Contacts of the helix formed by residues 235 - 247 (chain B) in PDB entry 3KQG
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 SER 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203B LYS* 5.9 0.9 - - - +
233B VAL* 3.6 2.7 - - - +
234B THR* 1.3 87.7 + - - +
236B GLU* 1.3 59.3 + - - +
237B SER* 3.7 11.5 - - - -
238B GLU* 2.9 25.4 + - - +
239B GLN* 2.8 27.0 + - - +
276B GLN* 4.0 7.8 + - - +
280B PHE* 4.0 5.8 - - - -
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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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235B SER* 1.3 72.3 - - - +
237B SER* 1.3 53.4 + - - +
239B GLN* 3.4 1.8 - - - +
240B GLU* 2.8 36.3 + - + +
276B GLN* 4.7 2.6 - - - +
279B ARG* 3.3 36.9 + - - +
280B PHE* 3.6 16.6 - - + -
303B LEU* 3.6 33.9 - - + +
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Residues in contact with SER 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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202B PHE* 3.2 25.9 - - - -
203B LYS* 3.1 30.8 + - - +
235B SER* 3.7 11.4 - - - -
236B GLU* 1.3 80.0 - - - +
238B GLU* 1.3 56.9 + - - +
240B GLU* 3.4 12.4 + - - +
241B PHE 3.1 21.5 + - - -
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Residues in contact with GLU 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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202B PHE* 4.0 13.0 - - + -
205B ASN* 5.8 0.7 - - - -
207B TYR* 2.7 31.5 + - + +
232B SER 3.1 14.3 - - - +
233B VAL* 3.5 2.1 - - + -
234B THR* 2.7 39.2 + - - +
235B SER* 2.9 20.8 + - - +
237B SER* 1.3 73.9 + - - +
239B GLN* 1.3 60.5 + - - +
241B PHE* 3.2 3.0 + - + +
242B LEU* 2.9 46.8 + - + +
320B LYS* 2.9 23.5 + - - -
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Residues in contact with GLN 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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233B VAL* 3.5 20.9 - - + +
235B SER 2.8 12.7 + - - +
236B GLU 3.4 8.1 - - - +
238B GLU* 1.3 76.4 - - - +
240B GLU* 1.3 57.5 + - - +
242B LEU* 3.4 3.1 + - - +
243B TYR* 3.0 28.5 + - + +
280B PHE* 3.6 19.2 + - + +
298B ILE* 4.4 6.3 - - - +
303B LEU* 2.8 44.5 + - + +
305B ALA* 3.6 19.7 - - - +
306B TRP* 3.0 34.0 + - - +
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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
----------------------------------------------------------
236B GLU* 2.8 22.3 + - + +
237B SER* 3.7 10.1 - - - +
239B GLN* 1.3 72.1 - - - +
241B PHE* 1.3 66.8 + - - +
243B TYR* 3.6 19.0 + - + -
244B LYS* 3.0 56.0 + - + +
303B LEU* 4.1 7.2 - - + +
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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
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197A GLN* 3.8 31.9 - - + -
200B LYS* 4.0 23.3 - - + -
201B TYR 4.3 1.8 - - - -
202B PHE* 3.6 51.6 - + + -
207B TYR* 3.6 31.2 - + - -
209B PHE* 4.2 8.1 - + - -
237B SER 3.1 10.1 + - - +
238B GLU* 3.2 6.5 + - - +
240B GLU* 1.3 76.8 - - - +
242B LEU* 1.3 75.0 + - + +
244B LYS* 3.9 3.2 - - - +
245B THR* 2.6 57.4 + - - -
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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
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207B TYR* 3.9 18.8 - - + -
209B PHE* 4.1 15.2 - - + -
231B THR* 4.2 14.8 - - + +
233B VAL* 3.6 31.6 - - + -
238B GLU* 2.9 31.6 + - + +
239B GLN* 3.8 3.4 - - - +
241B PHE* 1.3 98.6 - - + +
243B TYR* 1.3 59.9 + - - +
245B THR* 3.8 0.9 - - - -
246B ALA* 2.9 31.0 + - - +
298B ILE* 3.5 22.1 - - + +
318B ILE* 4.4 12.3 - - + +
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Residues in contact with TYR 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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226A ARG* 4.4 8.9 + - - -
239B GLN 3.0 24.9 + - - +
240B GLU* 3.6 22.8 + - + +
242B LEU* 1.3 77.3 - - - +
244B LYS* 1.3 96.7 + - + +
246B ALA* 3.5 8.5 + - - +
247B GLY* 3.5 11.3 + - - -
248B GLY 4.8 1.6 + - - -
298B ILE* 4.3 6.5 - - + +
300B ALA 4.2 4.5 - - - +
301B PRO* 3.5 22.5 - - + +
302B SER* 3.4 37.3 - - - +
303B LEU* 3.6 21.5 - - + -
305B ALA* 4.2 12.8 - - + -
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Residues in contact with LYS 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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208A TYR* 4.5 4.0 + - - -
225A SER* 3.9 19.4 + - - -
226A ARG* 2.6 58.0 + - - +
240B GLU* 3.0 47.4 + - + +
241B PHE* 3.9 3.8 - - - +
243B TYR* 1.3 107.7 + - + +
245B THR* 1.3 62.3 + - - +
247B GLY* 3.1 8.0 + - - -
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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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197A GLN* 4.0 19.7 + - - +
198A GLY* 5.0 0.9 - - - -
208A TYR* 4.5 5.7 + - - -
211A LEU* 4.1 12.6 - - - +
200B LYS* 4.0 23.6 - - + -
209B PHE* 3.4 37.1 - - + -
241B PHE* 2.6 41.2 + - + -
244B LYS* 1.3 72.0 - - - +
246B ALA* 1.3 66.1 + - - +
247B GLY* 3.0 4.1 + - - -
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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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211A LEU* 3.9 7.8 - - - +
209B PHE* 3.8 5.1 - - + -
242B LEU 2.9 19.1 + - - +
243B TYR 3.6 7.9 - - - +
244B LYS 3.3 0.2 - - - -
245B THR* 1.3 75.0 - - - +
247B GLY* 1.3 64.7 + - - +
248B GLY 3.3 2.2 - - - +
249B LEU* 3.2 21.6 + - - +
251B TYR* 3.6 39.1 - - + -
298B ILE* 4.3 13.9 - - + -
318B ILE* 5.3 0.9 - - + -
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Residues in contact with GLY 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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208A TYR* 3.7 18.4 + - - -
211A LEU* 4.4 4.6 + - - +
212A ILE* 3.2 26.9 + - - +
222A PHE* 5.0 6.7 - - - -
226A ARG* 4.1 8.3 - - - -
243B TYR 3.5 2.8 + - - -
244B LYS 3.1 15.2 + - - -
245B THR 3.0 2.4 - - - -
246B ALA* 1.3 79.7 - - - +
248B GLY* 1.3 57.0 + - - +
249B LEU* 3.5 4.2 + - - +
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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