Contacts of the helix formed by residues 224 - 235 (chain B) in PDB entry 4U2M
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 ASN 224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204B GLU* 6.1 4.0 - - + -
205B GLY* 6.3 0.4 - - - -
208B ILE* 3.4 25.9 - - + +
219B ASN 3.3 20.8 + - - -
220B LEU* 3.6 6.1 - - - +
221B ARG* 3.0 33.2 + - - +
223B GLY* 1.3 81.3 - - - +
225B ILE* 1.3 71.8 + - - +
226B MET 3.3 2.5 - - - -
227B ALA* 3.2 11.7 + - + +
228B VAL* 2.9 26.1 + - + +
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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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220B LEU* 4.8 8.5 - - + -
221B ARG 3.1 10.1 + - - +
222B GLU* 3.9 8.6 + - - +
224B ASN* 1.3 84.3 + - - +
226B MET* 1.3 59.9 + - + +
228B VAL* 3.8 4.3 - - - +
229B MET* 2.9 32.3 + - - +
244B CYS* 4.5 6.8 - - + +
247B PHE* 4.5 22.9 - - + -
248B ILE* 5.0 14.3 - - + +
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Residues in contact with MET 226 (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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222B GLU 5.2 2.7 + - - +
224B ASN 3.3 0.8 - - - -
225B ILE* 1.3 78.6 - - + +
227B ALA* 1.3 59.7 + - - +
229B MET* 3.5 11.0 + - - +
230B ALA* 3.0 30.0 + - - +
248B ILE* 4.6 20.0 - - - -
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Residues in contact with ALA 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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202B ASN* 4.0 33.4 - - + +
204B GLU* 6.2 0.2 - - + -
205B GLY* 4.5 5.4 - - - -
223B GLY 5.8 0.2 - - - +
224B ASN* 3.2 15.1 + - + +
226B MET* 1.3 79.7 - - - +
228B VAL* 1.3 56.7 + - + +
230B ALA* 3.8 4.9 - - - +
231B THR* 2.5 37.9 + - - -
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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
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205B GLY* 4.3 8.1 - - - -
208B ILE* 3.9 30.7 - - + -
209B LEU* 3.8 23.6 - - + +
218B LEU* 4.4 6.7 - - + -
220B LEU* 3.8 22.7 - - + -
224B ASN* 2.9 34.0 + - + +
225B ILE 3.8 3.4 - - - +
227B ALA* 1.3 74.8 - - - +
229B MET* 1.3 59.4 + - - +
231B THR* 3.2 5.5 + - - -
232B ALA* 2.9 28.6 + - - +
240B VAL* 4.6 0.7 - - + -
244B CYS* 3.9 8.5 - - - -
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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
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225B ILE 2.9 18.8 + - - +
226B MET* 3.7 12.8 - - - +
228B VAL* 1.3 77.6 - - - +
230B ALA* 1.3 61.1 + - - +
232B ALA* 3.3 4.4 + - - +
233B MET* 3.0 47.1 + - + +
241B VAL* 4.0 9.7 - - + +
244B CYS* 3.7 27.1 - - + -
245B ARG* 3.7 39.7 - - + +
248B ILE* 4.3 22.2 - - + -
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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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201B ILE* 5.8 2.9 - - + -
226B MET 3.0 17.7 + - - +
227B ALA* 3.8 6.5 - - - +
229B MET* 1.3 76.8 - - - +
231B THR* 1.3 64.8 + - - +
233B MET* 3.3 13.5 + - - +
234B TYR* 3.0 23.4 + - - +
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Residues in contact with THR 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 ILE* 4.0 23.7 - - + +
202B ASN* 4.2 8.8 + - - +
205B GLY* 3.9 10.7 - - - -
206B PHE* 3.8 22.9 - - + +
209B LEU* 3.5 20.9 - - + -
227B ALA 2.5 23.9 + - - -
228B VAL 3.7 0.4 - - - -
230B ALA* 1.3 78.3 - - - +
232B ALA* 1.3 56.5 + - - +
234B TYR* 3.4 7.3 + - + +
235B LEU* 2.9 37.3 + - + +
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Residues in contact with ALA 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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209B LEU* 3.4 12.0 - - + +
228B VAL 2.9 17.6 + - - +
229B MET* 3.7 3.4 - - - +
230B ALA 3.2 0.2 - - - -
231B THR* 1.3 72.3 - - - +
233B MET* 1.3 60.9 + - - +
235B LEU* 3.4 4.1 + - - +
236B GLN 2.9 7.6 + - - -
237B MET* 2.8 35.6 + - + +
240B VAL* 3.8 26.2 - - + -
241B VAL* 3.6 18.6 - - + +
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Residues in contact with MET 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* 3.0 42.4 + - + +
230B ALA* 3.5 14.4 - - - +
231B THR 3.3 0.2 - - - -
232B ALA* 1.3 75.5 - - - +
234B TYR* 1.3 65.4 + - - +
236B GLN* 3.0 19.5 + - - +
238B GLU* 5.5 1.3 - - - +
241B VAL* 3.6 24.9 - - + -
245B ARG* 6.3 0.7 - - - +
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Residues in contact with TYR 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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179B LEU* 3.7 40.0 - - + +
197B LEU* 3.7 25.3 - - + +
198B ASP* 3.1 38.6 + - + +
201B ILE* 3.7 36.3 - - + -
230B ALA 3.0 9.9 + - - +
231B THR* 3.5 8.7 - - + +
233B MET* 1.3 81.7 - - - +
235B LEU* 1.3 69.1 + - + +
236B GLN* 3.3 7.3 + - - +
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Residues in contact with LEU 235 (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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177B SER* 2.8 27.3 + - - +
178B GLY 3.4 0.7 + - - -
179B LEU* 3.3 18.0 + - + -
180B PHE* 3.9 24.0 - - + -
197B LEU* 4.5 2.2 - - + -
206B PHE* 3.9 29.2 - - + -
209B LEU* 4.0 21.3 - - + -
213B MET* 4.4 7.9 - - + -
231B THR* 2.9 23.6 + - + +
232B ALA 3.9 3.6 - - - +
233B MET 3.2 0.2 - - - -
234B TYR* 1.3 91.0 - - + +
236B GLN* 1.3 70.2 + - - +
237B MET* 3.9 19.1 - - + -
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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