Contacts of the helix formed by residues 224 - 235 (chain B) in PDB entry 2E7Y
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 224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209B CYS* 4.6 0.4 - - - -
211B PHE* 3.2 13.0 - - + +
212B LEU 5.0 0.4 - - - -
213B ASP 4.4 0.9 - - - +
214B ALA* 3.6 31.2 - - + +
217B ARG* 4.0 2.0 - - - +
223B ALA* 1.3 74.9 - - - +
225B ILE* 1.3 67.1 + - - +
226B ASP* 3.3 16.8 - - - +
227B GLU* 2.7 23.6 + - - +
228B VAL* 3.0 21.7 + - - +
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Residues in contact with ILE 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B CYS* 3.4 23.2 - - - -
211B PHE 3.0 6.9 + - - -
212B LEU* 3.4 36.6 - - + +
224B ALA* 1.3 71.2 - - - +
226B ASP* 1.3 65.7 + - + +
228B VAL* 3.1 4.8 + - - +
229B MET* 2.7 48.3 + - + +
242B LEU* 3.7 25.6 - - + -
256B VAL* 3.6 24.2 - - + -
257B ILE* 4.5 8.7 - - + -
260B TYR* 3.8 26.0 - - + +
269B ILE* 5.9 0.4 - - + -
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Residues in contact with ASP 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B LEU 5.8 1.6 - - - -
213B ASP* 6.5 0.2 - - - -
214B ALA* 4.7 8.9 + - - +
224B ALA* 3.3 12.8 - - - +
225B ILE* 1.3 79.0 - - + +
227B GLU* 1.3 85.5 + - - +
229B MET* 3.2 2.6 + - - +
230B GLU* 2.7 35.3 + - - +
260B TYR* 2.9 29.3 - - + +
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Residues in contact with GLU 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B LEU* 5.6 0.7 - - - +
193B ALA* 3.6 23.1 + - + +
214B ALA* 4.1 7.8 - - + +
217B ARG* 2.4 39.8 + - - -
223B ALA* 3.5 5.5 - - - +
224B ALA* 2.7 26.6 + - - +
226B ASP* 1.3 96.3 + - - +
228B VAL* 1.3 64.3 + - - +
230B GLU* 3.0 23.2 + - - +
231B SER* 3.1 5.5 + - - -
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Residues in contact with VAL 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ALA* 4.1 6.5 - - - -
205B LEU* 5.2 0.2 - - + -
207B HIS* 3.6 30.1 - - + +
208B GLU 3.6 13.5 - - - +
209B CYS* 4.9 2.5 - - - -
223B ALA* 3.5 24.7 - - + -
224B ALA 3.0 17.9 + - - +
225B ILE* 3.4 9.2 - - - +
227B GLU* 1.3 75.3 - - - +
229B MET* 1.3 69.6 + - + +
231B SER* 3.1 6.4 + - - -
232B VAL* 2.9 30.8 + - + +
240B VAL* 5.1 0.4 - - + -
242B LEU* 4.0 21.1 - - + -
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Residues in contact with MET 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B ILE* 2.7 31.4 + - + +
226B ASP 3.5 4.3 - - - +
228B VAL* 1.3 74.1 - - + +
230B GLU* 1.3 57.5 + - - +
232B VAL* 3.6 24.6 - - + +
233B LYS* 2.9 31.8 + - - +
240B VAL* 4.4 7.6 - - + -
242B LEU* 3.9 30.7 - - + -
260B TYR* 3.4 33.7 - - + -
264B MET* 3.6 21.2 - - + +
267B VAL* 5.6 0.7 - - - -
269B ILE* 4.1 29.6 - - + -
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Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B ASP 2.7 13.5 + - - +
227B GLU* 3.0 19.3 - - - +
229B MET* 1.3 77.1 - - - +
231B SER* 1.3 55.1 + - - +
233B LYS* 3.0 34.7 + - - +
234B ALA* 2.8 30.4 + - + +
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Residues in contact with SER 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B ALA* 3.6 17.7 - - - +
194B LEU 2.8 29.6 + - - -
196B PRO* 3.9 16.6 - - - +
199B ILE* 3.5 12.5 - - - +
207B HIS* 5.9 1.3 - - - -
227B GLU 3.1 2.0 + - - -
228B VAL* 3.1 9.2 + - - -
230B GLU* 1.3 74.8 - - - +
232B VAL* 1.3 67.0 + - - +
234B ALA* 3.8 1.1 - - - +
235B ALA* 2.9 27.5 + - - +
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Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ILE* 4.3 0.7 - - + -
205B LEU* 4.0 16.4 - - + -
228B VAL* 2.9 21.5 + - + +
229B MET* 3.6 24.2 - - + +
231B SER* 1.3 76.6 - - - +
233B LYS* 1.3 56.4 + - - +
235B ALA 3.0 20.1 - - - +
236B GLY 4.5 0.2 - - - -
237B VAL* 3.5 39.5 + - + +
240B VAL* 3.7 28.7 - - + -
264B MET* 5.1 2.9 - - + -
267B VAL* 4.0 18.9 - - + +
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Residues in contact with LYS 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B MET* 2.9 11.3 + - - +
230B GLU* 3.0 36.5 + - - +
232B VAL* 1.3 74.1 - - - +
234B ALA* 1.3 58.3 + - - +
235B ALA 2.4 23.9 - - - +
264B MET* 3.6 29.8 - - + +
267B VAL* 6.3 0.2 - - - -
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Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B PRO* 3.4 30.3 - - + -
200B ARG* 4.0 11.7 + - - +
230B GLU* 2.8 18.6 + - + +
231B SER* 3.3 0.4 + - - -
233B LYS* 1.3 73.6 - - - +
235B ALA* 1.3 60.0 + - - +
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Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B PRO* 3.6 26.2 - - + +
199B ILE* 3.9 3.6 - - + -
200B ARG* 3.8 18.6 - - - +
231B SER 2.9 17.6 + - - +
232B VAL 3.0 4.8 - - - +
233B LYS 2.4 27.0 - - - +
234B ALA* 1.3 77.3 - - - +
236B GLY* 1.3 60.1 + - - +
237B VAL* 3.3 20.4 - - + -
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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