Contacts of the helix formed by residues 224 - 232 (chain B) in PDB entry 4J1O
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 THR 224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223B ASN* 1.3 92.3 - - - +
225B LEU* 1.3 63.1 + - - +
226B GLU* 3.7 11.6 + - - +
227B GLU* 2.7 47.2 + - - +
228B ILE* 3.2 17.6 + - - +
244B SER* 4.0 2.9 - - - -
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Residues in contact with LEU 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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224B THR* 1.3 73.5 - - - +
226B GLU* 1.3 57.3 + - - +
228B ILE* 3.2 9.1 + - + -
229B ALA* 2.8 30.2 + - + +
241B LEU* 3.8 37.0 - - + -
244B SER* 3.5 17.7 + - - +
250B THR* 3.9 29.6 - - + +
253B ARG* 3.7 35.0 - - - +
254B ALA* 5.2 0.9 - - + -
259B LEU* 4.3 23.6 - - + -
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Residues in contact with GLU 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B THR* 3.1 10.7 - - - +
225B LEU* 1.3 80.3 - - + +
227B GLU* 1.3 61.7 + - + +
229B ALA* 3.4 6.9 + - - +
230B ALA* 3.1 22.7 + - - +
253B ARG* 2.7 40.4 + - - -
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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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199B LEU 4.4 4.9 - - - +
200B PRO* 4.8 2.8 - - - +
201B SER* 4.6 12.6 + - - -
222B CYS* 3.7 25.6 - - + +
223B ASN* 3.8 10.4 + - - +
224B THR* 2.7 43.7 + - - +
226B GLU* 1.3 72.6 - - + +
228B ILE* 1.3 66.7 + - - +
230B ALA* 3.2 7.9 + - - +
231B ILE* 3.1 28.4 + - - +
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Residues in contact with ILE 228 (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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220B GLN* 3.6 30.3 - - - +
221B PRO* 4.1 19.5 - - + -
222B CYS* 4.0 19.7 - - + +
224B THR 3.2 9.5 + - - +
225B LEU* 3.2 10.3 + - + +
227B GLU* 1.3 76.5 - - - +
229B ALA* 1.3 62.5 + - - +
231B ILE* 3.2 10.1 + - + +
232B ARG* 3.0 22.6 + - + +
239B ILE* 3.8 28.0 - - + -
241B LEU* 3.6 27.4 - - + -
244B SER* 4.6 1.3 - - - +
259B LEU 4.3 11.4 - - - +
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Residues in contact with ALA 229 (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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225B LEU* 2.8 20.4 + - + +
226B GLU* 3.7 9.9 - - - +
228B ILE* 1.3 75.0 - - - +
230B ALA* 1.3 60.8 + - - +
231B ILE 3.5 0.2 + - - -
232B ARG* 3.7 25.7 + - - +
233B GLY 4.9 1.2 + - - -
253B ARG* 5.2 6.5 - - - +
259B LEU* 4.3 29.8 - - + -
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Residues in contact with ALA 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 GLU 3.1 14.6 + - - +
227B GLU* 3.2 11.4 + - - +
229B ALA* 1.3 78.7 - - - +
231B ILE* 1.3 61.1 + - + +
232B ARG 3.9 0.2 + - - -
233B GLY 4.9 1.4 + - - -
234B ARG* 4.5 13.2 + - - -
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Residues in contact with ILE 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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201B SER* 3.4 30.5 - - - -
204B ALA* 3.9 26.5 - - + -
205B LEU* 4.4 11.7 - - + -
218B LEU* 5.4 0.9 - - + -
221B PRO* 4.3 12.6 - - + -
222B CYS* 4.0 12.6 - - - -
227B GLU 3.4 12.6 - - - +
228B ILE* 3.3 14.4 - - - +
230B ALA* 1.3 78.4 - - + +
232B ARG* 1.3 71.0 + - - +
233B GLY 3.3 2.7 - - - -
234B ARG* 2.9 26.0 + - - +
235B VAL* 3.4 25.8 + - + +
239B ILE* 4.5 6.5 - - + -
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Residues in contact with ARG 232 (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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228B ILE 3.0 16.8 + - - +
229B ALA* 4.1 13.4 + - - +
230B ALA 3.5 2.0 - - - -
231B ILE* 1.3 76.5 - - - +
233B GLY* 1.3 71.7 + - - +
234B ARG 3.2 1.0 + - - -
235B VAL* 3.2 21.0 + - - +
239B ILE* 3.9 23.3 - - + +
257B GLN 4.9 3.2 + - - -
258B GLY 3.4 24.5 + - - -
259B LEU* 3.4 41.6 - - - +
260B CYS* 4.4 2.5 - - - +
261B ASP* 5.5 5.8 - - - +
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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