Contacts of the helix formed by residues 190 - 198 (chain B) in PDB entry 1HJW
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 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B LYS* 4.2 11.3 + - + +
150B PHE* 5.8 0.2 - - - -
151B THR* 3.8 19.8 + - - +
189B TYR* 1.3 73.3 - - - +
191B ILE* 1.3 65.7 + - - +
192B ALA* 3.1 14.2 - - - +
193B LYS* 2.9 33.8 - - - +
194B ILE* 3.0 28.0 + - - +
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Residues in contact with ILE 191 (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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178B LEU* 4.3 6.3 - - + -
185B ILE* 4.6 6.3 - - + -
189B TYR* 3.5 35.9 - - + +
190B ASP* 1.3 73.6 - - - +
192B ALA* 1.3 64.6 + - - +
193B LYS 2.9 1.7 + - - -
194B ILE* 3.6 11.9 - - + -
195B SER* 2.8 35.4 + - - +
201B ILE* 5.0 2.2 - - + -
244B MET* 3.7 27.4 - - + +
247B LEU* 2.8 47.6 - - + +
249B ALA* 3.5 19.5 - - + +
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Residues in contact with ALA 192 (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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190B ASP* 3.9 13.0 - - - +
191B ILE* 1.3 81.7 - - - +
193B LYS* 1.3 58.2 + - + +
195B SER* 4.6 5.0 + - - -
196B GLN* 4.0 12.4 - - - +
247B LEU* 3.7 6.0 + - + +
248B GLY* 4.1 20.4 - - - +
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Residues in contact with LYS 193 (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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151B THR* 3.4 26.9 - - + +
152B THR* 5.9 0.4 + - - -
155B LYS* 3.6 29.0 - - - +
190B ASP* 2.9 22.3 + - - +
191B ILE 2.9 0.8 + - - -
192B ALA* 1.3 79.2 - - + +
194B ILE* 1.3 64.9 + - - +
195B SER 3.1 2.7 - - - -
196B GLN* 2.9 49.9 + - - +
197B HIS* 4.0 17.1 - - - +
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Residues in contact with ILE 194 (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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150B PHE* 4.3 19.1 - - + -
151B THR* 3.8 34.1 - - + +
154B ILE* 4.1 13.9 - - + +
178B LEU* 4.5 11.9 - - + -
189B TYR* 4.0 20.9 - - + -
190B ASP 3.0 21.0 + - - +
191B ILE* 3.6 19.5 - - + +
193B LYS* 1.3 74.7 - - - +
195B SER* 1.3 66.9 + - - +
196B GLN 3.0 1.2 + - - -
197B HIS* 3.2 19.8 + - - +
198B LEU* 3.3 30.3 + - + +
201B ILE* 5.0 0.7 - - + -
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Residues in contact with SER 195 (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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191B ILE* 2.8 36.7 + - - +
192B ALA 4.6 3.6 - - - -
193B LYS 3.1 1.0 + - - -
194B ILE* 1.3 77.7 - - - +
196B GLN* 1.3 58.0 + - - +
198B LEU* 3.5 11.9 - - - +
201B ILE* 4.0 13.5 - - - +
248B GLY 4.4 4.0 - - - -
249B ALA* 4.0 5.7 - - - -
250B PRO* 3.8 25.6 - - - +
253B LYS* 3.0 30.0 + - - +
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Residues in contact with GLN 196 (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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158B LYS* 5.6 0.9 - - - -
192B ALA 4.0 8.7 - - - +
193B LYS* 2.9 45.1 + - - +
194B ILE 3.0 0.4 - - - -
195B SER* 1.3 79.0 - - - +
197B HIS* 1.3 78.1 + - + +
253B LYS* 3.2 15.9 + - - +
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Residues in contact with HIS 197 (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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151B THR* 4.6 2.9 - - + -
154B ILE* 3.5 22.4 - - + -
155B LYS* 3.7 44.5 + - + +
158B LYS* 3.3 50.6 + - + +
174B LEU* 4.7 1.5 - - + +
193B LYS* 4.0 21.1 + - + -
194B ILE* 3.2 4.6 + - - -
196B GLN* 1.3 102.1 + - + +
198B LEU* 1.3 65.2 + - - +
199B ASP* 3.3 2.3 + - - +
253B LYS* 4.4 0.9 + - - -
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Residues in contact with LEU 198 (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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150B PHE* 6.0 0.4 - - + -
154B ILE* 3.5 26.0 - - + -
174B LEU* 3.4 11.0 - - + +
175B SER* 3.6 16.8 - - - +
176B ALA* 3.5 31.4 - - + -
178B LEU* 5.2 0.4 - - + -
194B ILE* 3.3 36.7 + - + +
195B SER 3.5 2.8 - - - +
197B HIS* 1.3 74.5 - - - +
199B ASP* 1.3 63.4 + - - +
200B PHE* 3.2 8.6 + - - +
201B ILE* 3.7 30.1 - - + -
253B LYS* 2.8 27.0 + - - +
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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