Contacts of the helix formed by residues 233 - 246 (chain B) in PDB entry 3QEL
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 233 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106B GLU* 3.7 25.8 + - - +
176B PHE* 3.3 44.6 - - + -
232B CYS* 1.3 79.6 - - - +
234B LYS* 1.3 59.5 + - - +
235B GLU* 3.6 6.6 + - - +
236B GLU* 2.8 39.8 + - - +
237B ALA* 2.8 26.2 + - - +
261B LEU* 4.1 6.7 - - + -
262B VAL* 4.4 2.2 - - - -
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Residues in contact with LYS 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ASP* 2.6 49.8 + - + +
106B GLU* 4.7 2.4 + - - +
132B MET* 6.2 0.2 - - - -
233B THR* 1.3 75.0 - - - +
235B GLU* 1.3 65.2 + - - +
237B ALA* 3.2 5.4 + - - +
238B THR* 2.9 29.8 + - + +
261B LEU 3.5 13.8 + - - +
262B VAL* 2.9 28.9 - - - +
263B ALA 2.9 23.9 + - - +
264B GLY* 4.2 1.6 - - - +
265B ASP 3.3 5.7 + - - -
268B THR* 3.0 27.4 + - - -
270B PRO* 4.0 19.7 - - + -
273B PHE* 4.2 7.0 - - + -
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Residues in contact with GLU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ASP* 5.9 2.8 - - - +
106B GLU* 5.5 1.9 + - - +
233B THR* 3.3 6.8 + - - +
234B LYS* 1.3 83.1 - - - +
236B GLU* 1.3 62.3 + - + +
238B THR* 3.5 23.6 + - - +
239B TYR* 3.6 10.2 + - - +
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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
----------------------------------------------------------
115A ARG* 5.4 7.4 + - - +
174B THR* 2.8 36.1 + - + -
176B PHE* 4.1 4.6 + - - +
207B MET* 3.4 31.3 - - + +
232B CYS* 3.2 6.6 - - + +
233B THR* 2.8 47.6 + - - +
235B GLU* 1.3 76.3 - - + +
237B ALA* 1.3 59.7 + - - +
239B TYR* 3.1 8.2 + - - +
240B ILE* 2.9 32.7 + - + +
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Residues in contact with ALA 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LEU* 4.0 2.5 - - + -
232B CYS* 3.5 15.0 - - - -
233B THR 2.8 17.0 + - - +
234B LYS 3.2 4.0 + - - +
236B GLU* 1.3 76.2 - - - +
238B THR* 1.3 58.1 + - - +
240B ILE* 3.8 5.8 - - - +
241B PHE* 2.8 49.0 + - + -
262B VAL* 3.5 28.9 - - + -
273B PHE* 4.1 2.0 - - + -
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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
----------------------------------------------------------
234B LYS* 2.9 21.8 - - + +
235B GLU* 3.8 20.4 + - - +
236B GLU 3.2 0.8 - - - -
237B ALA* 1.3 76.1 - - - +
239B TYR* 1.3 64.4 + - - +
241B PHE* 4.7 0.2 - - - -
242B GLU* 3.2 19.9 + - - +
270B PRO* 3.6 28.7 - - + -
272B GLU* 3.4 36.1 + - - +
273B PHE* 3.8 7.4 - - + -
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Residues in contact with TYR 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B MET* 4.4 19.5 - - + -
211B ASP* 2.9 43.5 + - + +
216B ILE* 4.5 11.4 - - + -
235B GLU 3.6 7.7 + - - +
236B GLU* 3.1 9.4 + - - +
238B THR* 1.3 80.1 + - - +
240B ILE* 1.3 70.3 + - + +
242B GLU* 3.4 25.4 + - - +
243B VAL* 3.2 42.4 + - + +
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Residues in contact with ILE 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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172B VAL* 4.8 0.7 - - + -
174B THR* 4.0 22.0 - - + -
205B LEU* 3.9 28.5 - - + -
207B MET* 4.6 10.5 - - + -
216B ILE* 5.5 1.6 - - + -
220B LEU* 4.1 18.5 - - + +
230B LEU* 4.1 30.7 - - + -
232B CYS* 4.1 8.5 - - - -
236B GLU* 2.9 20.1 + - + +
237B ALA* 3.8 4.7 - - - +
239B TYR* 1.3 81.0 - - + +
241B PHE* 1.3 58.4 + - - +
243B VAL* 3.0 8.0 + - - +
244B ALA* 2.9 24.8 + - - +
256B TRP* 4.5 16.8 - - + -
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Residues in contact with PHE 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B LEU* 3.7 15.9 - - + -
237B ALA* 2.8 42.7 + - + +
238B THR 4.2 1.1 - - - +
240B ILE* 1.3 72.5 - - - +
242B GLU* 1.3 63.1 + - - +
244B ALA* 3.2 3.3 + - - +
245B ASN* 3.0 25.9 + - - +
250B THR* 4.0 7.8 - - + +
256B TRP* 3.5 46.7 - + + -
258B VAL* 4.7 2.2 - - + -
262B VAL* 4.7 2.0 - - + -
272B GLU 3.3 20.4 - - - +
273B PHE* 3.6 25.4 - + - -
274B PRO* 3.5 23.8 - - + -
277B LEU* 4.0 23.8 - - + -
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Residues in contact with GLU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B THR 3.2 17.5 + - - +
239B TYR* 3.6 27.6 - - - +
240B ILE 3.3 0.2 - - - -
241B PHE* 1.3 77.1 - - - +
243B VAL* 1.3 62.2 + - - +
245B ASN* 3.8 6.0 + - - +
246B SER* 3.1 26.6 + - - +
272B GLU* 4.2 24.1 - - + +
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Residues in contact with VAL 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B ASP* 5.0 1.8 - - - +
216B ILE* 3.8 13.9 - - + -
217B GLN* 4.0 23.3 - - + +
220B LEU* 3.6 19.1 - - + -
239B TYR* 3.2 47.8 + - + +
240B ILE 3.0 7.0 + - - +
242B GLU* 1.3 78.2 - - + +
244B ALA* 1.3 66.7 + - - +
245B ASN 3.1 1.6 - - - -
246B SER* 3.1 17.7 + - - -
247B VAL* 3.3 14.4 + - + +
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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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220B LEU* 3.9 13.0 - - + +
240B ILE 2.9 14.7 + - - +
241B PHE* 3.2 8.0 + - - +
243B VAL* 1.3 75.7 - - - +
245B ASN* 1.3 62.3 + - - +
247B VAL* 3.0 14.0 + - - +
248B GLY 3.0 9.7 + - - -
249B LEU* 3.0 22.9 + - + +
250B THR* 4.4 4.7 - - + -
256B TRP* 3.8 33.2 - - + -
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Residues in contact with ASN 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 PHE 3.0 16.1 + - - +
242B GLU* 3.9 7.2 + - - +
244B ALA* 1.3 72.9 - - - +
246B SER* 1.3 58.3 + - - +
247B VAL 2.8 10.9 + - - -
248B GLY* 2.9 14.1 + - - +
250B THR* 3.3 29.7 + - + +
272B GLU 6.1 0.7 - - - +
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Residues in contact with SER 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217B GLN* 5.2 6.5 - - - +
242B GLU* 3.1 16.6 + - - +
243B VAL* 3.1 13.3 + - - -
245B ASN* 1.3 76.0 - - - +
247B VAL* 1.3 62.8 + - - +
248B GLY 3.6 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