Contacts of the helix formed by residues 229 - 243 (chain B) in PDB entry 1BK6
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 PRO 229 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227B ASN 3.0 11.8 - - - +
228B LYS* 1.3 84.5 - - + +
230B SER* 1.3 57.2 + - - +
232B ILE* 3.3 8.9 + - + +
233B ARG* 2.8 50.4 + - - +
270B ASP* 5.4 7.3 - - + +
273B THR* 4.7 1.2 + - - -
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Residues in contact with SER 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLU* 3.3 19.3 + - - +
228B LYS* 3.0 31.7 + - - +
229B PRO* 1.3 80.0 - - - +
231B LEU* 1.3 71.6 + - - +
233B ARG* 3.1 25.3 + - - +
234B THR* 3.1 19.8 + - - -
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Residues in contact with LEU 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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187B VAL* 3.9 24.7 - - + -
190B LYS* 4.1 14.4 - - + -
191B GLU* 3.3 44.0 - - + +
194B ILE* 4.2 11.2 - - + -
223B LEU* 4.4 28.9 - - + +
226B SER* 4.0 20.4 - - - +
228B LYS* 3.4 13.9 + - + +
230B SER* 1.3 81.2 + - - +
232B ILE* 1.3 58.5 + - - +
234B THR* 3.3 1.4 + - - -
235B ALA* 3.0 28.2 + - - +
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Residues in contact with ILE 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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223B LEU 4.3 7.4 - - - +
224B PHE* 4.0 26.4 - - + +
226B SER* 3.2 37.7 - - - +
227B ASN* 4.5 3.8 - - - +
228B LYS 3.2 17.3 + - - +
229B PRO* 3.7 9.9 - - + +
230B SER 3.2 0.2 - - - -
231B LEU* 1.3 77.5 - - - +
233B ARG* 1.3 53.8 + - - +
235B ALA* 4.0 6.4 - - - +
236B THR* 2.6 44.7 + - - +
265B LEU* 4.4 11.0 - - + -
273B THR* 4.7 8.1 - - + +
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Residues in contact with ARG 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 PRO* 2.8 29.7 + - - +
230B SER* 3.1 29.9 + - - +
232B ILE* 1.3 76.7 - - - +
234B THR* 1.3 63.2 + - - +
236B THR* 3.4 3.6 + - - -
237B TRP* 3.2 21.1 + - - +
270B ASP* 3.0 40.2 + - - +
272B GLU* 3.7 37.3 + - + +
273B THR* 3.4 14.7 - - - +
276B ASP* 5.1 1.8 - - - +
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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
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191B GLU* 2.9 27.4 + - - +
194B ILE* 3.6 20.2 - - + -
195B TRP* 3.8 36.1 - - + -
230B SER 3.1 6.7 + - - -
231B LEU 3.9 2.0 - - - -
233B ARG* 1.3 74.3 - - - +
235B ALA* 1.3 66.6 + - - +
237B TRP* 3.3 17.0 + - + +
238B THR* 3.0 22.8 + - - +
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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
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194B ILE* 3.8 13.4 - - + +
220B ILE* 4.9 3.4 - - + +
223B LEU* 4.1 25.8 - - + -
224B PHE* 3.5 27.8 - - + -
231B LEU 3.0 17.8 + - - +
232B ILE* 4.0 4.7 - - - +
233B ARG 3.3 0.2 - - - -
234B THR* 1.3 77.4 - - - +
236B THR* 1.3 57.5 + - - +
238B THR* 3.9 1.2 - - - -
239B LEU* 3.0 28.6 + - - +
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Residues in contact with THR 236 (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 PHE* 3.5 16.3 - - - -
232B ILE* 2.6 25.2 + - - +
233B ARG 3.7 4.9 - - - -
234B THR 3.2 0.4 - - - -
235B ALA* 1.3 75.2 - - - +
237B TRP* 1.3 67.9 + - - +
239B LEU* 3.4 7.2 + - + +
240B SER* 3.2 17.7 + - - -
265B LEU* 3.9 11.9 - - + +
273B THR* 3.6 41.4 - - + +
276B ASP* 4.0 4.8 - - + +
277B ALA* 3.8 20.4 - - - +
280B ALA* 5.6 0.7 - - - +
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Residues in contact with TRP 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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195B TRP* 3.9 23.8 - + - -
