Contacts of the helix formed by residues 224 - 242 (chain B) in PDB entry 2QU7
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 GLY 224 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ASP* 4.4 1.6 - - - -
102B GLU* 3.4 26.9 - - - -
103B GLU* 2.7 18.2 + - - +
223B LEU* 1.3 76.2 - - - +
225B THR* 1.3 66.5 + - - +
226B ASN 3.7 0.9 - - - -
227B ALA 4.0 0.7 - - - -
228B GLN* 2.9 32.6 + - - +
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Residues in contact with THR 225 (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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73B ASP* 3.6 0.8 - - - +
74B GLN* 2.7 68.1 + - + +
102B GLU* 3.0 10.6 + - - -
224B GLY* 1.3 67.9 - - - +
226B ASN* 1.3 77.5 + - - +
228B GLN* 3.1 16.2 + - - +
229B ILE* 3.3 16.2 + - + +
253B LEU* 3.8 29.3 - - + +
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Residues in contact with ASN 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A TYR* 3.9 31.8 + - - -
74B GLN* 5.6 3.0 - - - +
102B GLU* 5.1 0.2 + - - -
225B THR* 1.3 85.8 - - - +
227B ALA* 1.3 62.5 - - - +
229B ILE* 3.3 13.9 + - - +
230B TYR* 3.0 25.1 + - - +
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Residues in contact with ALA 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B GLU* 4.9 0.4 - - - +
219B SER* 4.3 2.9 - - - +
222B GLN* 3.6 31.4 - - + +
223B LEU 3.4 34.0 + - - +
224B GLY 3.6 2.6 + - - +
225B THR 3.2 0.2 - - - -
226B ASN* 1.3 78.7 - - - +
228B GLN* 1.3 62.7 + - - +
230B TYR* 3.3 5.1 + - - +
231B SER* 3.0 23.4 + - - -
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Residues in contact with GLN 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ASP* 3.0 31.3 + - - +
75B ASN* 5.8 0.2 + - - -
103B GLU* 3.4 25.5 + - - +
148B ARG* 5.5 1.6 + - - -
186B ALA* 4.4 6.9 - - + +
219B SER* 3.8 22.4 - - - +
224B GLY 2.9 22.2 + - - +
225B THR 3.1 6.8 + - - +
227B ALA* 1.3 75.9 - - - +
229B ILE* 1.3 63.1 + - - +
231B SER* 3.2 3.7 + - - -
232B GLY* 3.1 19.1 + - - -
251B ASN* 3.4 23.5 + - - +
253B LEU* 3.9 20.5 - - + +
254B LEU* 3.4 13.8 - - + +
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Residues in contact with ILE 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A TYR* 4.0 21.3 - - + -
225B THR* 3.3 12.0 + - + +
226B ASN* 3.3 28.5 + - - +
228B GLN* 1.3 76.0 - - - +
230B TYR* 1.3 59.0 + - - +
232B GLY 3.4 0.7 + - - -
233B TYR* 3.0 24.4 + - - +
253B LEU* 3.5 43.7 - - + +
256B LEU* 4.5 10.5 - - + -
257B GLY* 3.2 13.2 - - - +
260B GLN* 3.5 32.8 - - - +
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Residues in contact with TYR 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B ASN 3.0 17.3 + - - +
227B ALA* 3.9 4.9 - - - +
228B GLN 3.3 0.2 - - - -
229B ILE* 1.3 78.3 - - - +
231B SER* 1.3 56.1 + - - +
233B TYR* 3.5 27.1 - + + +
234B GLU* 2.8 64.1 + - + +
237B LYS* 4.9 1.0 + - - -
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Residues in contact with SER 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU 4.6 0.2 + - - -
217B HIS* 5.7 1.0 - - - +
218B TYR 3.7 6.3 + - - -
219B SER* 3.2 39.3 + - - -
227B ALA 3.0 14.3 + - - -
228B GLN 3.4 9.4 - - - -
230B TYR* 1.3 79.5 - - - +
232B GLY* 1.3 56.1 + - - +
234B GLU* 5.1 1.6 - - - -
235B ALA* 2.9 35.8 + - - +
254B LEU* 3.9 4.9 - - - +
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Residues in contact with GLY 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 4.2 9.4 - - - -
228B GLN 3.1 13.3 + - - -
229B ILE 3.8 1.8 - - - -
231B SER* 1.3 71.6 + - - +
233B TYR* 1.3 59.3 + - - +
235B ALA* 3.9 1.7 - - - +
236B THR* 2.8 37.7 + - - -
254B LEU* 3.8 27.9 - - - +
257B GLY 3.7 7.0 - - - -
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Residues in contact with TYR 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ILE 3.0 16.8 + - - +
