Contacts of the helix formed by residues 230 - 242 (chain B) in PDB entry 3ZZY
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 ASP 230 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B PRO* 4.4 1.6 - - - -
209B THR 6.0 0.4 - - - +
228B TYR* 3.6 6.8 - - - +
229B ALA* 1.3 83.0 - - + +
231B PRO* 1.3 75.9 - - - +
232B VAL* 2.9 41.4 + - - +
233B SER* 3.0 32.4 + - - +
234B ALA 3.4 3.3 + - - -
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Residues in contact with PRO 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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180B GLN 3.3 48.2 - - - +
181B SER 4.1 2.6 - - - +
182B PRO* 4.0 22.6 - - + -
229B ALA 4.3 4.0 - - - +
230B ASP* 1.3 92.7 - - - +
232B VAL* 1.3 62.9 + - + +
234B ALA* 3.1 3.5 + - + +
235B GLN* 2.9 30.8 + - - +
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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
----------------------------------------------------------
230B ASP* 2.9 23.0 + - - +
231B PRO* 1.3 76.2 - - + +
233B SER* 1.3 62.9 + - - +
235B GLN* 3.3 19.1 + - - +
236B HIS* 3.0 24.4 + - + +
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Residues in contact with SER 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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207B PHE* 3.0 28.0 + - - +
208B GLY* 3.7 7.4 - - - -
209B THR 4.8 0.7 + - - -
228B TYR* 3.6 25.0 - - - -
230B ASP* 3.0 21.9 + - - +
232B VAL* 1.3 79.6 - - - +
234B ALA* 1.3 57.3 + - - +
236B HIS* 3.3 4.9 + - - +
237B ALA* 2.9 31.0 + - - +
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Residues in contact with ALA 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181B SER 3.9 18.8 - - - +
182B PRO* 4.0 13.7 - - + +
184B LEU* 3.8 19.9 - - + +
228B TYR* 3.5 24.1 - - + -
230B ASP 3.4 2.0 + - - +
231B PRO* 3.1 9.9 + - + +
233B SER* 1.3 80.2 - - - +
235B GLN* 1.3 60.5 + - - +
237B ALA* 3.4 2.3 + - - +
238B LYS* 3.1 23.0 + - - +
257B PHE* 4.1 3.6 - - + -
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Residues in contact with GLN 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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180B GLN* 3.7 34.0 - - + +
181B SER 5.3 0.4 + - - -
231B PRO* 2.9 26.7 + - - +
232B VAL* 3.6 18.5 - - + +
233B SER 3.2 0.2 - - - -
234B ALA* 1.3 74.1 - - - +
236B HIS* 1.3 65.8 - - - +
238B LYS* 3.3 3.5 + - - +
239B LEU* 3.1 31.3 + - + +
257B PHE* 3.8 26.9 - - + -
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Residues in contact with HIS 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B PHE* 3.3 45.3 - + + -
232B VAL* 3.0 20.4 + - + +
233B SER* 3.8 6.5 - - - +
235B GLN* 1.3 74.8 - - - +
237B ALA* 1.3 58.9 + - - +
239B LEU* 3.2 13.6 + - + +
240B SER* 2.9 32.8 + - - -
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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
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184B LEU* 4.0 7.9 - - + -
204B PHE* 4.2 8.7 - - + -
207B PHE* 3.7 17.9 - - + -
228B TYR* 3.4 28.5 - - + +
233B SER 2.9 17.2 + - - +
234B ALA 3.7 5.2 - - - +
236B HIS* 1.3 77.3 - - - +
238B LYS* 1.3 57.1 + - - +
241B LEU* 2.8 36.1 + - + +
255B ILE* 4.0 2.0 - - - +
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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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184B LEU* 4.6 1.1 - - + +
234B ALA 3.1 16.5 + - - +
235B GLN 3.7 5.4 - - - +
236B HIS 3.2 0.2 - - - -
237B ALA* 1.3 77.1 - - - +
239B LEU* 1.3 68.8 + - + +
242B ASP* 3.1 36.8 + - + +
255B ILE* 3.5 45.5 - - + +
256B ASP* 4.0 15.0 - - - +
257B PHE* 3.4 38.5 - - + -
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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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235B GLN* 3.1 24.7 + - + +
236B HIS* 3.6 11.7 - - + +
238B LYS* 1.3 84.0 - - + +
240B SER* 1.3 60.3 + - - +
242B ASP* 4.7 3.6 + - - +
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Residues in contact with SER 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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206B LYS* 5.4 0.3 + - - -
207B PHE* 3.4 30.6 - - - -
236B HIS* 2.9 24.8 + - - -
239B LEU* 1.3 80.2 - - - +
241B LEU* 1.3 61.6 + - - +
242B ASP 3.6 1.8 + - - +
244B GLN* 3.3 17.3 - - - +
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Residues in contact with LEU 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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203B ILE* 4.0 19.5 - - + -
204B PHE* 3.8 31.4 - - + -
206B LYS* 4.7 2.5 - - + -
207B PHE* 3.8 30.1 - - + -
237B ALA 2.8 21.6 + - - +
240B SER* 1.3 78.3 - - - +
242B ASP* 1.3 64.3 + - - +
243B GLY 3.0 0.7 + - - -
244B GLN* 2.9 24.0 + - + +
253B LEU* 3.7 13.8 - - + +
255B ILE* 3.6 11.2 - - + -
500D LEU* 3.8 38.1 - - + -
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Residues in contact with ASP 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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238B LYS* 3.1 29.9 + - + +
239B LEU 4.7 3.0 + - - +
240B SER 3.6 2.5 - - - +
241B LEU* 1.3 75.5 - - - +
243B GLY* 1.3 62.4 + - - +
244B GLN* 3.6 3.6 + - - +
253B LEU 3.9 2.0 - - - -
254B ARG* 3.5 10.1 - - - -
255B ILE* 2.9 44.7 + - + +
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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
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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