Contacts of the helix formed by residues 237 - 256 (chain B) in PDB entry 2BKU
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 ASP 237 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B LYS* 3.2 47.7 + - + +
198B ARG* 6.0 0.7 - - - +
235B ALA* 3.4 4.4 - - + +
236B GLU* 1.3 76.9 - - - +
238B ILE* 1.3 63.0 + - - +
239B GLU 3.0 25.8 + - - -
240B VAL* 3.2 19.7 + - + +
241B GLN* 3.3 25.0 + - - +
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Residues in contact with ILE 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 LYS* 5.9 0.7 - - - +
236B GLU 3.5 4.3 + - - +
237B ASP* 1.3 72.5 + - - +
239B GLU* 1.3 76.6 + - + +
241B GLN* 3.3 11.2 + - - +
242B ALA* 3.0 22.5 + - - +
279B ASN* 3.3 29.4 - - - +
281B LYS* 4.1 15.9 - - + -
282B VAL* 3.4 24.0 - - + -
285B MET* 3.6 16.9 - - + +
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Residues in contact with GLU 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASN* 5.7 1.4 - - - +
195B LYS* 2.4 32.2 + - - +
199B LEU* 3.6 27.3 - - + +
237B ASP* 3.0 7.2 + - - +
238B ILE* 1.3 88.9 - - + +
240B VAL* 1.3 62.1 + - - +
242B ALA* 3.1 8.7 + - - +
243B ALA* 2.9 28.1 + - - +
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Residues in contact with VAL 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B LYS* 4.2 22.2 - - + +
198B ARG* 3.9 30.5 - - + +
199B LEU* 4.0 14.1 - - + +
202B LEU* 3.6 15.8 - - + +
232B ALA* 4.0 6.1 - - + +
235B ALA* 3.6 20.6 - - + -
237B ASP* 3.2 27.9 + - + +
239B GLU* 1.3 76.6 - - - +
241B GLN* 1.3 57.3 + - - +
243B ALA* 3.3 4.3 + - - +
244B ALA* 3.0 26.7 + - - +
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Residues in contact with GLN 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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232B ALA 3.6 8.1 - - - -
233B THR 2.7 28.0 + - - +
234B GLN* 4.2 3.2 + - - +
235B ALA 3.3 30.4 + - - +
236B GLU 4.8 2.1 - - - +
237B ASP 3.3 7.6 + - - +
238B ILE* 3.4 19.1 - - - +
239B GLU 3.2 0.4 - - - -
240B VAL* 1.3 78.8 - - - +
242B ALA* 1.3 57.6 + - - +
244B ALA* 3.1 3.2 + - - +
245B PHE* 2.9 35.0 + - + -
274B THR* 5.2 5.5 - - - +
282B VAL* 3.3 36.3 - - - +
285B MET* 3.6 11.2 - - - -
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Residues in contact with ALA 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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238B ILE 3.0 14.0 + - - +
239B GLU* 3.1 12.1 + - - +
241B GLN* 1.3 75.8 - - - +
243B ALA* 1.3 57.7 + - - +
245B PHE* 3.7 1.4 + - - +
246B GLY* 3.0 24.3 + - - -
281B LYS* 6.4 0.2 - - + -
285B MET* 3.4 26.8 - - + +
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Residues in contact with ALA 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B LEU* 4.1 12.1 - - + -
202B LEU* 3.5 26.9 - - + -
203B ASN* 4.1 16.8 - - - +
239B GLU 2.9 12.8 + - - +
240B VAL 3.5 8.7 - - - +
242B ALA* 1.3 75.5 - - - +
244B ALA* 1.3 63.9 + - - +
246B GLY* 3.2 3.4 + - - -
247B CYS* 3.0 26.2 + - - -
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Residues in contact with ALA 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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202B LEU* 4.0 7.2 - - - +
229B VAL* 3.6 17.2 - - + +
232B ALA* 3.5 19.7 - - + -
233B THR* 3.4 33.0 - - + +
240B VAL 3.0 7.6 + - - +
241B GLN 3.4 7.2 - - - +
243B ALA* 1.3 74.0 - - - +
245B PHE* 1.3 65.9 + - - +
247B CYS* 3.0 7.6 + - - +
248B LEU* 2.9 18.7 + - - +
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Residues in contact with PHE 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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233B THR* 4.0 30.5 - - + -
234B GLN* 5.4 0.7 - - - -
241B GLN* 2.9 29.3 + - + +
242B ALA 4.2 2.9 - - - +
244B ALA* 1.3 72.0 - - - +
246B GLY* 1.3 57.6 + - - +
248B LEU* 3.1 21.7 + - + +
249B CYS* 2.8 36.7 + - - -
270B LEU* 5.5 0.9 - - + -
271B THR* 4.2 18.8 - - + -
274B THR* 3.7 27.4 - - + -
282B VAL* 5.0 2.5 - - + -
285B MET* 3.6 48.0 - - + +
286B THR* 3.9 19.7 - - + -
289B PHE* 4.3 10.3 - - + -
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Residues in contact with GLY 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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206B ALA* 5.8 3.1 - - - -
242B ALA 3.0 16.3 + - - -
243B ALA* 3.4 6.3 - - - -
244B ALA 3.1 0.4 - - - -
245B PHE* 1.3 77.1 - - - +
247B CYS* 1.3 59.3 + - - +
249B CYS* 3.5 7.6 + - - +
250B LYS* 3.2 24.1 + - - +
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Residues in contact with CYS 247 (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 LEU* 3.1 36.3 - - - -
205B LEU* 4.3 12.6 - - + -
206B ALA* 4.0 19.5 - - - -
209B LEU* 5.0 1.3 - - + -
229B VAL* 4.0 15.0 - - + -
