Contacts of the helix formed by residues 235 - 249 (chain B) in PDB entry 2QB0
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 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198B GLN* 3.2 29.0 + - - +
231B TRP* 3.3 15.4 + - - -
232B TYR 3.5 3.1 - - - -
234B GLN* 1.3 86.9 - - + +
236B PRO* 1.4 66.3 - - - +
237B ASN 3.5 1.7 + - - -
238B ARG* 3.5 15.8 + - + +
239B ALA* 3.0 19.8 + - - +
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Residues in contact with PRO 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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232B TYR* 3.1 27.7 - - + +
233B ASN* 3.5 12.3 - - - +
234B GLN 3.6 3.8 - - - +
235B THR* 1.4 86.2 - - - +
237B ASN* 1.3 67.9 + - - +
239B ALA* 3.2 2.5 + - + +
240B LYS* 2.9 50.7 + - - +
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Residues in contact with ASN 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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235B THR 3.5 0.4 - - - -
236B PRO* 1.3 85.6 - - - +
238B ARG* 1.3 61.1 + - - +
240B LYS* 3.7 20.8 + - - +
241B ARG* 3.4 41.6 + - - +
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Residues in contact with ARG 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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100B LEU* 3.4 12.9 - - - +
103B ASP* 3.4 40.2 + - - +
104B GLU* 2.8 34.9 + - - -
194B ASN* 2.8 28.9 + - - -
198B GLN* 3.2 50.9 + - - +
235B THR* 3.5 15.9 + - - +
236B PRO 3.3 0.2 - - - -
237B ASN* 1.3 76.0 - - - +
239B ALA* 1.3 66.4 + - - +
241B ARG* 3.2 19.2 + - - +
242B VAL* 3.0 26.1 + - + +
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Residues in contact with ALA 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 TRP* 3.7 31.2 - - + +
232B TYR* 3.6 34.5 - - + -
235B THR* 3.0 19.9 + - - +
236B PRO 3.7 0.4 - - - +
238B ARG* 1.3 75.9 - - - +
240B LYS* 1.3 56.5 - - - +
242B VAL* 3.3 1.6 + - - +
243B ILE* 2.8 37.9 + - - +
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Residues in contact with LYS 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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232B TYR* 3.1 37.4 - - + +
236B PRO* 2.9 35.5 + - - +
237B ASN* 3.7 18.8 + - - +
239B ALA* 1.3 76.8 - - - +
241B ARG* 1.3 58.1 + - + +
243B ILE* 3.7 5.1 - - - +
244B THR* 2.8 36.6 + - - +
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Residues in contact with ARG 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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102B ILE* 4.5 14.6 + - - +
103B ASP* 3.0 33.1 + - - +
237B ASN* 3.4 29.4 + - - +
238B ARG* 3.2 22.8 + - - +
240B LYS* 1.3 77.8 - - + +
242B VAL* 1.3 63.2 + - - +
244B THR* 3.4 3.1 + - - -
245B THR* 2.8 27.5 + - - -
253B ALA* 3.6 34.8 - - + +
254B TYR* 3.4 30.1 - - + +
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Residues in contact with VAL 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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99B MET* 4.4 1.8 - - + -
103B ASP* 4.4 1.6 - - - +
191B ALA* 3.5 27.7 - - + +
194B ASN* 3.8 24.7 - - + +
195B MET* 3.9 3.8 - - + -
231B TRP* 3.8 25.1 - - + -
238B ARG* 3.0 18.4 + - + +
239B ALA 3.7 6.1 - - - +
241B ARG* 1.3 74.4 - - - +
243B ILE* 1.3 62.5 + - - +
245B THR* 3.2 9.4 + - - -
246B PHE* 3.1 35.0 + - + -
254B TYR* 3.7 14.1 - - - +
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Residues in contact with ILE 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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223B ALA* 3.7 34.0 - - + +
226B LEU* 3.9 22.4 - - + +
227B ALA* 3.7 36.3 - - + +
231B TRP* 4.1 12.8 - - + -
232B TYR* 3.9 15.9 - - + -
239B ALA 2.8 21.7 + - - +
240B LYS* 3.7 5.2 - - - +
242B VAL* 1.3 72.2 - - - +
244B THR* 1.3 60.6 + - - +
246B PHE* 3.0 10.2 + - + +
247B ARG* 2.8 28.1 + - + +
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Residues in contact with THR 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 LYS* 2.8 28.1 + - - +
241B ARG 3.7 4.9 - - - -
243B ILE* 1.3 73.6 - - - +
245B THR* 1.3 56.5 + - - +
247B ARG* 3.7 31.8 + - - +
248B THR* 2.8 44.4 + - + +
250B THR 6.1 0.2 - - - +
252B ASP* 5.0 5.6 - - + +
253B ALA* 3.9 27.0 - - + +
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Residues in contact with THR 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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99B MET* 4.4 1.1 - - + -
187B VAL* 3.8 23.6 - - + +
188B ARG* 3.9 3.2 - - - +
191B ALA* 3.8 19.5 - - + -
241B ARG 2.8 18.9 + - - -
242B VAL* 3.3 10.1 - - - -
243B ILE 3.2 0.2 - - - -
244B THR* 1.3 76.5 - - - +
246B PHE* 1.3 56.3 + - - +
249B GLY* 2.9 28.2 + - - -
250B THR 3.8 24.6 + - - +
251B TRP* 4.2 10.5 - - + -
253B ALA* 5.0 1.2 - - - +
254B TYR* 3.5 19.8 - - - -
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Residues in contact with PHE 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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184B LEU* 4.2 9.2 - - + -
188B ARG* 2.8 54.7 + - + +
191B ALA* 3.5 12.1 - - + -
192B LEU* 3.4 29.8 - - + -
195B MET* 3.6 26.5 - - - -
214B LEU* 3.7 43.5 - - + -
219B TRP* 3.6 13.5 - - - +
222B ALA* 6.0 0.9 - - + -
223B ALA* 6.1 2.5 - - - -
226B LEU* 4.2 18.8 - - + -
242B VAL* 3.1 28.3 + - + -
243B ILE* 3.0 9.9 + - + +
245B THR* 1.3 76.3 - - - +
247B ARG* 1.3 59.0 + - - +
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Residues in contact with ARG 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B ARG* 3.5 10.7 + - - -
219B TRP* 3.5 21.4 - - - +
220B ASP* 3.6 26.1 + - - +
223B ALA* 4.0 23.5 - - + +
243B ILE* 2.8 16.8 + - - +
244B THR* 3.3 25.3 + - - +
246B PHE* 1.3 77.9 - - - +
248B THR* 1.3 80.7 + - - +
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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
----------------------------------------------------------
188B ARG* 3.6 6.9 + - - -
244B THR* 2.8 31.2 + - + +
247B ARG* 1.3 108.8 - - - +
249B GLY* 1.3 62.8 + - - +
250B THR* 2.9 34.0 + - - +
252B ASP* 4.6 7.9 + - + +
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Residues in contact with GLY 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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185B ASP* 4.6 3.1 - - - +
187B VAL* 3.7 24.8 - - - +
188B ARG* 3.6 24.5 - - - +
245B THR 2.9 18.4 + - - -
248B THR* 1.3 78.6 + - - +
250B THR* 1.3 62.5 + - - +
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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