Contacts of the helix formed by residues 224 - 234 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A ARG 5.3 0.2 - - - -
190A LYS* 3.2 44.6 - - + +
223B SER* 1.3 82.7 - - - +
225B PRO* 1.3 76.1 - - + +
226B GLY* 3.2 0.9 - - - -
227B ASP* 3.2 39.8 + - - +
228B VAL* 3.5 12.6 + - - +
244B MET* 3.5 9.7 - - - +
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Residues in contact with PRO 225 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A LYS 3.7 6.3 - - - +
191A LYS* 3.4 35.2 - - + +
224B CYS* 1.3 87.6 - - + +
226B GLY* 1.3 60.3 + - - +
228B VAL* 3.2 13.7 + - + +
229B ALA* 3.1 20.4 + - - +
244B MET* 3.9 4.9 - - + -
307B ASP* 4.0 12.1 - - + +
308B ILE* 3.9 43.5 - - + +
311B GLY* 4.3 0.9 - - - -
312B ILE* 4.3 4.0 - - - +
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Residues in contact with GLY 226 (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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189A ARG 4.3 0.9 - - - -
190A LYS 2.8 24.3 + - - -
191A LYS 3.5 1.4 + - - -
192A THR 3.7 5.2 - - - -
193A GLY* 3.5 24.2 - - - -
224B CYS* 4.2 1.8 - - - -
225B PRO* 1.3 72.0 - - - +
227B ASP* 1.3 55.8 + - - +
229B ALA* 3.3 3.4 + - - +
230B LYS* 2.9 38.8 + - - +
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Residues in contact with ASP 227 (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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12B PHE* 3.3 31.5 - - + +
13B LYS* 5.0 0.7 + - - -
221B GLY 3.7 3.1 - - - +
222B CYS* 3.7 21.4 - - - -
223B SER* 2.9 31.9 + - - -
224B CYS* 3.2 22.7 + - - +
226B GLY* 1.3 74.5 - - - +
228B VAL* 1.3 58.2 + - - +
230B LYS* 3.2 15.9 + - - +
231B ALA* 2.9 28.6 + - - +
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Residues in contact with VAL 228 (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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50B ILE* 4.2 8.3 - - + -
222B CYS* 3.9 10.3 - - + -
224B CYS 3.6 14.6 - - - +
225B PRO* 3.2 12.3 + - + +
227B ASP* 1.3 76.4 - - - +
229B ALA* 1.3 57.8 + - - +
231B ALA* 3.4 4.6 + - - +
232B PHE* 3.1 41.7 + - + -
239B VAL* 3.9 13.5 - - + -
241B LEU* 4.0 27.4 - - + -
244B MET* 4.3 7.9 - - + -
308B ILE* 4.7 3.4 - - + -
312B ILE* 3.6 25.4 - - + -
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Residues in contact with ALA 229 (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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192A THR 3.7 9.2 - - - +
17B LEU* 4.8 4.6 - - + +
225B PRO 3.1 11.9 + - - +
226B GLY* 3.4 9.2 - - - +
227B ASP 3.2 0.2 - - - -
228B VAL* 1.3 75.4 - - - +
230B LYS* 1.3 60.1 + - - +
232B PHE* 3.3 9.3 + - - +
233B GLY* 2.8 28.2 + - - -
312B ILE* 4.5 9.8 - - + +
315B THR* 3.5 34.8 - - + +
327B LEU* 4.0 5.9 - - + +
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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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189A ARG 5.0 3.2 + - - -
193A GLY* 3.8 25.1 - - - -
12B PHE* 2.8 51.5 + - + +
13B LYS* 4.4 5.1 - - - +
15B VAL* 2.8 31.9 + - + +
16B LEU* 4.6 4.8 - - - +
17B LEU* 3.8 16.2 - - + -
199B LEU* 4.0 1.1 - - + +
226B GLY 2.9 22.6 + - - +
227B ASP* 3.2 11.0 + - - +
229B ALA* 1.3 76.8 - - - +
231B ALA* 1.3 58.2 + - - +
234B ALA* 2.9 30.8 + - - +
333B PHE* 3.6 15.8 - - + -
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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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12B PHE* 3.9 19.9 - - + -
202B VAL* 3.9 3.2 - - - +
218B SER* 3.9 19.1 - - - +
222B CYS* 4.8 0.2 - - - -
227B ASP 2.9 16.0 + - - +
228B VAL* 3.7 6.1 - - - +
229B ALA 3.2 0.2 - - - -
230B LYS* 1.3 76.8 - - - +
232B PHE* 1.3 61.4 + - - +
234B ALA* 3.2 12.4 + - - +
235B GLY 3.4 0.7 + - - -
236B ALA* 3.1 23.1 + - - +
239B VAL* 3.8 19.3 - - + -
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Residues in contact with PHE 232 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B PRO* 3.4 32.1 - - + -
50B ILE* 3.8 15.0 - - + -
228B VAL* 3.1 44.0 + - + +
229B ALA* 3.3 1.1 + - - +
231B ALA* 1.3 77.0 - - - +
233B GLY* 1.3 56.4 + - - +
235B GLY* 2.9 21.5 + - - -
236B ALA 3.5 17.2 + - - +
237B ASP 3.5 21.5 - - - -
239B VAL* 3.7 18.2 - - + -
312B ILE* 4.1 13.9 - - + -
324B LEU* 4.1 26.5 - - + -
327B LEU* 3.7 19.0 - - + +
328B SER* 3.7 8.7 + - - -
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Residues in contact with GLY 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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17B LEU* 5.0 0.9 - - - -
229B ALA 2.8 20.0 + - - -
230B LYS* 3.7 2.9 - - - -
232B PHE* 1.3 73.0 - - - +
234B ALA* 1.3 59.3 + - - +
235B GLY 3.2 0.4 - - - -
327B LEU* 4.0 6.7 - - - +
328B SER* 3.3 23.6 - - - +
331B THR* 3.3 32.6 - - - +
333B PHE* 4.0 6.3 - - - -
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Residues in contact with ALA 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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199B LEU* 3.5 24.2 - - + -
202B VAL* 3.9 10.3 - - + +
203B MET* 3.9 34.3 - - + +
206B ALA* 4.1 3.8 - - - +
207B ASP* 5.8 0.2 - - - +
230B LYS 2.9 16.8 + - - +
231B ALA 3.6 5.8 - - - +
232B PHE 3.2 0.2 - - - -
233B GLY* 1.3 76.6 - - - +
235B GLY* 1.3 55.3 + - - +
236B ALA 3.7 1.1 - - - -
328B SER* 4.8 0.7 - - - -
333B PHE* 3.8 10.3 - - + -
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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