Contacts of the helix formed by residues 224 - 234 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223G SER* 1.3 81.9 - - - +
225G PRO* 1.3 76.6 - - + +
226G GLY* 4.2 0.7 - - - -
227G ASP* 3.1 43.5 + - - +
228G VAL* 3.5 8.3 + - - +
244G MET* 3.5 10.3 - - - +
189H ARG 5.3 0.2 - - - -
190H LYS* 3.1 44.6 - - + +
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Residues in contact with PRO 225 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224G CYS* 1.3 88.1 - - + +
226G GLY* 1.3 61.5 + - - +
228G VAL* 3.2 12.7 + - + +
229G ALA* 3.0 21.7 + - - +
244G MET* 4.3 5.2 - - + -
307G ASP* 3.7 33.7 - - - +
308G ILE* 4.0 28.5 - - + +
311G GLY* 4.3 2.5 - - - -
312G ILE* 4.2 3.6 - - - +
190H LYS* 3.7 4.9 - - + +
191H LYS* 3.2 31.6 - - + +
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Residues in contact with GLY 226 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224G CYS* 4.2 1.3 - - - -
225G PRO* 1.3 72.8 - - - +
227G ASP* 1.3 57.1 + - - +
229G ALA* 3.4 3.4 + - - +
230G LYS* 3.0 37.1 + - - +
189H ARG 4.3 1.1 - - - -
190H LYS 2.7 24.2 + - - -
191H LYS 3.6 0.6 + - - -
192H THR 3.7 4.7 - - - -
193H GLY* 3.6 24.4 - - - -
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Residues in contact with ASP 227 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G PHE* 3.2 32.6 - - + +
13G LYS* 4.9 0.5 + - - -
221G GLY 3.7 5.0 - - - +
222G CYS* 3.7 19.2 - - - -
223G SER* 2.9 31.4 + - - -
224G CYS* 3.1 22.5 + - - +
226G GLY* 1.3 74.2 - - - +
228G VAL* 1.3 65.6 + - - +
230G LYS* 3.1 15.2 + - - +
231G ALA* 3.0 23.7 + - - +
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Residues in contact with VAL 228 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G ILE* 4.4 8.1 - - + -
222G CYS* 3.8 11.4 - - + -
224G CYS 3.8 11.7 - - - +
225G PRO* 3.2 9.8 + - + +
227G ASP* 1.3 76.4 - - - +
229G ALA* 1.3 63.8 + - - +
231G ALA* 3.3 4.9 + - - +
232G PHE* 3.1 36.0 + - + -
239G VAL* 4.0 13.5 - - + -
241G LEU* 3.8 30.5 - - + -
244G MET* 4.3 9.9 - - + -
308G ILE* 4.6 3.6 - - + -
312G ILE* 3.6 25.1 - - + -
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Residues in contact with ALA 229 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G LEU* 4.8 4.0 - - + +
225G PRO 3.0 12.5 + - - +
226G GLY* 3.6 8.7 - - - +
227G ASP 3.2 0.2 - - - -
228G VAL* 1.3 76.8 - - - +
230G LYS* 1.3 51.8 + - - +
232G PHE* 3.3 7.8 + - - +
233G GLY* 2.8 32.4 + - - -
312G ILE* 4.3 13.6 - - + +
315G THR* 3.4 35.4 - - + +
327G LEU* 3.8 7.9 - - + +
192H THR 3.7 7.4 - - - +
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Residues in contact with LYS 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G PHE* 2.9 43.0 + - + +
13G LYS* 4.4 4.9 + - - +
15G VAL* 2.7 37.3 + - + +
16G LEU* 4.6 5.3 - - - +
17G LEU* 3.8 16.8 - - + -
199G LEU* 3.8 8.5 - - + +
226G GLY 3.0 19.3 + - - +
227G ASP* 3.1 13.3 + - - +
229G ALA* 1.3 72.3 - - - +
231G ALA* 1.3 60.5 + - - +
233G GLY* 3.3 1.8 + - - +
234G ALA* 2.9 27.2 + - - +
333G PHE* 3.5 13.6 - - + -
189H ARG 5.0 3.2 + - - -
193H GLY* 3.9 24.7 - - - -
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Residues in contact with ALA 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G PHE* 3.9 16.0 - - + -
199G LEU* 4.8 0.2 - - - -
202G VAL* 3.7 3.7 - - + +
218G SER* 3.8 21.5 - - - +
222G CYS* 4.8 0.2 - - - -
227G ASP 3.0 12.7 + - - +
228G VAL* 3.5 9.4 - - - +
230G LYS* 1.3 77.0 - - - +
232G PHE* 1.3 61.4 + - - +
234G ALA* 3.2 14.4 + - - +
235G GLY 3.4 0.3 + - - -
236G ALA* 3.1 22.8 + - - +
239G VAL* 3.7 20.2 - - + -
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Residues in contact with PHE 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G PRO* 3.5 32.1 - - + -
50G ILE* 3.9 11.2 - - + -
228G VAL* 3.1 42.5 + - + -
229G ALA* 3.6 7.6 - - - +
231G ALA* 1.3 75.1 - - - +
233G GLY* 1.3 57.7 + - - +
235G GLY* 3.0 19.2 + - - -
236G ALA 3.3 19.7 + - - +
237G ASP 3.6 20.6 - - - -
238G PHE* 4.0 1.3 - - - -
239G VAL* 3.7 16.8 - - + -
312G ILE* 4.1 16.2 - - + -
324G LEU* 4.2 27.6 - - + -
327G LEU* 3.8 16.1 - - + +
328G SER* 3.5 11.9 + - - -
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Residues in contact with GLY 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G LEU* 5.0 1.3 - - - -
229G ALA 2.8 18.8 + - - -
230G LYS* 3.3 5.6 + - - -
232G PHE* 1.3 73.3 - - - +
234G ALA* 1.3 58.0 + - - +
327G LEU* 4.1 5.0 - - - +
328G SER* 3.4 21.5 - - - +
331G THR* 3.5 33.1 - - - +
333G PHE* 4.0 6.9 - - - -
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Residues in contact with ALA 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199G LEU* 3.8 16.2 - - + -
202G VAL* 3.6 15.5 - - + -
203G MET* 3.7 38.4 - - + +
206G ALA* 4.0 4.9 - - - +
207G ASP* 5.4 1.4 - - - +
230G LYS 2.9 15.1 + - - +
231G ALA 3.2 6.2 + - - +
233G GLY* 1.3 76.0 - - - +
235G GLY* 1.3 57.3 + - - +
236G ALA 3.7 0.7 - - - -
328G SER* 4.7 0.4 - - - -
333G PHE* 3.9 7.6 - - + -
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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