Contacts of the helix formed by residues 230 - 248 (chain B) in PDB entry 3BLR
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 230 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222B TRP* 4.4 2.5 - - - +
227B ALA 5.7 0.7 - - - +
228B THR 3.5 12.8 + - - +
229B VAL* 1.3 83.5 - - - +
231B LEU* 1.3 65.9 + - - +
232B GLU* 3.3 25.8 + - - +
233B LEU* 2.9 30.5 + - - +
234B LEU* 3.1 11.8 + - - +
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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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202B HIS* 4.1 16.6 - - + -
222B TRP* 3.9 36.6 - - + -
230B THR* 1.3 73.7 - - - +
232B GLU* 1.3 71.8 + - + +
234B LEU* 3.8 7.0 - - + -
235B ASP* 3.0 48.0 + - - +
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Residues in contact with GLU 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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230B THR* 3.0 25.9 + - - +
231B LEU* 1.3 90.2 + - + +
233B LEU* 1.3 60.2 + - - +
235B ASP* 4.4 3.4 - - - +
236B GLU* 3.5 20.8 + - - +
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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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191B TYR* 4.4 17.3 - - + +
195B VAL* 4.4 16.8 - - + -
228B THR* 5.5 3.8 - - - +
229B VAL* 5.2 8.1 - - + -
230B THR* 2.9 21.9 + - - +
232B GLU* 1.3 75.7 - - - +
234B LEU* 1.3 70.0 + - + +
235B ASP 3.1 1.1 - - - -
236B GLU* 2.9 19.3 + - - +
237B LEU* 2.8 59.4 + - + +
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Residues in contact with LEU 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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195B VAL* 4.7 2.5 - - + +
198B CYS* 3.8 5.4 - - + -
199B VAL* 3.8 37.2 - - + +
202B HIS* 4.1 29.4 - - + +
221B TRP* 4.5 5.2 - - + -
222B TRP* 3.9 39.3 - - + -
229B VAL* 3.7 27.1 - - + -
230B THR 3.1 7.3 + - - +
231B LEU* 3.9 8.1 - - - +
233B LEU* 1.3 78.9 - - + +
235B ASP* 1.3 57.9 + - - +
237B LEU* 4.7 3.1 - - + +
238B THR* 2.8 36.4 + - - +
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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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202B HIS* 3.0 23.9 + - - -
206B LYS* 3.6 20.4 + - - +
231B LEU* 3.0 34.6 + - - +
232B GLU* 4.4 3.4 - - - +
234B LEU* 1.3 73.1 - - - +
236B GLU* 1.3 64.4 + - - +
238B THR* 3.4 4.9 + - - -
239B HIS* 3.2 25.1 + - - +
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Residues in contact with GLU 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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16B ARG* 4.3 13.9 + - - -
191B TYR* 4.9 1.4 + - - -
232B GLU 3.5 14.7 + - - +
233B LEU* 2.9 20.3 + - - +
235B ASP* 1.3 77.5 - - - +
237B LEU* 1.3 64.6 + - - +
239B HIS* 3.7 5.3 - - + +
240B GLU* 3.1 51.9 + - + +
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Residues in contact with LEU 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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16B ARG* 4.3 8.5 - - - +
187B PHE* 3.7 17.6 - - + -
191B TYR* 3.4 50.7 - - + +
195B VAL* 4.5 2.7 - - + -
196B VAL* 6.2 0.4 - - + -
199B VAL* 3.5 35.7 - - + -
233B LEU* 2.8 44.6 + - + +
234B LEU 4.2 0.4 - - - +
236B GLU* 1.3 79.5 - - - +
238B THR* 1.3 59.1 + - - +
239B HIS 3.1 1.8 - - - -
240B GLU* 3.3 6.8 + - - +
241B LEU* 2.9 30.3 + - - +
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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
----------------------------------------------------------
199B VAL* 3.3 36.3 - - + +
202B HIS* 3.5 24.5 - - + -
203B LEU* 3.6 26.9 - - + +
206B LYS* 4.1 9.6 + - - +
234B LEU 2.8 28.3 + - - +
235B ASP* 3.4 9.7 + - - -
237B LEU* 1.3 76.1 - - - +
239B HIS* 1.3 59.5 + - - +
241B LEU* 4.0 3.0 - - - +
242B LEU* 3.0 28.5 + - - +
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Residues in contact with HIS 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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235B ASP 3.2 19.7 + - - +
236B GLU* 3.7 6.7 - - + +
237B LEU 3.1 0.4 - - - -
238B THR* 1.3 78.1 + - - +
240B GLU* 1.3 65.3 + - + +