243B ALA 3.0 13.1 + - - +
244B ALA 3.0 9.2 + - - +
246B GLY* 1.3 72.6 - - - +
248B LEU* 1.3 56.6 + - - +
250B LYS* 3.2 7.1 + - - +
251B ILE* 2.7 48.4 + - + +
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Residues in contact with LEU 248 (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 MET* 4.0 18.4 - - + -
229B VAL* 3.9 18.2 - - + -
230B CYS* 4.7 4.3 - - - -
233B THR* 3.7 24.7 - - + -
244B ALA 2.9 11.8 + - - +
245B PHE* 3.4 23.3 - - + +
247B CYS* 1.3 76.2 - - - +
249B CYS* 1.3 57.0 + - - +
251B ILE* 3.3 5.9 + - + +
252B MET* 2.8 31.4 + - - +
259B MET* 6.1 0.9 - - - -
267B LEU* 3.5 43.5 - - + -
289B PHE* 3.9 18.8 - - + -
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Residues in contact with CYS 249 (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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245B PHE* 2.8 21.5 + - - -
246B GLY* 3.6 10.8 - - - +
248B LEU* 1.3 73.3 - - - +
250B LYS* 1.3 63.7 + - + +
252B MET* 3.2 6.2 + - - +
253B SER* 2.9 26.0 + - - -
285B MET 5.1 1.3 - - - -
288B GLU* 4.2 11.0 - - - -
289B PHE* 3.7 28.9 - - - -
292B THR* 3.4 27.2 - - + +
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Residues in contact with LYS 250 (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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206B ALA* 3.1 38.4 + - + +
207B ASP* 4.9 3.8 + - - +
209B LEU* 3.4 22.1 - - + +
210B ILE* 4.6 15.5 - - - +
211B PHE* 6.2 0.4 - - - -
246B GLY 3.2 12.4 + - - +
247B CYS* 3.2 5.2 + - - +
249B CYS* 1.3 79.4 - - + +
251B ILE* 1.3 54.3 + - - +
253B SER* 3.0 8.2 + - - -
254B LYS* 2.7 58.3 + - - +
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Residues in contact with ILE 251 (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 LEU* 5.3 0.7 - - + -
209B LEU* 3.8 25.4 - - + -
216B MET* 4.2 14.6 - - + -
225B LEU* 4.1 13.5 - - + -
226B MET* 3.3 35.9 - - + -
229B VAL* 4.7 2.9 - - + -
247B CYS* 2.7 40.7 + - + +
248B LEU* 3.6 7.0 - - + +
250B LYS* 1.3 73.1 - - - +
252B MET* 1.3 55.8 + - - +
255B TYR* 2.7 37.3 + - - +
259B MET* 3.6 32.3 - - + -
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Residues in contact with MET 252 (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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248B LEU 2.8 17.1 + - - +
249B CYS* 3.2 6.3 + - - +
251B ILE* 1.3 76.2 - - - +
253B SER* 1.3 64.4 + - - +
256B TYR* 3.1 54.5 + - + +
259B MET* 3.6 36.6 - - + -
263B MET* 4.0 8.7 - - - -
267B LEU* 5.5 0.4 - - + -
289B PHE* 3.7 30.1 - - + -
292B THR* 4.5 5.8 - - + +
293B ILE* 3.7 40.4 - - + +
296B GLU* 4.4 2.9 - - + +
317B PHE* 4.4 3.6 - - + -
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Residues in contact with SER 253 (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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249B CYS 2.9 16.0 + - - -
250B LYS* 3.4 9.2 - - - -
252B MET* 1.3 77.1 - - - +
254B LYS* 1.3 79.1 + - - +
292B THR* 3.2 16.1 - - - +
296B GLU* 3.0 39.2 - - - +
309D GLN 5.4 0.5 - - - +
311D PRO* 3.9 9.0 - - - +
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Residues in contact with LYS 254 (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* 4.6 5.4 - - + -
210B ILE* 3.6 37.0 - - + -
250B LYS* 2.7 41.9 + - - +
253B SER* 1.3 91.9 + - - +
255B TYR* 1.3 91.4 + - + +
256B TYR 3.7 0.7 - - - -
257B THR* 5.0 0.3 - - - +
296B GLU* 5.6 0.4 + - - -
311D PRO* 3.8 17.9 - - - +
313D GLN* 5.4 4.3 + - - -
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Residues in contact with TYR 255 (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* 2.5 36.9 + - + -
210B ILE* 4.0 4.1 - - - -
213B LYS* 3.3 28.9 - - + +
216B MET* 3.4 52.9 - - + -
217B GLU* 5.1 4.9 - - + -
251B ILE* 2.7 26.2 + - + +
254B LYS* 1.3 108.5 - - + +
256B TYR* 1.3 65.7 + - - +
257B THR* 3.1 8.3 - - + -
258B PHE* 3.0 31.3 + + + -
259B MET* 3.4 12.5 - - + +
313D GLN* 5.0 10.3 + - - -
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Residues in contact with TYR 256 (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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252B MET* 3.1 35.5 + - - +
254B LYS 3.7 2.0 + - - -
255B TYR* 1.3 73.9 - - - +
257B THR* 1.3 68.5 + - - +
259B MET* 2.9 24.8 + - - +
293B ILE 4.9 3.1 - - - -
296B GLU* 4.5 12.6 - - + +
297B GLU* 2.9 35.1 + - + +
300B ILE* 3.8 21.3 - - + -
312B LEU* 4.9 4.9 - - + -
313B GLN 3.8 16.6 - - - -
314B SER 3.7 0.5 - - - -
315B TYR* 2.7 53.0 + + - +
317B PHE* 3.6 18.6 - + - -
311D PRO* 4.0 18.6 - - + +
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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
------------------------------------------------------------
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