Contacts of the helix formed by residues 229 - 236 (chain B) in PDB entry 4A8W
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 229 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B TRP* 3.9 6.7 - - - -
227B VAL 4.1 0.4 + - - -
228B ALA* 1.3 77.2 - - - +
230B PHE* 1.3 64.9 + - - +
231B GLU* 3.6 6.5 + - - +
232B TYR* 3.0 20.3 + - - +
233B ALA* 3.1 18.4 + - - +
240B GLY* 3.6 4.6 - - - -
241B SER* 2.9 46.7 + - - -
243B PHE* 3.9 16.8 - - + -
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Residues in contact with PHE 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ARG* 4.2 5.8 - - - -
6B ALA* 3.7 28.0 - - + -
100B TRP* 3.6 52.1 - + + +
229B ASP* 1.3 72.7 - - - +
231B GLU* 1.3 83.5 + - + +
233B ALA* 3.3 3.3 + - - +
234B VAL* 3.0 52.9 + - + +
377B THR* 4.2 8.5 - - + -
379B LEU* 3.8 5.6 - - + -
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Residues in contact with GLU 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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3B ARG* 2.7 46.7 + - - -
229B ASP* 3.3 6.3 + - - +
230B PHE* 1.3 88.9 - - + +
232B TYR* 1.3 55.6 + - - +
234B VAL* 3.6 1.9 - - - +
235B THR* 2.7 38.4 + - - +
239B GLN* 3.7 20.7 - - - +
240B GLY* 3.6 19.1 - - - +
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Residues in contact with TYR 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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102B LEU* 3.7 20.9 - - + -
228B ALA* 3.6 14.6 - - + -
229B ASP* 3.0 24.8 + - - +
231B GLU* 1.3 75.9 - - - +
233B ALA* 1.4 57.2 + - - +
236B GLY* 3.0 10.9 + - - -
237B GLY* 3.0 52.0 + - - -
239B GLN 3.2 22.4 + - - +
240B GLY 4.0 2.0 - - - -
241B SER* 3.6 25.4 - - - +
242B LEU* 3.8 38.8 - - + +
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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
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100B TRP* 3.6 32.1 - - + +
101B PRO 3.3 21.5 - - - +
102B LEU* 3.7 12.9 - - - +
103B ALA* 2.9 25.6 + - - +
228B ALA* 4.4 0.8 - - + +
229B ASP 3.1 5.8 + - - +
230B PHE 3.5 7.2 - - - +
232B TYR* 1.4 75.7 - - - +
234B VAL* 1.4 61.8 + - + +
236B GLY 3.5 7.8 + - - -
379B LEU* 4.8 5.6 - - + -
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Residues in contact with VAL 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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2B ARG 4.4 0.7 - - - +
3B ARG* 3.3 33.4 - - - +
4B ALA* 2.8 56.0 + - + +
6B ALA* 4.4 1.3 - - + -
103B ALA* 4.5 1.8 - - - +
230B PHE* 3.0 39.5 + - + +
231B GLU* 3.6 12.8 - - - +
233B ALA* 1.4 74.3 - - - +
235B THR* 1.3 56.6 - - - +
236B GLY 3.5 0.2 - - - -
379B LEU* 3.6 33.7 - - + -
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Residues in contact with THR 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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2B ARG 5.1 4.4 - - - +
3B ARG* 3.6 38.4 - - + +
104B SER* 5.9 0.9 - - - -
107B LYS* 5.8 0.2 - - - +
231B GLU* 2.7 22.4 + - - +
232B TYR 3.4 2.6 + - - -
234B VAL* 1.3 79.7 - - - +
236B GLY* 1.3 56.5 + - - +
238B GLU* 3.1 32.0 + - - +
239B GLN* 2.9 49.3 + - + +
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Residues in contact with GLY 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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102B LEU* 4.5 8.4 - - - +
104B SER* 3.6 31.8 - - - +
107B LYS* 3.6 24.9 - - - +
108B LYS* 4.4 5.2 + - - +
232B TYR* 3.0 9.2 + - - -
233B ALA 3.5 7.2 + - - -
234B VAL 3.5 2.8 - - - -
235B THR* 1.3 77.4 - - - +
237B GLY* 1.3 56.3 + - - +
238B GLU 3.5 0.4 - - - -
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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