Contacts of the helix formed by residues 232 - 246 (chain B) in PDB entry 2BT4
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 232 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220B LEU* 3.5 17.0 - - - +
221B GLY* 4.8 3.8 - - - -
222B GLN* 6.0 3.1 - - + +
230B SER 4.7 5.2 - - - +
231B ASP* 1.3 75.3 - - - +
233B LEU* 1.3 67.3 + - - +
234B ALA* 3.5 10.1 + - - +
235B ASP* 3.1 32.5 + - - +
236B VAL* 3.0 25.3 + - - +
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Residues in contact with LEU 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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213B ASN* 3.9 15.7 - - + +
217B LEU* 3.7 32.3 - - + +
218B ASN* 4.1 12.5 + - + +
220B LEU* 4.0 22.4 + - + +
232B THR* 1.3 74.5 - - - +
234B ALA* 1.3 55.9 + - - +
236B VAL* 3.2 6.4 + - + +
237B GLU* 2.9 27.0 + - - +
253B PHE* 3.8 29.7 - - + -
255B GLN* 3.7 33.0 - - + -
338B TYR* 4.8 2.9 - - - +
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Residues in contact with ALA 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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232B THR* 3.2 10.1 + - - +
233B LEU* 1.3 75.5 - - - +
235B ASP* 1.3 65.6 + - - +
237B GLU* 3.4 13.2 + - - +
238B ALA* 3.1 22.2 + - - +
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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
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230B SER 4.6 1.2 - - - +
231B ASP* 3.6 24.8 - - + +
232B THR* 3.1 39.0 + - - +
234B ALA* 1.3 75.2 - - - +
236B VAL* 1.3 63.9 + - - +
238B ALA* 3.2 9.0 + - - +
239B LEU* 3.0 24.2 + - - +
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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
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220B LEU* 3.6 22.2 - - + -
231B ASP* 4.5 4.3 - - + -
232B THR 3.0 14.0 + - - +
233B LEU* 3.4 9.6 - - + +
235B ASP* 1.3 73.3 - - - +
237B GLU* 1.3 65.3 + - - +
239B LEU* 3.2 10.5 + - + +
240B CYS* 3.0 23.5 + - - -
253B PHE* 4.0 14.8 - - + -
335B VAL* 3.6 22.7 - - + -
338B TYR* 3.6 39.5 - - + -
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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 LEU 2.9 14.2 + - - +
234B ALA* 3.5 14.9 - - - +
235B ASP 3.3 0.2 - - - -
236B VAL* 1.3 74.7 - - - +
238B ALA* 1.3 57.7 + - - +
240B CYS* 3.2 3.1 + - - +
241B VAL* 3.0 42.9 + - + +
251B VAL* 4.9 0.9 - - + +
253B PHE* 3.6 55.7 + - + +
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Residues in contact with ALA 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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234B ALA 3.1 10.0 + - - +
235B ASP* 3.5 11.2 - - - +
237B GLU* 1.3 77.7 - - - +
239B LEU* 1.3 64.1 + - - +
241B VAL* 3.3 9.0 + - - +
242B LYS* 3.2 32.4 + - + +
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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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231B ASP* 5.6 3.4 - - - +
235B ASP 3.0 13.7 + - - +
236B VAL* 3.4 12.8 - - + +
238B ALA* 1.3 75.1 - - - +
240B CYS* 1.3 59.2 + - - +
242B LYS* 3.5 9.2 + - + +
243B ALA* 2.9 29.7 + - - +
335B VAL* 3.8 36.3 - - + +
336B GLN* 4.8 1.6 - - - +
338B TYR* 5.6 0.9 - - + -
339B VAL* 3.9 26.6 - - + +
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Residues in contact with CYS 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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211B ILE* 3.4 33.2 - - + -
236B VAL 3.0 16.9 + - - +
237B GLU 3.6 7.6 - - - +
238B ALA 3.2 0.2 - - - -
239B LEU* 1.3 77.2 - - - +
241B VAL* 1.3 65.2 + - - +
243B ALA* 4.0 5.2 - - - +
244B ALA* 2.9 27.0 + - - +
251B VAL* 3.6 7.8 - - + +
253B PHE* 4.2 9.0 - - + -
338B TYR* 3.6 40.8 - - - -
339B VAL* 5.8 1.3 - - - +
342B VAL* 4.6 4.2 - - + +
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Residues in contact with VAL 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 31.0 + - + +
238B ALA* 3.6 9.4 - - - +
240B CYS* 1.3 75.9 - - - +
242B LYS* 1.3 62.6 + - + +
244B ALA* 3.8 2.1 - - - +
245B ALA* 3.0 29.6 + - + +
249B GLY 4.9 0.7 - - - +
250B THR* 5.8 0.9 - - - +
251B VAL* 4.0 22.7 - - + +
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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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238B ALA* 3.2 19.4 + - - +
239B LEU* 3.9 8.3 - - + +
241B VAL* 1.3 80.5 - - + +
243B ALA* 1.3 63.8 + - - +
245B ALA* 3.3 6.5 + - - +
246B ALA* 3.0 24.1 + - - +
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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
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239B LEU 2.9 18.6 + - - +
240B CYS* 3.3 5.1 + - - +
242B LYS* 1.3 74.6 - - - +
244B ALA* 1.3 60.6 + - - +
246B ALA* 3.3 9.8 + - - +
247B HIS* 2.9 29.7 - - + +
339B VAL* 4.0 33.9 - - + +
342B VAL* 3.8 14.6 - - + -
343B GLU* 5.8 0.4 - - + -
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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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204B LEU* 4.5 1.1 - - - +
209B ILE* 4.8 4.3 - - + -
240B CYS 2.9 8.6 + - - +
241B VAL 3.8 2.5 - - - +
243B ALA* 1.3 77.7 - - - +
245B ALA* 1.4 54.6 + - - +
247B HIS* 3.0 15.5 + - - +
248B GLY 3.2 0.2 + - - -
249B GLY* 2.8 43.7 + - - +
250B THR* 3.9 2.7 - - - +
251B VAL* 3.4 32.3 - - + -
342B VAL* 3.6 15.8 - - + +
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Residues in contact with ALA 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 VAL* 3.0 20.3 + - + +
242B LYS* 3.3 7.8 + - - +
244B ALA* 1.4 70.7 - - - +
246B ALA* 1.3 62.2 + - - +
247B HIS 2.9 5.6 - - - -
248B GLY* 3.0 13.6 + - - +
249B GLY 3.5 12.0 + - - +
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Residues in contact with ALA 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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242B LYS 3.0 12.9 + - - +
243B ALA* 3.3 15.0 - - - +
244B ALA 3.1 0.2 - - - -
245B ALA* 1.3 76.3 - - - +
247B HIS* 1.3 72.3 + - + +
248B GLY 3.7 0.2 - - - -
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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