Contacts of the helix formed by residues 226 - 236 (chain E) in PDB entry 1QZW
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 ALA 226 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E ILE* 4.7 10.8 - - + -
222E ILE* 3.1 36.6 - - + +
223E GLY 2.5 19.3 + - - +
225E LYS* 1.3 73.8 - - - +
227E TYR* 1.3 72.6 + - - +
228E ASP* 2.4 10.2 - - - +
229E LEU* 2.6 23.3 + - + +
230E ALA* 4.5 2.9 - - + -
256E ALA* 5.4 5.4 - - + +
260E VAL* 6.0 2.9 - - + -
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Residues in contact with TYR 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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224E GLN 2.8 19.9 + - - +
225E LYS 2.7 4.1 + - - +
226E ALA* 1.3 84.3 - - - +
228E ASP* 1.3 81.8 + - + +
230E ALA* 2.9 9.2 + - - +
231E SER* 2.6 31.8 + - - -
259E ALA* 3.1 40.2 - - + +
260E VAL* 4.6 2.9 - - - +
262E ALA* 2.8 37.9 + - + +
263E THR* 3.2 9.3 - - + +
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Residues in contact with ASP 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E GLU* 4.1 10.5 - - - +
222E ILE* 5.0 1.2 - - - +
225E LYS* 2.5 23.6 - - - +
226E ALA* 2.4 22.9 - - - +
227E TYR* 1.3 83.7 - - + +
229E LEU* 1.3 74.2 + - - +
231E SER* 2.6 22.3 + - - -
232E ARG* 2.7 13.1 + - - -
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Residues in contact with LEU 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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104E VAL* 3.1 28.5 - - + -
192E TYR* 3.4 30.7 - - + -
195E GLU* 3.3 24.0 + - + +
198E LEU* 4.5 9.2 - - + -
199E LEU* 5.4 1.0 - - - +
216E LEU* 3.5 19.5 - - + +
218E ILE* 3.4 30.7 - - + -
226E ALA* 2.6 21.0 + - + +
228E ASP* 1.3 83.9 + - - +
230E ALA* 1.3 63.9 + - + +
232E ARG* 2.5 30.1 + - - +
233E PHE* 4.4 0.2 - - - +
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Residues in contact with ALA 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216E LEU* 4.0 20.2 - - + -
218E ILE* 5.8 2.0 - - + -
226E ALA* 4.6 1.6 - - + +
227E TYR* 2.9 11.4 + - - +
229E LEU* 1.3 90.6 - - + +
231E SER* 1.3 71.0 + - - +
232E ARG 2.6 10.7 - - - +
233E PHE* 2.9 16.5 - - + +
234E HIS* 3.4 3.4 + - - -
242E VAL* 5.6 7.9 - - + -
260E VAL* 5.9 6.1 - - + -
263E THR* 6.0 1.1 - - + +
265E ALA* 5.9 7.2 - - + -
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Residues in contact with SER 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227E TYR* 2.6 36.6 + - - -
228E ASP* 2.6 19.1 + - - -
230E ALA* 1.3 68.8 - - - +
232E ARG* 1.3 49.2 + - - -
233E PHE 2.5 19.4 + - - -
234E HIS* 2.5 27.2 + - - +
235E GLN* 3.6 8.7 + - - +
263E THR* 3.6 26.5 + - - +
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Residues in contact with ARG 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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193E GLY 3.9 1.0 + - - -
195E GLU* 3.0 38.6 + - - +
196E THR* 2.5 43.5 + - - +
199E LEU* 3.7 34.4 - - + +
228E ASP 2.7 11.9 + - - +
229E LEU 2.5 22.5 - - - +
231E SER* 1.3 68.9 - - - +
233E PHE* 1.3 69.8 + - - +
235E GLN* 4.6 14.3 + - - +
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Residues in contact with PHE 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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102E VAL* 5.2 4.3 - - + -
199E LEU* 5.7 6.1 - - + -
202E MET* 5.2 9.2 - - - -
214E VAL* 4.7 15.9 - - + -
216E LEU* 4.0 31.9 - - + -
230E ALA* 2.9 21.8 - - + +
231E SER 2.5 2.8 + - - -
232E ARG* 1.3 84.9 - - - +
234E HIS* 1.3 55.2 + - - -
235E GLN* 2.4 10.9 - - - +
236E ALA* 2.4 41.6 + - + +
237E SER* 2.4 51.2 + - - -
240E GLY* 3.2 29.8 - - - -
242E VAL* 4.2 10.1 - - + -
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Residues in contact with HIS 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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230E ALA 3.4 1.9 + - - +
231E SER* 2.5 23.6 + - - +
233E PHE* 1.3 79.8 - - - +
235E GLN* 1.3 58.8 + - + +
237E SER 3.5 5.4 - - - -
238E PRO* 3.0 58.1 + - + +
240E GLY 4.3 8.5 - - - -
263E THR* 2.8 21.8 + - - -
264E GLY* 2.9 41.1 + - - -
265E ALA* 3.9 5.7 + - - -
266E THR* 3.7 8.6 + - - -
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Residues in contact with GLN 235 (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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231E SER* 3.8 13.1 - - - +
232E ARG* 4.6 14.3 + - - +
233E PHE 2.9 3.4 - - - +
234E HIS* 1.3 82.5 - - + +
236E ALA* 1.3 69.5 + - - +
237E SER* 3.2 1.3 + - - -
238E PRO* 4.2 6.9 - - - +
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Residues in contact with ALA 236 (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* 5.5 10.1 - - + -
202E MET* 5.0 16.2 - - + -
233E PHE* 2.4 39.4 + - + +
235E GLN* 1.3 76.7 - - - +
237E SER* 1.3 63.8 + - - +
238E PRO* 4.2 2.3 - - - +
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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