Contacts of the helix formed by residues 232 - 246 (chain B) in PDB entry 3EIJ
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 SER 232 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197B LYS* 5.3 5.1 + - - +
227B CYS* 4.0 4.3 - - - -
228B GLY* 5.7 0.2 - - - -
231B MET* 1.3 75.2 - - - +
233B THR* 1.3 65.2 + - - +
234B THR* 3.3 19.9 + - - -
235B ASP* 2.9 35.3 + - - +
236B VAL* 3.2 12.1 + - - +
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Residues in contact with THR 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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227B CYS* 3.8 17.9 - - - -
232B SER* 1.3 72.5 - - - +
234B THR* 1.3 66.1 + - - +
236B VAL* 3.2 4.8 + - - +
237B GLU* 3.1 22.0 + - - +
272B GLY 4.6 5.8 - - - +
273B ILE* 3.9 27.4 - - - +
274B LEU* 5.8 0.2 - - - +
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Residues in contact with THR 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B SER* 3.0 11.6 + - - -
233B THR* 1.3 82.1 + - - +
235B ASP* 1.3 65.5 + - - +
237B GLU* 3.1 9.0 + - + +
238B LYS* 3.0 47.1 + - + +
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Residues in contact with ASP 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B GLU 4.9 2.8 - - - +
197B LYS* 3.7 39.1 + - - +
198B SER* 3.7 21.9 + - - -
201B PRO* 5.2 0.4 - - - -
231B MET* 3.7 15.7 - - + +
232B SER* 2.9 32.2 + - - +
234B THR* 1.3 76.9 - - - +
236B VAL* 1.3 53.5 + - - +
238B LYS* 3.3 17.3 + - - +
239B SER* 2.6 36.7 + - - -
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B PRO* 4.8 3.4 - - + -
223B LEU* 5.4 3.8 - - + -
227B CYS* 3.9 23.1 - - + -
231B MET* 4.0 21.5 - - + -
232B SER 3.2 13.7 + - - +
233B THR 3.5 7.0 - - - +
234B THR 3.2 0.6 - - - -
235B ASP* 1.3 77.0 - - - +
237B GLU* 1.3 61.5 + - - +
239B SER* 3.2 8.6 + - - -
240B PHE* 3.0 53.2 + - + -
273B ILE* 3.7 32.8 - - + +
274B LEU* 4.7 2.5 - - + -
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Residues in contact with GLU 237 (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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233B THR 3.1 12.4 + - - +
234B THR* 3.1 11.2 + - + +
236B VAL* 1.3 73.6 - - - +
238B LYS* 1.3 66.0 + - - +
240B PHE* 3.1 5.0 + - - +
241B ASP* 3.0 33.4 + - - +
274B LEU* 4.5 16.2 - - + +
275B CYS* 5.1 9.4 + - - +
278B TYR* 3.5 33.1 + - + +
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Residues in contact with LYS 238 (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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195B GLU* 5.2 14.7 + - - +
198B SER* 3.9 24.2 - - - +
234B THR* 3.0 36.7 + - + +
235B ASP* 3.5 16.9 + - - +
237B GLU* 1.3 75.3 - - + +
239B SER* 1.3 63.9 + - - +
241B ASP* 3.2 12.2 + - - +
242B LYS* 3.1 23.0 + - - +
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Residues in contact with SER 239 (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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198B SER 2.7 19.7 + - - -
201B PRO* 3.2 33.7 - - - +
202B VAL* 3.6 21.2 - - - +
235B ASP 2.6 20.8 + - - -
236B VAL* 3.3 9.2 - - - -
238B LYS* 1.3 76.3 - - - +
240B PHE* 1.3 60.7 + - - +
242B LYS 3.4 0.3 + - - -
243B LEU* 2.9 31.6 + - - +
