Contacts of the helix formed by residues 196 - 204 (chain B) in PDB entry 2QUH
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 THR 196 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B ARG 3.2 6.1 + - - -
163B GLY* 3.3 18.7 + - - -
164B PRO* 3.6 7.9 - - - +
194B GLN* 3.8 9.9 - - - -
195B MET* 1.3 67.8 - - - +
197B ASP* 1.3 63.4 + - - +
198B ASP 3.1 3.1 - - - -
199B GLU* 2.7 42.3 + - - +
200B LYS* 3.2 9.2 + - - +
237B ASP* 3.2 20.4 - - - +
280B PHE* 3.7 12.3 - - + -
818B TRP* 3.6 27.0 - - + +
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Residues in contact with ASP 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B PRO* 3.7 9.6 - - - +
195B MET 2.8 8.9 + - - -
196B THR* 1.3 72.5 - - - +
198B ASP* 1.3 61.9 + - - -
200B LYS* 3.7 1.6 + - - +
201B TYR* 3.0 21.1 + - - +
211B ALA* 3.2 39.8 - - - +
212B TYR* 3.7 8.7 - - - -
215B ALA* 4.0 6.9 - - + +
236B SER* 2.5 28.2 + - - -
237B ASP* 3.2 6.1 + - - +
238B LEU* 3.1 39.5 + - + +
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Residues in contact with ASP 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A TYR* 3.3 25.3 + - - +
252A VAL* 4.5 9.0 - - + -
196B THR* 3.5 2.8 - - - -
197B ASP* 1.3 74.2 + - - +
199B GLU* 1.3 80.8 + - - -
201B TYR* 3.1 8.5 + - - +
202B LEU* 2.8 31.6 + - + +
237B ASP* 2.8 42.1 - - - +
238B LEU* 3.7 22.2 - - + -
280B PHE* 3.9 8.5 - - - -
283B ILE* 3.8 8.8 - - - +
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Residues in contact with GLU 199 (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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196B THR* 2.7 33.3 + - - +
198B ASP* 1.3 81.7 + - - +
200B LYS* 1.3 74.8 + - + +
202B LEU* 2.9 11.2 + - - +
203B TRP* 2.9 48.2 + - + -
280B PHE* 3.4 43.5 - - + -
316B TYR* 4.1 8.5 + - - -
818B TRP 3.0 35.6 + - - +
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Residues in contact with LYS 200 (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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163B GLY* 3.6 25.1 - - - -
164B PRO 3.7 15.3 - - - +
165B SER* 3.6 40.3 + - - +
196B THR 3.2 13.2 + - - +
197B ASP* 4.1 4.7 - - - +
199B GLU* 1.3 97.3 + - + +
201B TYR* 1.3 61.6 + - - +
203B TRP* 3.8 9.3 - - + +
204B LYS* 2.9 40.5 + - + +
206B LEU* 4.0 10.8 - - + +
211B ALA* 5.2 0.7 - - + -
818B TRP 3.7 9.4 + - - -
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Residues in contact with TYR 201 (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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252A VAL* 3.4 32.3 - - + -
253A LYS* 3.7 25.0 - - - +
256A LYS* 2.7 65.1 + - + +
257A HIS* 4.0 9.7 + - - -
327A ILE* 5.3 0.2 - - - +
197B ASP 3.0 16.1 + - - +
198B ASP* 3.1 10.3 + - - +
200B LYS* 1.3 76.2 - - - +
202B LEU* 1.3 61.1 + - + +
204B LYS 3.2 3.3 - - - +
206B LEU* 3.3 28.9 - - - -
207B THR* 3.9 2.9 - - - -
208B LEU* 3.6 41.5 - - + -
211B ALA* 4.2 8.5 - - + +
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Residues in contact with LEU 202 (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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248A TYR* 5.9 1.3 - - - +
252A VAL* 3.9 28.7 - - + +
255A GLN* 4.6 5.2 - - + +
256A LYS* 3.9 44.7 - - + +
198B ASP* 2.8 22.1 + - + +
199B GLU* 3.1 12.3 - - - +
201B TYR* 1.3 81.3 - - + +
203B TRP* 1.3 67.2 + - + +
274B CYS* 4.5 3.2 - - - -
276B GLY* 3.8 37.7 - - - +
277B LYS* 3.7 17.7 - - + +
280B PHE* 4.8 10.3 - - + -
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Residues in contact with TRP 203 (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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199B GLU* 2.9 53.2 + - + +
200B LYS* 4.5 8.3 - - + +
202B LEU* 1.3 78.2 - - + +
204B LYS* 1.3 67.6 + - + +
269B PHE* 3.6 28.0 - + - -
277B LYS* 3.7 69.9 + - + +
280B PHE* 4.0 19.3 - + + -
316B TYR* 5.1 6.7 - - - -
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Residues in contact with LYS 204 (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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256A LYS* 2.8 26.3 + - - -
165B SER* 3.4 46.1 + - - +
166B SER* 5.3 1.6 - - - -
200B LYS* 2.9 27.1 + - + +
201B TYR 3.2 2.8 - - - +
203B TRP* 1.3 84.5 - - + +
205B ASP* 1.3 61.9 + - - +
206B LEU* 2.8 19.2 + - + +
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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