242B LEU* 3.3 9.5 + - - +
243B GLN* 3.0 63.9 + - + +
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Residues in contact with GLU 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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16B ARG* 3.1 29.3 + - - -
187B PHE* 4.0 15.8 - - + -
236B GLU* 3.1 43.4 + - + +
237B LEU* 3.7 7.8 - - - +
239B HIS* 1.3 83.3 - - + +
241B LEU* 1.3 61.6 + - - +
243B GLN* 3.3 12.7 + - - +
244B ILE* 3.3 27.2 + - + +
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Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B MET* 4.3 23.6 - - + +
180B ASN 4.8 2.9 - - - +
181B SER* 4.1 23.6 - - - +
184B LEU* 5.3 3.1 - - + -
185B THR* 3.8 27.4 - - + -
187B PHE* 4.1 7.9 - - + -
199B VAL* 4.3 18.2 - - + +
200B CYS* 4.7 3.6 - - - -
203B LEU* 4.0 21.8 - - + -
237B LEU 2.9 17.2 + - - +
238B THR* 4.0 4.7 - - - +
240B GLU* 1.3 76.4 - - - +
242B LEU* 1.3 63.0 + - - +
243B GLN 3.4 0.2 + - - -
244B ILE* 3.4 2.3 + - - +
245B LEU* 3.1 32.8 + - + +
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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
----------------------------------------------------------
177B MET* 6.4 0.4 - - + -
203B LEU* 4.1 26.0 - - + +
207B TRP* 4.5 26.2 - - + -
238B THR 3.0 20.3 + - - +
239B HIS* 3.6 10.3 - - - +
240B GLU 3.3 0.4 - - - -
241B LEU* 1.3 78.3 - - - +
243B GLN* 1.3 62.6 + - - +
245B LEU* 3.3 6.9 + - + +
246B GLU* 3.1 50.7 + - + +
252B LEU* 4.6 7.6 - - + -
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Residues in contact with GLN 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 HIS* 3.0 52.6 + - + +
240B GLU* 3.7 8.4 - - - +
241B LEU 3.3 0.4 - - - -
242B LEU* 1.3 77.7 - - + +
244B ILE* 1.3 62.6 + - + +
246B GLU* 3.3 18.3 + - - +
247B LYS* 3.3 47.2 + - - +
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Residues in contact with ILE 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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35B LEU* 5.7 7.9 - - + -
39B GLN* 3.7 24.0 - - - +
184B LEU* 3.4 33.7 - - + +
185B THR* 3.7 20.2 - - + -
240B GLU* 3.3 17.4 + - + +
241B LEU* 4.0 4.9 - - - +
242B LEU 3.3 0.4 - - - -
243B GLN* 1.3 75.8 - - + +
245B LEU* 1.3 62.6 + - - +
247B LYS* 3.1 27.5 + - + +
248B THR* 2.8 24.7 + - - +
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Residues in contact with LEU 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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176B PHE* 4.4 7.0 - - + -
177B MET* 3.9 28.9 - - + -
180B ASN* 4.2 15.9 - - + -
184B LEU* 3.5 24.2 - - + -
203B LEU* 4.3 6.1 - - + -
241B LEU* 3.1 33.7 + - + +
242B LEU* 3.5 7.4 - - + +
243B GLN 3.3 0.4 - - - -
244B ILE* 1.3 77.2 - - - +
246B GLU* 1.3 61.1 + - - +
248B THR* 3.2 23.9 + - - +
251B ARG* 4.3 20.1 - - + +
252B LEU* 3.8 33.0 - - + +
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Residues in contact with GLU 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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207B TRP* 6.0 0.5 - - - -
242B LEU* 3.1 35.3 + - + +
243B GLN* 3.5 21.2 - - - +
244B ILE 3.2 0.2 - - - -
245B LEU* 1.3 75.6 - - - +
247B LYS* 1.3 61.2 + - + +
248B THR 3.2 3.0 + - - +
252B LEU* 3.7 21.8 - - + -
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Residues in contact with LYS 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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243B GLN* 3.3 40.7 + - - +
244B ILE* 3.1 22.3 + - + +
246B GLU* 1.3 77.0 - - + +
248B THR* 1.3 59.4 + - - +
249B PRO* 3.1 14.0 - - - +
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Residues in contact with THR 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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39B GLN* 5.5 0.3 + - - -
184B LEU* 3.6 21.4 - - + +
244B ILE* 2.8 20.0 + - - +
245B LEU* 3.2 19.2 + - - +
246B GLU 3.2 3.0 - - - +
247B LYS* 1.3 75.9 - - - +
249B PRO* 1.3 73.0 - - + +
250B ASN 3.3 2.4 + - - -
251B ARG* 3.3 54.2 + - + +
252B LEU 4.7 0.5 + - - -
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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