Contacts of the helix formed by residues 228 - 240 (chain B) in PDB entry 4UT2
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 228 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210B ASP 3.5 5.2 - - - -
213B VAL* 3.3 24.6 + - - +
214B LEU 3.8 6.5 + - - -
215B GLY 3.1 12.1 + - - -
227B PHE* 1.3 76.0 - - - +
229B ALA* 1.3 65.2 + - - -
230B GLU 3.3 2.7 - - - -
231B VAL* 3.3 14.1 + - - +
232B VAL* 3.3 13.0 + - - +
258B PHE* 4.0 3.8 - - - -
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Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B ASP 4.6 0.2 + - - -
211B LYS* 6.0 0.4 - - - +
213B VAL 4.5 1.8 + - - -
214B LEU* 4.6 1.6 + - - +
228B GLY* 1.3 70.7 - - - -
230B GLU* 1.3 59.1 + - - +
232B VAL* 3.3 5.1 + - - +
233B ALA* 2.9 26.7 + - - +
258B PHE* 3.8 18.6 - - + -
259B ALA* 3.5 29.6 - - + +
260B LYS* 4.7 8.5 - - - +
262B GLN* 4.7 0.9 + - - -
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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
----------------------------------------------------------
214B LEU* 4.1 30.0 + - + +
215B GLY* 5.8 0.2 - - - -
228B GLY 3.3 0.6 - - - -
229B ALA* 1.3 74.6 - - - +
231B VAL* 1.3 61.3 + - + +
233B ALA* 3.2 7.8 + - + +
234B LYS* 2.9 67.5 + - + +
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Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LEU* 3.9 15.5 - - + -
214B LEU 4.2 0.9 - - - +
215B GLY* 3.6 38.8 - - - +
216B TRP* 3.6 38.4 - - + +
227B PHE* 4.1 9.0 - - + -
228B GLY 3.3 9.3 + - - +
230B GLU* 1.3 78.4 - - + +
232B VAL* 1.3 62.4 + - - +
234B LYS* 3.5 7.6 + - + +
235B PHE* 3.1 23.3 + - + +
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Residues in contact with VAL 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LEU* 4.3 7.0 - - + -
227B PHE* 3.7 27.8 - - + -
228B GLY 3.3 12.5 + - - +
229B ALA* 3.3 9.1 + - - +
230B GLU 3.2 0.2 - - - -
231B VAL* 1.3 77.4 - - - +
233B ALA* 1.3 63.4 + - - +
235B PHE* 3.2 2.9 + - - +
236B LEU* 3.0 26.4 + - + +
244B ILE* 3.9 17.3 - - + -
258B PHE* 4.1 13.7 - - + -
259B ALA* 4.5 2.9 - - + -
262B GLN* 3.8 35.0 - - + +
263B LEU* 4.2 9.2 - - + -
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Residues in contact with ALA 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ALA 2.9 13.6 + - - +
230B GLU* 3.2 13.9 + - + +
232B VAL* 1.3 78.2 - - - +
234B LYS* 1.3 62.3 + - + +
236B LEU* 3.5 2.3 + - - +
237B HIS* 3.1 24.7 + - - +
262B GLN* 4.0 27.3 - - - +
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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
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230B GLU* 2.9 55.1 + - + +
231B VAL* 4.0 7.0 - - + +
232B VAL 3.3 0.2 - - - -
233B ALA* 1.3 75.1 - - + +
235B PHE* 1.3 60.0 + - - +
237B HIS* 3.9 5.6 - - - +
238B LYS* 2.9 33.4 + - - +
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Residues in contact with PHE 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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170B PHE* 4.2 13.9 - + + -
176B LEU* 3.7 36.6 - - + -
180B LEU* 3.6 35.0 - - + -
183B MET* 3.8 22.0 - - + -
231B VAL* 3.1 18.2 + - + +
232B VAL 3.2 4.0 + - - +
234B LYS* 1.3 77.1 - - - +
236B LEU* 1.3 63.8 + - + +
238B LYS* 4.5 2.2 - - - -
239B HIS* 3.1 55.6 + + - +
241B LEU* 3.7 23.1 - - + -
244B ILE* 4.1 13.0 - - + -
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Residues in contact with LEU 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 VAL* 3.0 19.7 + - + +
233B ALA 3.9 3.8 - - - +
235B PHE* 1.3 79.3 - - + +
237B HIS* 1.3 58.6 + - - +
240B ASP* 2.8 25.8 + - - -
241B LEU* 2.9 43.5 + - + +
242B ASP* 3.5 21.1 - - - +
243B LEU 3.8 21.3 - - - +
244B ILE* 4.0 14.1 - - + -
262B GLN* 3.6 44.6 - - + +
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Residues in contact with HIS 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 ALA 3.1 16.0 + - - +
234B LYS* 3.9 6.3 - - - +
236B LEU* 1.3 76.9 - - - +
238B LYS* 1.3 69.1 + - + +
239B HIS 3.4 0.2 + - - -
240B ASP* 3.4 11.5 + - - +
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Residues in contact with LYS 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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180B LEU 5.1 0.4 + - - -
181B GLN* 3.1 51.0 + - - +
234B LYS 2.9 20.7 + - - +
235B PHE* 3.8 4.7 - - - +
236B LEU 3.4 0.2 - - - -
237B HIS* 1.3 83.1 - - + +
239B HIS* 1.3 73.8 + - + +
240B ASP* 3.8 0.9 + - - +
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Residues in contact with HIS 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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167B GLU 5.3 0.2 - - - +
180B LEU* 4.8 3.3 - - + +
181B GLN 3.3 30.2 + - - -
182B SER* 4.2 5.4 - - - -
183B MET* 4.1 30.9 + - + +
235B PHE* 3.1 51.0 + + - +
238B LYS* 1.3 95.8 - - + +
240B ASP* 1.3 72.7 + - - +
241B LEU* 3.4 23.9 - - + +
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Residues in contact with ASP 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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167B GLU 3.6 10.2 - - - +
168B LYS* 3.1 30.3 + - - -
236B LEU 2.8 10.4 + - - -
237B HIS* 3.4 7.2 + - - +
238B LYS 3.4 3.9 - - - +
239B HIS* 1.3 81.6 - - - +
241B LEU* 1.3 56.6 + - - +
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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