230B TYR* 3.5 34.8 - + - +
232B GLY* 1.3 74.7 - - - +
234B GLU* 1.3 70.4 + - - +
237B LYS* 2.9 60.7 + - + +
257B GLY 3.1 19.3 - - - +
260B GLN* 3.8 20.6 - - + +
261B ALA* 3.3 34.6 - - - +
264B GLU* 2.8 41.6 + - - -
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Residues in contact with GLU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B TYR* 2.8 52.2 + - + +
231B SER* 4.4 2.7 - - - +
233B TYR* 1.3 75.7 - - - +
235B ALA* 1.3 62.6 + - - +
237B LYS* 2.8 40.6 + - - +
238B THR* 3.0 36.4 + - - +
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Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 3.5 17.5 - - + -
217B HIS* 3.5 38.9 + - + +
231B SER* 2.9 22.0 + - - +
232B GLY 3.9 0.2 - - - +
234B GLU* 1.3 76.9 - - - +
236B THR* 1.3 56.6 + - - +
238B THR* 3.3 5.5 + - - -
239B LEU* 2.9 32.4 + - - +
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Residues in contact with THR 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LEU* 3.5 11.6 - - - +
232B GLY 2.8 21.6 + - - -
235B ALA* 1.3 73.1 - - - +
237B LYS* 1.3 57.7 + - - +
239B LEU* 3.1 8.9 + - - +
240B LEU* 2.7 46.5 + - + +
247B ILE* 3.6 23.7 - - + +
258B ALA* 3.4 29.1 - - + +
261B ALA* 3.7 18.8 - - + -
262B ILE* 4.1 4.3 - - + -
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Residues in contact with LYS 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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230B TYR* 4.9 1.0 + - - -
233B TYR* 2.9 52.0 + - + +
234B GLU* 2.8 37.6 + - - +
236B THR* 1.3 75.3 - - - +
238B THR* 1.3 60.3 + - - +
240B LEU* 3.7 6.7 + - - +
241B SER* 3.2 22.5 + - - -
261B ALA* 3.7 12.9 - - + +
264B GLU* 4.3 11.4 + - - +
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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
----------------------------------------------------------
217B HIS* 4.3 13.8 - - + -
234B GLU* 3.0 23.8 + - - +
235B ALA* 3.4 9.3 - - - -
237B LYS* 1.3 73.9 - - - +
239B LEU* 1.3 65.7 + - - +
241B SER* 2.5 26.7 + - - +
242B LYS* 3.2 31.3 + - + +
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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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182B GLY* 4.0 30.3 - - - -
184B LEU* 4.1 18.4 - - + -
215B LEU* 4.1 12.8 - - + +
217B HIS* 3.6 29.4 - - + +
235B ALA 2.9 19.1 + - - +
236B THR* 3.1 8.0 + - - +
238B THR* 1.3 75.3 - - - +
240B LEU* 1.3 63.0 + - - +
242B LYS* 3.2 13.6 + - - +
244B ILE* 3.0 52.3 + - + +
247B ILE* 4.2 17.9 - - + -
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Residues in contact with LEU 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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236B THR* 2.7 32.1 + - + +
237B LYS* 4.1 5.4 - - - +
239B LEU* 1.3 72.9 - - - +
241B SER* 1.3 57.6 + - - +
243B GLY* 2.9 17.2 + - - -
244B ILE 3.8 18.2 - - - +
247B ILE* 4.7 5.6 - - + -
261B ALA* 4.1 5.8 - - + +
262B ILE* 3.8 27.4 - - + -
265B SER* 3.7 27.6 - - - +
267B LYS* 3.1 41.6 + - + +
273B VAL* 4.3 23.1 - - + -
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Residues in contact with SER 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 LYS 3.2 12.3 + - - -
238B THR* 2.5 25.1 + - - +
240B LEU* 1.3 79.2 - - - +
242B LYS* 1.3 59.2 + - - +
243B GLY 3.2 1.5 + - - -
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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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214B SER* 3.3 35.3 + - - -
215B LEU* 5.5 2.4 - - + +
217B HIS* 4.5 6.7 + - - -
238B THR* 3.6 32.2 - - + +
239B LEU* 3.2 14.1 + - + +
240B LEU 3.2 1.0 - - - -
241B SER* 1.3 78.9 + - - +
243B GLY* 1.3 60.0 + - - +
244B ILE* 3.6 19.7 + - + +
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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