -
233C LEU* 2.8 17.7 + - - +
234C LEU* 2.8 35.7 + - + +
243C ILE* 4.8 7.9 - - + -
253C GLY 3.9 3.6 - - - +
254C VAL* 3.2 50.9 - - + +
257C GLY* 3.5 26.5 - - - +
258C ALA* 3.7 3.6 - - + +
261C ARG* 4.5 0.4 - - + +
269C LEU* 5.8 0.9 - - + -
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Residues in contact with GLU 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 ILE* 3.2 10.0 + - - +
228C GLU* 4.0 3.6 - - - +
230C VAL* 1.3 81.3 - - - +
232C LYS* 1.3 67.0 + - + +
235C GLU* 2.8 47.4 + - + +
261C ARG* 2.8 33.8 + - - +
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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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217C VAL* 4.8 16.4 - - + -
228C GLU* 3.1 25.8 + - + +
229C ALA* 3.9 4.9 - - - +
230C VAL 2.9 1.4 + - - -
231C GLU* 1.3 84.6 - - + +
233C LEU* 1.3 58.9 + - - +
236C GLU* 2.4 49.4 + - + +
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Residues in contact with LEU 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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181C ALA* 3.3 37.9 - - + -
183C VAL* 4.2 9.0 - - + -
214C SER 5.8 0.4 - - - +
215C TYR* 4.4 16.6 - - + -
217C VAL* 3.7 29.1 - - + +
229C ALA 3.0 14.8 + - - +
230C VAL* 2.8 10.2 + - - +
232C LYS* 1.3 75.0 - - - +
234C LEU* 1.3 66.2 + - + +
236C GLU* 3.7 11.2 - - - +
237C ASP 4.0 3.3 + - - +
240C PRO* 3.4 31.2 - - + +
243C ILE* 4.1 21.5 - - + -
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Residues in contact with LEU 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 VAL* 2.8 34.7 + - + +
232C LYS 3.2 0.2 + - - -
233C LEU* 1.3 78.2 - - + +
235C GLU* 1.3 83.6 + - - +
236C GLU 3.1 0.2 + - - -
237C ASP 3.6 4.7 + - - -
239C LYS* 3.3 43.3 - - + +
240C PRO* 5.0 5.6 - - + +
243C ILE* 6.3 2.2 - - + -
257C GLY 4.5 0.7 - - - +
258C ALA* 4.6 4.7 - - + -
261C ARG* 3.4 36.1 - - + -
263C LEU* 3.7 32.3 - - + -
269C LEU* 4.8 6.7 - - + -
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Residues in contact with GLU 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 GLU* 2.8 30.0 + - + +
234C LEU* 1.3 90.7 - - - +
236C GLU* 1.3 73.2 + - - +
237C ASP* 3.1 1.7 + - - -
239C LYS* 4.7 8.7 + - - +
261C ARG* 3.2 34.2 + - - +
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Residues in contact with GLU 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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232C LYS* 2.4 48.4 + - + +
233C LEU* 3.7 8.1 - - - +
234C LEU 3.1 0.6 + - - -
235C GLU* 1.3 85.9 - - - +
237C ASP* 1.3 59.7 + - - +
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Residues in contact with ASP 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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215C TYR* 4.3 7.3 + - - -
233C LEU 4.1 1.7 - - - +
234C LEU 3.6 1.8 + - - -
235C GLU 3.1 5.2 + - - -
236C GLU* 1.3 83.6 - - - +
238C GLU* 1.3 61.9 + - - +
239C LYS* 2.7 20.9 + - - +
240C PRO* 4.0 7.3 - - - +
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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