Contacts of the helix formed by residues 225 - 234 (chain E) in PDB entry 6ACQ
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 GLY 225 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213E ASP* 3.4 28.7 - - - -
216E MET* 4.5 1.1 - - - -
217E LYS* 3.6 6.0 - - - +
224E MET* 1.3 76.1 - - - +
226E PRO* 1.3 70.5 - - - +
227E LEU 3.4 2.8 + - - -
228E GLU* 3.4 12.7 + - - +
229E LEU* 2.9 27.1 + - - +
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Residues in contact with PRO 226 (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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190D ILE* 4.1 4.7 - - + -
194E MET* 4.3 12.6 - - + +
195E ILE* 3.6 26.4 - - + +
198E ALA* 3.6 28.7 - - + -
212E ILE* 4.0 5.2 - - + -
213E ASP* 3.5 8.5 - - - +
216E MET* 3.5 33.9 - - + -
222E HIS* 5.8 1.8 - - - +
224E MET 4.5 1.3 - - - +
225E GLY* 1.3 83.3 - - - +
227E LEU* 1.3 58.2 + - - +
229E LEU* 3.3 10.2 + - + +
230E GLY* 2.8 24.3 + - - -
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Residues in contact with LEU 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E ILE* 4.5 2.5 - - + +
198E ALA* 3.7 24.5 - - + +
199E VAL* 4.0 15.3 - - + +
202E LEU* 4.5 9.4 - - + -
209E VAL* 3.6 38.6 - - + +
212E ILE* 4.1 18.4 - - + -
213E ASP* 3.1 10.6 + - - +
226E PRO* 1.3 73.4 - - - +
228E GLU* 1.3 68.0 - - - +
230E GLY* 3.0 4.9 + - - +
231E ASP* 2.9 25.6 + - - +
277E PHE* 4.0 39.6 - - + -
278E TYR* 4.4 5.2 - - + -
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Residues in contact with GLU 228 (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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213E ASP* 3.0 21.1 + - - +
217E LYS* 3.6 22.6 + - - -
224E MET* 3.3 26.7 - - + +
225E GLY 3.4 19.3 + - - +
227E LEU* 1.3 74.4 - - - +
229E LEU* 1.3 56.5 + - - +
231E ASP* 3.1 6.9 + - - +
232E PHE* 2.9 27.7 + - - +
271E ARG* 4.3 15.3 + - - +
278E TYR* 3.7 21.5 + - + -
280E TYR* 4.6 4.0 + - - +
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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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220D ALA 6.0 1.3 - - - +
222D HIS* 6.1 0.7 - - - +
191E LEU* 4.0 35.4 - - + -
194E MET* 5.6 2.0 - - - -
195E ILE* 4.0 11.4 - - + -
224E MET* 4.0 33.6 - - + +
225E GLY 2.9 21.5 + - - +
226E PRO* 3.4 8.3 - - + +
228E GLU* 1.3 72.3 - - - +
230E GLY* 1.3 54.7 + - - +
232E PHE* 3.1 9.6 + - + +
233E ILE* 2.8 54.3 + - + +
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Residues in contact with GLY 230 (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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195E ILE* 3.9 17.9 - - - +
226E PRO 2.8 13.7 + - - -
227E LEU 3.0 5.8 + - - -
229E LEU* 1.3 77.7 - - - +
231E ASP* 1.3 50.9 + - - +
233E ILE* 3.4 1.0 + - - +
234E GLY 2.8 40.4 + - - +
235E LEU* 3.5 17.0 - - - -
238E CYS* 4.2 4.7 - - - -
277E PHE* 5.5 0.2 - - - -
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Residues in contact with ASP 231 (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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227E LEU 2.9 11.4 + - - -
228E GLU 3.1 5.8 + - - +
230E GLY* 1.3 75.0 - - - +
232E PHE* 1.3 61.8 + - - +
234E GLY* 3.5 6.8 + - - -
235E LEU* 3.7 4.3 - - - +
269E LEU 3.9 3.1 - - - +
270E GLY* 3.7 19.0 - - - -
271E ARG* 3.2 22.0 + - - +
272E LYS* 4.7 1.6 + - - +
276E GLY* 3.4 5.5 - - - -
277E PHE* 2.9 30.2 + - - -
278E TYR* 3.0 34.0 + - - -
280E TYR* 3.0 27.1 + - + +
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Residues in contact with PHE 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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141E ASN 6.0 1.8 - - - -
224E MET* 4.3 19.7 - - + -
228E GLU 2.9 12.5 + - - +
229E LEU* 3.1 24.0 + - + +
231E ASP* 1.3 77.5 - - - +
233E ILE* 1.3 68.6 + - + +
271E ARG* 3.4 47.8 - - - +
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Residues in contact with ILE 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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191E LEU* 4.4 9.2 - - + -
192E ILE* 4.3 15.0 - - + -
195E ILE* 4.0 14.6 - - + -
229E LEU* 2.8 46.4 + - + +
230E GLY 3.9 2.7 - - - +
232E PHE* 1.3 80.5 - - + +
234E GLY* 1.3 63.0 + - - +
237E ILE* 3.6 38.7 - - + +
238E CYS* 3.8 8.7 - - - -
241E ILE* 5.7 0.7 - - + -
272E LYS* 4.9 2.6 + - - -
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Residues in contact with GLY 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 GLY 2.8 10.2 + - - -
231E ASP 3.5 3.5 + - - -
232E PHE 3.3 3.0 - - - -
233E ILE* 1.3 78.5 - - - +
235E LEU* 1.3 60.4 + - - -
236E ASP* 3.2 13.5 - - - -
237E ILE* 3.2 5.5 + - - +
238E CYS* 3.0 27.0 + - - -
269E LEU 3.4 12.6 - - - -
272E LYS* 4.0 9.4 - - - -
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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