Contacts of the helix formed by residues 224 - 234 (chain E) in PDB entry 2BZN
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 CYS 224 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223E SER* 1.3 81.6 - - - +
225E PRO* 1.3 74.0 - - + +
226E GLY* 4.3 1.1 - - - -
227E ASP* 3.1 44.3 + - - +
228E VAL* 3.4 5.0 + - - +
230E LYS* 6.2 0.2 - - - -
244E MET* 3.5 14.5 - - - +
189G ARG 5.2 0.4 - - - -
190G LYS* 3.2 45.5 - - + +
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Residues in contact with PRO 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E CYS* 1.3 90.0 - - + +
226E GLY* 1.3 56.1 + - - +
228E VAL* 3.0 13.6 + - + +
229E ALA* 2.9 27.4 + - - +
244E MET* 4.2 4.5 - - + -
307E ASP* 3.7 27.1 - - - +
308E ILE* 3.9 35.9 - - + +
311E GLY* 4.3 3.1 - - - -
312E ILE* 4.1 3.9 - - - +
190G LYS 3.7 4.9 - - - +
191G LYS* 3.2 28.9 - - + +
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Residues in contact with GLY 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E CYS* 4.3 0.7 - - - -
225E PRO* 1.3 76.1 - - - +
227E ASP* 1.3 57.3 + - - +
229E ALA* 3.3 2.8 + - - +
230E LYS* 2.9 38.0 + - - +
189G ARG 4.2 1.1 - - - -
190G LYS 2.9 19.6 + - - -
191G LYS 3.5 1.0 + - - -
192G THR 3.6 5.8 - - - -
193G GLY* 3.5 24.5 - - - -
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Residues in contact with ASP 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E PHE* 3.4 30.4 - - + +
13E LYS* 5.1 0.5 + - - -
221E GLY 3.8 3.1 - - - +
222E CYS* 3.7 21.6 - - - -
223E SER* 2.9 30.7 + - - -
224E CYS* 3.1 25.0 + - - +
226E GLY* 1.3 75.1 - - - +
228E VAL* 1.3 64.4 + - - +
230E LYS* 3.2 17.1 + - - +
231E ALA* 3.0 23.2 + - - +
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Residues in contact with VAL 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E ILE* 4.3 8.1 - - + -
222E CYS* 3.9 10.5 - - + -
224E CYS 3.8 12.6 - - - +
225E PRO* 3.0 9.1 + - + +
227E ASP* 1.3 76.6 - - - +
229E ALA* 1.3 64.6 + - - +
231E ALA* 3.2 4.7 + - - +
232E PHE* 3.1 37.3 + - + -
239E VAL* 4.1 13.2 - - + -
241E LEU* 3.9 27.1 - - + -
244E MET* 4.3 9.6 - - + -
308E ILE* 4.5 7.0 - - + -
312E ILE* 3.5 24.7 - - + -
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Residues in contact with ALA 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E LEU* 4.8 3.8 - - + +
225E PRO 2.9 11.8 + - - +
226E GLY* 3.6 9.0 - - - +
228E VAL* 1.3 77.6 - - - +
230E LYS* 1.3 57.1 + - - +
232E PHE* 3.4 7.0 + - - +
233E GLY* 2.9 25.3 + - - -
312E ILE* 4.1 14.7 - - + +
315E THR* 3.4 36.3 - - + +
327E LEU* 3.9 7.2 - - + +
192G THR 3.6 7.0 - - - +
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Residues in contact with LYS 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E PHE* 2.9 42.4 + - + +
13E LYS* 4.5 4.4 - - - +
15E VAL* 2.9 36.7 + - + -
16E LEU* 4.6 5.8 - - - +
17E LEU* 3.8 20.6 - - + -
199E LEU* 3.8 4.4 - - + +
226E GLY 2.9 20.1 + - - +
227E ASP* 3.2 13.3 + - - +
229E ALA* 1.3 75.3 - - - +
231E ALA* 1.3 58.0 + - - +
233E GLY 3.2 0.5 + - - -
234E ALA* 2.9 30.1 + - - +
333E PHE* 3.5 12.0 - - + -
189G ARG 4.9 4.0 + - - -
193G GLY* 3.8 24.7 - - - -
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Residues in contact with ALA 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E PHE* 3.9 16.0 - - + -
199E LEU* 4.7 0.2 - - - -
202E VAL* 3.7 2.9 - - - +
218E SER* 3.8 20.6 - - - +
227E ASP 3.0 12.4 + - - +
228E VAL* 3.6 9.2 - - - +
230E LYS* 1.3 72.0 - - - +
232E PHE* 1.3 66.2 + - - +
234E ALA* 3.3 12.9 + - - +
235E GLY 3.4 0.9 + - - -
236E ALA* 3.1 22.6 + - - +
239E VAL* 3.7 20.9 - - + -
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Residues in contact with PHE 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E ARG* 5.9 1.8 - - - -
49E PRO* 3.6 30.5 - - + -
50E ILE* 3.8 15.7 - - + -
228E VAL* 3.1 38.6 + - + -
229E ALA* 3.7 7.9 - - - +
231E ALA* 1.3 79.5 - - - +
233E GLY* 1.3 61.6 + - - +
235E GLY* 3.0 15.2 + - - -
236E ALA 3.4 19.1 + - - +
237E ASP 3.5 22.0 - - - -
239E VAL* 3.8 14.8 - - + -
312E ILE* 4.2 13.0 - - + -
324E LEU* 4.2 28.3 - - + -
327E LEU* 3.8 15.4 - - + +
328E SER* 3.6 9.2 + - - -
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Residues in contact with GLY 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17E LEU* 5.2 0.7 - - - -
229E ALA 2.9 16.4 + - - -
230E LYS* 3.2 4.4 + - - -
232E PHE* 1.3 75.5 - - - +
234E ALA* 1.3 56.0 + - - +
235E GLY 3.2 0.4 - - - -
327E LEU* 4.1 5.1 - - - +
328E SER* 3.3 25.2 - - - +
331E THR* 3.4 33.7 - - - +
333E PHE* 4.1 6.5 - - - -
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Residues in contact with ALA 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E LEU* 3.6 22.7 - - + -
202E VAL* 3.8 11.1 - - + +
203E MET* 3.6 38.4 - - + +
206E ALA* 4.1 3.1 - - - +
207E ASP* 5.6 0.7 - - - +
230E LYS 2.9 15.3 + - - +
231E ALA 3.6 6.5 - - - +
232E PHE 3.1 0.4 - - - -
233E GLY* 1.3 76.5 - - - +
235E GLY* 1.3 55.8 + - - +
236E ALA 3.7 0.7 - - - -
328E SER* 4.8 0.4 - - - -
333E PHE* 3.9 10.1 - - + -
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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