Contacts of the helix formed by residues 224 - 234 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189F ARG 5.2 0.4 - - - -
190F LYS* 3.2 42.6 - - + +
223H SER* 1.3 81.3 - - - +
225H PRO* 1.3 75.8 - - + +
226H GLY* 4.2 0.9 - - - -
227H ASP* 3.2 45.3 + - - +
228H VAL 3.5 3.6 + - - -
244H MET* 3.5 14.5 - - - +
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Residues in contact with PRO 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F LYS 3.6 6.1 - - - +
191F LYS* 3.4 30.7 - - + +
224H CYS* 1.3 87.4 - - + +
226H GLY* 1.3 58.7 + - - +
228H VAL* 3.1 18.9 + - + +
229H ALA* 3.1 13.2 + - - +
244H MET* 4.2 7.6 - - + -
307H ASP* 3.6 25.6 - - - +
308H ILE* 4.0 36.8 - - + +
311H GLY* 4.5 0.9 - - - -
312H ILE* 4.2 3.9 - - - +
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Residues in contact with GLY 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F ARG 4.3 0.9 - - - -
190F LYS 2.8 24.2 + - - -
191F LYS 3.4 1.4 + - - -
192F THR 3.7 6.1 - - - -
193F GLY* 3.6 24.1 - - - -
224H CYS* 4.2 1.1 - - - -
225H PRO* 1.3 73.4 - - - +
227H ASP* 1.3 57.2 + - - +
229H ALA* 3.4 3.8 + - - +
230H LYS* 3.0 37.2 + - - +
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Residues in contact with ASP 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H PHE* 3.3 32.0 - - + +
13H LYS* 5.0 0.5 + - - -
221H GLY 3.8 3.3 - - - +
222H CYS* 3.7 21.8 - - + -
223H SER* 2.9 31.9 + - - -
224H CYS* 3.2 24.9 + - - +
226H GLY* 1.3 73.4 - - - +
228H VAL* 1.3 65.8 + - - +
230H LYS* 3.3 16.4 + - - +
231H ALA* 3.1 23.4 + - - +
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Residues in contact with VAL 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H ILE* 4.4 8.7 - - + -
222H CYS* 3.9 10.3 - - + -
224H CYS 3.7 13.2 - - - +
225H PRO* 3.1 9.6 + - + +
227H ASP* 1.3 76.6 - - - +
229H ALA* 1.3 61.0 - - - +
231H ALA* 3.3 4.3 + - - +
232H PHE* 3.1 36.6 + - + -
239H VAL* 3.9 14.1 - - + +
241H LEU* 3.9 25.8 - - + -
244H MET* 4.2 10.8 - - + -
308H ILE* 4.5 6.1 - - + -
312H ILE* 3.4 26.0 - - + -
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Residues in contact with ALA 229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192F THR 3.9 3.4 - - - +
17H LEU* 4.8 3.9 - - + +
225H PRO 3.1 11.5 + - - +
226H GLY* 3.6 8.3 - - - +
228H VAL* 1.3 75.5 - - - +
230H LYS* 1.3 54.6 + - - +
232H PHE* 3.4 8.0 + - - -
233H GLY* 2.8 32.2 + - - -
312H ILE* 4.4 10.5 - - + +
315H THR* 3.4 38.6 - - + +
327H LEU* 3.7 10.2 - - + +
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Residues in contact with LYS 230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F ARG 5.0 3.0 + - - -
193F GLY* 3.7 26.2 - - - -
12H PHE* 2.7 48.4 + - + +
13H LYS* 4.4 4.6 - - - +
15H VAL* 2.9 30.1 + - + -
16H LEU* 4.7 4.6 - - - +
17H LEU* 3.6 21.3 - - + -
199H LEU* 3.9 4.7 - - + +
224H CYS* 6.2 0.2 - - - -
226H GLY* 3.0 20.5 + - - +
227H ASP* 3.6 13.1 + - - +
228H VAL 3.3 0.2 - - - -
229H ALA* 1.3 72.2 - - - +
231H ALA* 1.3 60.7 + - - +
233H GLY 3.3 0.5 + - - -
234H ALA* 2.8 30.5 + - - +
333H PHE* 3.5 12.1 - - + -
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Residues in contact with ALA 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H PHE* 3.9 15.8 - - + -
199H LEU* 4.8 0.2 - - - -
202H VAL* 3.7 4.2 - - + +
218H SER* 3.7 24.9 - - - +
227H ASP 3.1 14.0 + - - +
228H VAL* 3.6 8.7 - - - +
230H LYS* 1.3 75.7 - - - +
232H PHE* 1.3 62.6 + - - +
234H ALA* 3.2 13.4 + - - +
235H GLY 3.4 0.7 + - - -
236H ALA* 3.1 21.7 + - - +
239H VAL* 3.8 16.8 - - + -
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Residues in contact with PHE 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H ARG* 6.4 0.2 - - - -
49H PRO* 3.5 32.1 - - + -
50H ILE* 3.9 11.4 - - + -
228H VAL* 3.1 45.1 + - + -
229H ALA* 3.8 4.0 - - - +
231H ALA* 1.3 76.1 - - - +
233H GLY* 1.3 63.6 + - - +
235H GLY* 3.0 13.3 + - - -
236H ALA 3.3 20.3 + - - +
237H ASP 3.5 22.4 - - - -
239H VAL* 3.7 15.7 - - + -
312H ILE* 4.0 14.1 - - + -
324H LEU* 4.1 26.2 - - + -
327H LEU* 3.7 17.7 - - + +
328H SER* 3.6 11.4 + - - -
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Residues in contact with GLY 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H LEU* 5.0 1.1 - - - -
229H ALA 2.8 21.6 + - - -
230H LYS* 3.6 3.1 - - - -
232H PHE* 1.3 73.6 - - - +
234H ALA* 1.3 58.7 + - - +
327H LEU* 3.8 5.8 - - - +
328H SER* 3.3 23.7 - - - +
331H THR* 3.3 31.9 + - - +
333H PHE* 4.1 5.7 - - - -
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Residues in contact with ALA 234 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199H LEU* 3.7 21.5 - - + -
202H VAL* 3.7 13.5 - - + +
203H MET* 3.8 33.1 - - + +
206H ALA* 4.2 1.9 - - - +
230H LYS 2.8 17.7 + - - +
231H ALA 3.5 6.1 - - - +
232H PHE 3.1 0.8 - - - -
233H GLY* 1.3 77.3 - - - +
235H GLY* 1.3 56.6 + - - +
236H ALA 3.7 0.4 - - - -
328H SER* 4.8 0.4 - - - -
333H PHE* 3.8 9.6 - - + -
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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