Contacts of the helix formed by residues 207 - 217 (chain D) in PDB entry 3UO9
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 ASN 207 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174D ARG 3.2 21.2 + - - +
175D LEU* 3.3 25.3 - - + -
177D GLU* 3.6 22.8 + - - +
178D CYS* 3.0 33.8 + - + +
204D VAL 3.0 8.1 + - - +
206D SER* 1.3 87.9 + - - +
208D ILE* 1.3 64.1 + - - +
209D VAL 3.4 2.7 - - - -
210D LEU* 3.4 9.0 + - + +
211D LEU* 3.1 27.3 + - + +
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Residues in contact with ILE 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D LEU* 3.8 29.8 - - + +
140D GLU* 3.7 43.5 - - + +
143D LEU* 3.7 20.0 - - + -
204D VAL* 3.0 12.6 + - + +
205D GLN 3.3 20.4 - - - +
206D SER 3.6 0.8 - - - -
207D ASN* 1.3 74.3 - - - +
209D VAL* 1.3 76.5 + - + +
211D LEU* 3.3 1.9 + - - -
212D THR* 2.9 37.8 + - + +
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Residues in contact with VAL 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D LEU* 5.6 7.2 - - + -
207D ASN 3.4 1.0 - - - -
208D ILE* 1.3 84.3 - - + +
210D LEU* 1.3 63.8 + - - +
212D THR* 3.2 8.5 + - - +
213D GLN* 3.2 44.8 + - + +
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Residues in contact with LEU 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D LEU* 4.6 9.2 - - + -
172D ASP* 4.7 0.4 - - - +
174D ARG* 3.6 63.5 - - + +
175D LEU* 4.3 20.2 - - + -
207D ASN* 3.4 10.3 + - + +
208D ILE 3.3 0.4 - - - -
209D VAL* 1.3 77.8 - - - +
211D LEU* 1.3 63.5 + - - +
213D GLN* 3.4 13.8 + - - +
214D ALA* 3.0 22.1 + - - +
219D PHE* 3.9 24.2 - - + -
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Residues in contact with LEU 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D LEU* 3.9 14.6 - - + -
159D PHE* 4.4 8.1 - - + -
163D LEU* 3.5 33.4 - - + -
168D LEU* 5.5 0.9 - - + -
175D LEU* 3.7 17.7 - - + -
178D CYS* 4.1 12.6 - - - -
204D VAL* 3.7 37.5 - - + +
207D ASN* 3.1 28.8 + - + +
208D ILE* 3.3 4.5 + - - +
210D LEU* 1.3 77.4 - - - +
212D THR* 1.3 57.7 + - - +
214D ALA* 3.4 3.6 + - + +
215D PHE* 2.9 41.9 + - + -
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Residues in contact with THR 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139D LEU* 3.9 32.1 - - + +
142D LEU* 6.4 0.4 - - + -
143D LEU* 4.4 16.4 - - + +
208D ILE* 2.9 37.9 + - + +
209D VAL* 3.2 13.9 + - - +
210D LEU 3.3 0.2 - - - -
211D LEU* 1.3 76.8 - - - +
213D GLN* 1.3 56.2 + - - +
215D PHE* 4.5 0.4 - - - +
216D ARG* 2.8 51.0 + - - +
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Residues in contact with GLN 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D VAL* 3.2 34.9 + - + +
210D LEU* 3.5 22.9 - - - +
211D LEU 3.4 0.2 - - - -
212D THR* 1.3 75.6 - - - +
214D ALA* 1.3 62.2 + - - +
217D ARG 3.2 4.0 + - - -
218D LYS* 3.0 44.0 + - + +
219D PHE* 3.9 18.5 + - + -
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Residues in contact with ALA 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D LEU* 4.9 2.5 - - + -
166D THR* 3.4 31.9 - - + +
168D LEU* 4.0 8.5 - - + -
210D LEU 3.0 14.5 + - - +
211D LEU* 3.5 11.2 - - - +
213D GLN* 1.3 77.2 - - - +
215D PHE* 1.3 63.4 + - + +
217D ARG* 3.6 12.1 + - - +
219D PHE* 3.6 32.9 - - + -
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Residues in contact with PHE 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D LEU* 3.5 29.4 - - + -
146D THR* 5.2 10.6 - - + +
147D ILE* 4.1 25.8 - - + -
159D PHE* 4.2 14.1 - + - -
162D ALA* 3.6 31.2 - - + -
163D LEU* 3.5 44.6 - - + -
166D THR* 4.7 4.3 - - + -
211D LEU* 2.9 31.4 + - + +
212D THR 4.0 1.1 - - - +
214D ALA* 1.3 75.7 - - + +
216D ARG* 1.3 70.5 + - - +
217D ARG* 3.6 8.1 + - - +
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Residues in contact with ARG 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D LEU* 5.5 3.8 - - - -
146D THR* 4.3 28.5 + - - +
212D THR* 2.8 34.8 + - - +
215D PHE* 1.3 80.8 + - - +
217D ARG* 1.3 72.4 + - - +
218D LYS* 3.8 30.5 + - + +
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Residues in contact with ARG 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D GLN 3.2 4.5 + - - -
214D ALA 3.6 7.8 + - - +
215D PHE 3.4 10.4 - - - +
216D ARG* 1.3 83.1 - - - +
218D LYS* 1.3 63.2 + - - +
219D PHE 3.3 4.6 - - - +
222D PRO* 3.5 49.0 + - + +
223D ASP* 3.9 22.0 + - - +
545D GLU* 3.1 36.1 + - - +
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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