198B GLY* 3.9 22.7 - - - -
199B ASN* 3.7 20.4 - - - -
233B ARG 3.2 10.8 + - - +
234B THR* 3.3 16.6 + - + +
236B THR* 1.3 77.8 - - - +
238B THR* 1.3 71.0 + - - +
240B SER* 2.7 34.3 + - - -
241B ASN* 3.3 24.2 + - - +
276B ASP* 3.7 28.0 + - - +
127E LYS* 3.5 35.6 - - + +
128E LYS* 4.1 0.2 - - - -
129E LYS* 3.4 57.3 - - + +
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Residues in contact with THR 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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194B ILE* 2.8 44.4 + - + +
197B LEU* 4.3 6.5 - - + +
198B GLY* 3.4 29.1 - - - +
201B ALA* 5.3 0.9 - - + -
220B ILE* 4.9 1.8 - - + -
234B THR 3.0 16.9 + - - -
235B ALA 3.9 4.5 - - - +
237B TRP* 1.3 82.4 - - - +
239B LEU* 1.3 62.4 + - - +
241B ASN* 3.2 8.6 + - - +
242B LEU* 3.2 33.9 + - + +
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Residues in contact with LEU 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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217B MET* 4.2 24.2 - - + -
220B ILE* 4.6 12.3 - - + -
221B LEU* 5.3 2.9 - - + -
224B PHE* 4.3 18.4 - - + -
235B ALA 3.0 17.6 + - - +
236B THR* 3.5 8.5 - - + +
237B TRP 3.1 0.2 - - - -
238B THR* 1.3 76.3 - - - +
240B SER* 1.3 62.8 + - - +
242B LEU* 3.1 14.8 + - + +
243B CYS* 3.1 29.8 + - - -
258B ALA* 4.1 18.6 - - + -
261B THR* 5.4 1.8 - - + -
262B LEU* 3.3 34.3 - - + -
265B LEU* 4.7 5.6 - - + -
280B ALA* 5.0 4.5 - - + -
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Residues in contact with SER 240 (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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236B THR 3.2 9.2 + - - -
237B TRP* 2.7 26.5 + - - -
239B LEU* 1.3 73.2 - - - +
241B ASN* 1.3 62.3 + - - -
243B CYS* 3.1 2.8 + - - -
244B ARG* 3.0 23.8 + - - +
276B ASP* 3.8 24.6 + - - -
279B TRP* 4.0 7.1 - - - +
280B ALA* 4.1 12.1 + - - +
283B TYR* 3.7 20.5 - - - -
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Residues in contact with ASN 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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198B GLY* 3.3 22.2 + - - +
201B ALA* 4.2 11.7 - - + +
202B GLY* 4.0 19.9 - - - +
208B ARG* 3.7 8.3 - - - +
237B TRP* 3.3 28.8 + - - -
238B THR* 3.2 7.6 + - - +
240B SER* 1.3 80.0 - - - +
242B LEU* 1.3 64.0 + - - +
243B CYS 3.4 0.3 + - - -
244B ARG* 3.4 29.7 + - - +
127E LYS* 3.3 33.2 + - - +
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Residues in contact with LEU 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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201B ALA* 3.7 22.9 - - + -
208B ARG* 3.2 34.4 - - - +
211B VAL* 4.0 18.2 - - + -
212B LEU* 3.9 30.4 - - + +
216B ALA* 5.9 0.2 - - + -
217B MET* 4.4 13.7 - - + -
220B ILE* 3.9 28.3 - - + -
238B THR* 3.2 20.9 + - + +
239B LEU* 3.1 16.9 + - + +
241B ASN* 1.3 75.9 - - - +
243B CYS* 1.3 59.4 + - - +
250B PRO* 3.7 10.9 - - - +
255B VAL* 4.1 4.9 - - + +
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Residues in contact with CYS 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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217B MET* 6.0 0.2 - - - -
239B LEU* 3.1 27.8 + - - +
240B SER 3.1 6.5 + - - +
242B LEU* 1.3 77.7 - - - +
244B ARG* 1.3 64.0 + - - +
245B GLY 3.6 2.9 + - - +
249B GLN* 5.4 0.3 - - - +
250B PRO* 3.6 16.4 - - - +
255B VAL* 4.2 19.3 - - - -
258B ALA* 5.4 2.9 - - - -
262B LEU* 5.4 0.9 - - - -
280B ALA* 4.2 13.7 - - - +
283B TYR* 3.7 23.9 - - + +
284B LEU* 3.8 35.0 - - + +
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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