Contacts of the helix formed by residues 224 - 234 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189B ARG 5.3 0.2 - - - -
190B LYS* 3.2 34.5 - - + +
223D SER* 1.3 81.5 - - - +
225D PRO* 1.3 80.5 - - + +
226D GLY* 4.2 0.9 - - - -
227D ASP* 3.1 44.1 + - - +
228D VAL* 3.4 8.7 + - - +
244D MET* 3.5 9.3 - - - +
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Residues in contact with PRO 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B LYS 3.7 6.3 - - - +
191B LYS* 3.3 28.0 - - + +
224D CYS* 1.3 89.5 - - + +
226D GLY* 1.3 53.1 + - - +
228D VAL* 3.1 9.9 + - + +
229D ALA* 3.0 26.5 + - - +
244D MET* 3.9 8.9 - - + -
307D ASP* 3.8 33.2 - - - +
308D ILE* 4.0 32.8 - - + +
311D GLY* 4.4 0.9 - - - -
312D ILE* 4.2 3.8 - - - +
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Residues in contact with GLY 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B ARG 4.4 0.9 - - - -
190B LYS 2.9 20.4 + - - -
191B LYS 3.5 1.0 + - - -
192B THR 3.8 5.2 - - - -
193B GLY* 3.6 23.8 - - - -
224D CYS* 4.2 1.3 - - - -
225D PRO* 1.3 73.2 - - - +
227D ASP* 1.3 60.5 + - - +
229D ALA* 3.4 3.9 + - - +
230D LYS* 3.0 37.7 + - - +
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Residues in contact with ASP 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PHE* 3.6 30.5 - - + +
13D LYS* 5.2 0.7 + - - -
221D GLY 3.7 3.8 - - - +
222D CYS* 3.7 22.6 - - + -
223D SER* 2.9 31.2 + - - -
224D CYS* 3.1 25.2 + - - +
226D GLY* 1.3 74.0 - - - +
228D VAL* 1.3 65.5 + - - +
230D LYS* 3.3 16.0 + - - +
231D ALA* 3.1 23.2 + - - +
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Residues in contact with VAL 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ILE* 4.5 8.1 - - + -
222D CYS* 3.9 10.3 - - + -
224D CYS 3.4 11.9 + - - +
225D PRO* 3.1 10.6 + - + +
227D ASP* 1.3 74.7 - - - +
229D ALA* 1.3 63.1 + - - +
231D ALA* 3.2 5.7 + - - +
232D PHE* 3.1 46.2 + - + -
239D VAL* 4.0 13.5 - - + -
241D LEU* 3.9 27.1 - - + -
244D MET* 4.3 10.1 - - + -
308D ILE* 4.6 6.3 - - + -
312D ILE* 3.7 15.7 - - + -
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Residues in contact with ALA 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B THR 3.6 9.0 - - - +
17D LEU* 4.7 4.6 - - + +
225D PRO 3.0 11.5 + - - +
226D GLY* 3.4 9.4 - - - +
228D VAL* 1.3 74.1 - - - +
230D LYS* 1.3 59.7 + - - +
232D PHE* 3.4 10.5 + - - +
233D GLY* 2.9 26.3 + - - -
312D ILE* 4.4 9.5 - - + +
315D THR* 3.4 35.4 - - + +
327D LEU* 3.8 8.3 - - + +
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Residues in contact with LYS 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B ARG 5.0 3.6 + - - -
193B GLY* 3.8 25.5 - - - -
12D PHE* 2.7 50.2 + - + +
13D LYS* 4.5 4.6 - - - +
15D VAL* 2.8 31.8 + - + -
16D LEU* 4.7 4.8 - - - +
17D LEU* 3.7 19.5 - - + -
199D LEU* 3.9 3.9 - - + +
226D GLY 3.0 20.8 + - - +
227D ASP* 3.3 11.9 + - - +
229D ALA* 1.3 74.9 - - - +
231D ALA* 1.3 54.8 + - - +
233D GLY 3.2 0.7 + - - -
234D ALA* 2.8 32.2 + - - +
333D PHE* 3.4 15.8 - - + -
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Residues in contact with ALA 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PHE* 4.0 15.0 - - + -
202D VAL* 3.7 3.3 - - - +
218D SER* 3.9 20.9 - - - +
227D ASP 3.1 13.1 + - - +
228D VAL 3.3 9.6 - - - +
230D LYS* 1.3 78.0 - - - +
232D PHE* 1.3 63.3 + - - +
234D ALA* 3.3 11.0 + - - +
235D GLY 3.5 0.5 + - - -
236D ALA* 3.2 23.0 + - - +
239D VAL* 3.7 21.3 - - + -
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Residues in contact with PHE 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D ARG* 6.2 0.9 - - - -
49D PRO* 3.6 28.0 - - + -
50D ILE* 4.0 11.7 - - + -
228D VAL* 3.1 39.2 + - + -
229D ALA* 3.7 6.7 - - - +
231D ALA* 1.3 77.6 - - - +
233D GLY* 1.3 59.2 + - - +
235D GLY* 3.0 17.5 + - - -
236D ALA 3.2 19.7 + - - +
237D ASP 3.5 21.5 - - - -
239D VAL* 3.6 19.5 - - + -
312D ILE* 4.0 16.4 - - + -
324D LEU* 4.0 29.4 - - + -
327D LEU* 3.8 13.2 - - + +
328D SER* 3.5 12.8 + - - -
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Residues in contact with GLY 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D LEU* 5.0 1.1 - - - -
229D ALA 2.9 15.2 + - - -
230D LYS* 3.2 5.1 + - - -
232D PHE* 1.3 76.8 - - - +
234D ALA* 1.3 55.8 + - - +
235D GLY 3.2 0.7 - - - -
327D LEU* 4.1 4.7 - - - +
328D SER* 3.3 25.1 - - - +
331D THR* 3.3 38.5 - - - +
333D PHE* 4.5 0.6 - - - -
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Residues in contact with ALA 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D LEU* 3.5 23.3 - - + -
202D VAL* 3.7 18.6 - - + +
203D MET* 3.8 32.7 - - + +
206D ALA* 4.2 3.5 - - - +
207D ASP* 5.7 0.5 - - - +
230D LYS 2.8 16.4 + - - +
231D ALA 3.7 0.4 - - - +
232D PHE 3.2 0.6 - - - -
233D GLY* 1.3 75.3 - - - +
235D GLY* 1.3 56.3 + - - +
236D ALA 3.7 0.9 - - - -
328D SER* 4.8 0.7 - - - -
333D PHE* 3.8 8.9 - - + -
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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