Contacts of the helix formed by residues 229 - 240 (chain B) in PDB entry 2HDH
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 LYS 229 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222B TYR* 3.1 55.1 + - + +
228B SER* 1.3 73.2 - - - +
230B GLU* 1.3 67.8 + - - +
232B ILE* 3.3 2.8 + - - +
233B ASP* 2.9 28.6 + - - +
247B PHE* 3.8 25.5 - - + -
298B PHE* 2.9 41.4 + - + +
299B TYR* 3.4 33.2 + - - +
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Residues in contact with GLU 230 (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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228B SER* 3.4 20.5 - - - +
229B LYS* 1.3 90.4 + - - +
231B ASP* 1.3 61.1 + - - +
233B ASP* 3.4 4.7 + - - +
234B THR* 3.0 31.9 + - - -
299B TYR* 3.5 31.2 + - + +
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Residues in contact with ASP 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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196A PRO 4.8 2.1 - - - +
197A VAL* 3.8 24.1 - - + +
198A SER* 3.0 42.9 + - - +
206A ILE* 4.5 4.7 - - + -
228B SER* 3.2 23.9 + - - +
230B GLU* 1.3 78.4 - - - +
232B ILE* 1.3 56.0 + - - +
234B THR* 3.2 3.5 + - - -
235B ALA* 2.7 37.9 + - - +
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Residues in contact with ILE 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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206A ILE* 4.2 10.1 - - + -
210A LEU* 3.8 22.4 - - + -
218B ALA* 3.9 19.7 - - + +
221B LEU* 4.1 18.6 - - + -
222B TYR* 4.2 6.3 - - + +
227B ALA* 3.9 24.2 - - + +
228B SER 3.0 18.6 + - - +
229B LYS 3.6 4.3 - - - +
231B ASP* 1.3 74.5 - - - +
233B ASP* 1.3 63.1 + - - +
235B ALA* 3.2 7.4 + - - +
236B MSE 3.1 23.4 + - - +
246B PRO* 3.6 23.3 - - + -
247B PHE* 4.0 12.6 - - + -
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Residues in contact with ASP 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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229B LYS 2.9 16.4 + - - +
230B GLU* 3.6 5.8 - - - +
232B ILE* 1.3 78.6 - - - +
234B THR* 1.3 63.5 + - - +
236B MSE 3.4 0.3 + - - -
237B LYS* 3.1 31.2 + - - +
245B GLY* 2.9 23.4 - - - -
246B PRO* 2.9 4.3 - - - +
247B PHE* 2.8 27.2 + - - -
248B GLU* 3.0 30.6 + - - +
299B TYR* 2.9 25.9 + - - +
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Residues in contact with THR 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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168A LEU* 4.4 1.1 - - + -
195A HIS* 3.3 36.7 + - + -
197A VAL* 4.0 13.7 - - + -
230B GLU 3.0 18.5 + - - -
231B ASP* 3.6 5.5 + - - -
233B ASP* 1.3 75.4 - - - +
235B ALA* 1.3 64.2 + - - +
237B LYS* 4.1 13.4 + - - +
238B LEU* 3.0 40.1 + - + +
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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
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168A LEU* 3.5 18.8 - - + +
197A VAL* 4.4 3.3 - - + +
206A ILE* 3.4 31.2 - - + -
207A VAL* 3.8 13.8 - - + +
231B ASP 2.7 21.5 + - - +
232B ILE 3.2 6.0 + - - +
234B THR* 1.3 73.8 - - - +
236B MSE 1.3 55.4 + - - +
239B GLY* 2.7 35.3 + - - -
240B ALA 3.6 0.2 + - - -
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Residues in contact with MSE 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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206A ILE* 4.6 2.5 - - - -
207A VAL* 4.1 31.2 - - - +
210A LEU* 4.1 31.4 - - + -
211A LEU* 4.5 7.6 - - + +
214B TYR* 3.6 23.8 - - + +
232B ILE 3.1 16.4 + - - +
233B ASP 4.1 0.4 - - - +
235B ALA* 1.3 75.5 - - - +
237B LYS* 1.3 61.6 + - - +
240B ALA* 3.0 33.7 + - + +
242B TYR* 3.1 47.7 + - + +
245B GLY* 4.8 0.9 - - - -
246B PRO* 3.7 15.5 - - + -
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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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233B ASP* 3.1 27.1 + - - +
234B THR* 3.9 10.8 + - - +
236B MSE 1.3 77.0 - - - +
238B LEU* 1.3 66.2 + - + +
241B GLY* 2.9 27.4 + - - -
242B TYR 3.4 21.4 - - - +
243B PRO 4.0 10.5 - - - +
244B MSE 3.8 0.9 - - - -
245B GLY 3.6 13.5 - - - +
248B GLU* 3.0 36.8 + - - +
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Residues in contact with LEU 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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166A MSE 3.2 20.4 - - - +
167A LYS* 4.5 21.1 + - + -
168A LEU* 4.0 21.0 + - + +
195A HIS* 3.6 33.9 - - + -
234B THR* 3.0 33.2 + - + +
237B LYS* 1.3 84.9 - - + +
239B GLY* 1.3 60.1 + - - +
241B GLY* 4.2 2.3 + - - -
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Residues in contact with GLY 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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160A PHE* 4.6 10.8 - - - -
166A MSE 3.5 18.9 - - - +
168A LEU* 3.7 17.8 - - - +
207A VAL* 4.5 11.3 - - - +
211A LEU* 5.8 1.2 - - - +
235B ALA 2.7 22.6 + - - -
238B LEU* 1.3 77.1 - - - +
240B ALA* 1.3 56.7 + - - -
241B GLY 3.5 0.2 - - - -
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Residues in contact with ALA 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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207A VAL* 5.1 1.8 - - + -
211A LEU* 5.0 15.0 - - + -
243A PRO* 3.9 9.5 - - - +
249A LEU* 6.0 3.1 - - + +
235B ALA 3.6 1.2 + - - -
236B MSE 3.0 32.5 + - + +
239B GLY* 1.3 76.5 - - - +
241B GLY* 1.3 64.0 + - - +
242B TYR* 3.4 33.8 + - + -
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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