Contacts of the helix formed by residues 196 - 204 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A ARG 3.1 6.5 + - - -
163A GLY* 3.3 16.5 - - - -
164A PRO* 3.6 8.8 - - - +
194A GLN* 3.6 23.3 - - + +
195A MET* 1.3 69.0 - - - +
197A ASP* 1.3 63.6 + - - +
198A ASP 3.2 2.2 - - - -
199A GLU* 2.6 35.9 + - - +
200A LYS* 3.2 8.8 + - - +
237A ASP* 3.5 20.9 - - - +
280A PHE* 3.7 13.5 - - + -
817B TRP* 3.6 18.2 + - + -
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Residues in contact with ASP 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A PRO* 4.0 6.6 - - - +
195A MET 3.0 7.1 + - - -
196A THR* 1.3 72.1 - - - +
198A ASP* 1.3 63.1 + - - -
200A LYS* 3.2 3.3 + - - +
201A TYR* 2.8 26.5 + - - +
211A ALA* 3.4 37.0 - - - +
212A TYR* 3.4 11.0 - - - -
215A ALA* 4.0 5.8 - - + +
236A SER* 2.4 29.0 + - - -
237A ASP* 3.2 6.9 + - - +
238A LEU* 3.1 40.9 + - + +
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Residues in contact with ASP 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A THR* 3.4 4.2 - - - -
197A ASP* 1.3 77.8 + - - +
199A GLU* 1.3 62.1 + - - -
201A TYR* 3.3 7.2 + - - +
202A LEU* 2.9 37.0 + - + +
237A ASP* 2.7 39.6 - - - +
238A LEU* 3.4 25.6 - - + -
280A PHE* 3.8 6.0 - - - -
283A ILE* 3.4 15.8 - - - +
248B TYR* 3.3 22.2 + - - +
252B VAL* 4.5 9.2 - - + -
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Residues in contact with GLU 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A THR* 2.6 32.1 + - - +
198A ASP* 1.3 83.7 + - - +
200A LYS* 1.3 69.5 + - + +
202A LEU* 3.2 2.8 + - - -
203A TRP* 2.8 54.8 + - + +
280A PHE* 3.3 35.9 - - + -
316A TYR* 3.5 20.6 + - - -
817B TRP 3.1 30.1 + - - +
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Residues in contact with LYS 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A GLY* 3.4 23.7 + - - -
164A PRO* 3.6 28.5 - - + +
165A SER* 3.0 29.0 + - - +
196A THR 3.2 9.8 + - - +
197A ASP* 3.2 8.8 + - - +
199A GLU* 1.3 90.4 + - + +
201A TYR* 1.3 58.8 + - - +
203A TRP* 4.3 4.8 - - + +
204A LYS* 2.6 48.2 + - + +
206A LEU* 4.3 13.6 - - + +
211A ALA* 4.7 2.0 - - + -
817B TRP 3.5 16.4 + - - -
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Residues in contact with TYR 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A ASP 2.8 17.8 + - - +
198A ASP 3.6 4.0 - - - +
200A LYS* 1.3 76.0 - - - +
202A LEU* 1.3 62.7 + - + +
204A LYS 3.2 5.6 - - - +
206A LEU* 3.4 26.9 - - - -
207A THR* 3.8 2.5 - - - -
208A LEU* 3.4 37.9 - - + -
211A ALA* 4.1 11.8 - - + +
252B VAL* 3.4 35.2 - - + -
253B LYS* 3.5 28.1 - - + +
256B LYS* 2.9 62.5 + - + +
257B HIS* 3.7 12.0 + - - -
327B ILE* 5.4 0.2 - - - +
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Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ASP* 2.9 21.1 + - + +
199A GLU* 3.4 6.1 - - - +
201A TYR* 1.3 87.6 - - + +
203A TRP* 1.3 65.7 + - + +
274A CYS* 4.5 6.5 - - - -
276A GLY* 3.5 41.3 - - - +
277A LYS* 3.6 19.3 - - + +
280A PHE* 4.5 13.2 - - + -
283A ILE* 6.3 2.0 - - + -
252B VAL* 3.4 39.9 - - + +
255B GLN* 5.0 3.8 - - + +
256B LYS* 4.1 24.0 - - + +
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Residues in contact with TRP 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A GLU* 2.8 54.9 + - + +
200A LYS* 4.2 6.1 - - + +
202A LEU* 1.3 82.6 - - + +
204A LYS* 1.3 66.5 + - + +
269A PHE* 3.7 28.3 - + - -
277A LYS* 3.6 66.0 + - + +
280A PHE* 4.0 26.2 - + + -
316A TYR* 5.1 5.6 - + - -
256B LYS* 5.9 0.2 - - - -
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Residues in contact with LYS 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A SER* 3.3 48.0 + - - +
166A SER* 5.3 2.6 - - - -
200A LYS* 2.6 28.2 + - + +
201A TYR 3.2 4.2 - - - +
203A TRP* 1.3 85.7 - - + +
205A ASP* 1.3 59.4 + - - +
206A LEU* 2.8 28.4 + - + +
353A SER* 6.4 0.2 - - - -
256B LYS* 3.0 19.6 + - - -
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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