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Residues in contact with PHE 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B PRO* 5.8 0.4 - - + -
205B VAL* 5.4 0.9 - - + -
223B LEU* 4.3 19.5 - - + -
236B VAL* 3.0 48.7 + - + +
237B GLU* 3.1 3.1 + - - +
239B SER* 1.3 78.4 - - - +
241B ASP* 1.3 64.8 + - - +
243B LEU* 3.7 23.2 - - + +
244B LEU* 3.1 30.2 + - + +
261B VAL* 4.7 1.8 - - + -
264B PHE* 4.0 16.4 - - + -
265B ILE* 3.6 36.8 - - + -
268B ALA* 4.0 25.1 - - + -
274B LEU* 4.1 12.6 - - + -
278B TYR* 3.2 21.9 + - + +
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Residues in contact with ASP 241 (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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237B GLU* 3.0 27.1 + - - +
238B LYS* 3.4 12.7 - - - +
240B PHE* 1.3 74.3 - - - +
242B LYS* 1.3 65.1 + - - +
244B LEU 3.2 2.4 + - - -
245B LYS* 3.1 29.2 + - - +
278B TYR* 2.6 32.6 + - - -
282B TYR* 3.4 27.5 + - + -
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Residues in contact with LYS 242 (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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161B GLU* 3.6 22.5 + - - -
199B GLY* 6.1 2.4 - - - -
202B VAL* 4.0 27.1 - - + +
238B LYS 3.1 9.5 + - - +
239B SER 3.8 6.5 - - - +
241B ASP* 1.3 79.0 - - - +
243B LEU* 1.3 53.8 + - - +
245B LYS* 3.0 12.5 + - + +
246B ASP* 2.8 63.0 + - - +
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Residues in contact with LEU 243 (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 PRO 4.9 3.1 - - - +
202B VAL* 3.8 35.2 - - + +
205B VAL* 3.7 37.7 - - + -
206B SER* 5.0 2.7 - - - +
239B SER* 2.9 19.7 + - - +
240B PHE* 3.7 30.3 - - + +
242B LYS* 1.3 77.0 - - - +
244B LEU* 1.3 57.7 + - - +
246B ASP* 3.6 4.5 + - + +
247B LEU* 3.2 27.8 + - - +
250B LEU* 4.0 20.7 - - + +
261B VAL* 4.5 18.2 - - + -
264B PHE* 5.7 0.2 - - + -
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Residues in contact with LEU 244 (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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240B PHE 3.1 21.1 + - - +
241B ASP 3.7 0.4 - - - +
242B LYS 3.2 0.2 - - - -
243B LEU* 1.3 76.4 - - - +
245B LYS* 1.3 64.1 + - - +
247B LEU* 3.3 18.4 - - + +
248B PRO* 4.1 3.3 - - - +
261B VAL* 4.3 13.0 - - + -
265B ILE* 4.3 9.4 - - + -
278B TYR* 3.7 18.2 - - + +
282B TYR* 3.5 40.6 - - + +
288B CYS* 4.8 1.6 - - - -
291B ALA* 4.0 28.9 - - + +
294B ALA* 4.0 26.9 - - + -
295B LEU* 4.2 14.6 - - + -
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Residues in contact with LYS 245 (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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241B ASP* 3.1 23.9 + - - +
242B LYS* 3.0 12.4 + - + +
244B LEU* 1.3 72.5 - - - +
246B ASP* 1.3 64.3 + - - +
247B LEU 3.1 5.2 - - - -
248B PRO* 3.3 18.9 - - - +
282B TYR* 4.0 15.0 - - - +
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Residues in contact with ASP 246 (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 VAL* 4.7 5.2 - - - +
242B LYS* 2.8 50.3 + - - +
243B LEU* 3.7 6.3 - - + +
245B LYS* 1.3 81.7 - - - +
247B LEU* 1.3 56.7 + - - +
248B PRO* 3.5 2.0 - - - -
249B GLU* 3.1 26.7 - - + +
250B LEU* 3.0 38.2 + - + +
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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