Contacts of the helix formed by residues 209 - 216 (chain D) in PDB entry 1YXU
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 PRO 209 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201D PHE* 5.8 3.4 - - + -
207D TYR 4.3 2.7 - - - +
208D SER* 1.3 92.4 - - - +
210D PRO* 1.3 78.5 - - + +
211D GLU* 3.4 29.2 - - + +
212D TRP* 3.1 24.4 + - + +
213D ILE* 3.2 11.3 + - - +
218D TYR* 4.4 4.0 - - + -
223D ALA* 4.1 25.4 - - + +
226D TRP* 3.7 20.4 - - + -
248D ILE* 4.1 0.9 - - - -
278D ARG* 3.9 2.9 - - - +
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Residues in contact with PRO 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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209D PRO* 1.3 90.0 - - + +
211D GLU* 1.3 61.8 + - - +
213D ILE* 3.1 5.1 + - + +
214D ARG* 3.0 40.9 + - - +
226D TRP* 3.4 39.3 - - + -
248D ILE* 3.7 19.7 - - + +
249D ILE* 4.2 10.8 - - + -
273D LEU* 3.8 22.4 - - + +
278D ARG* 3.8 4.9 - - - +
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Residues in contact with GLU 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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209D PRO* 3.4 16.5 - - - +
210D PRO* 1.3 71.6 - - - +
212D TRP* 1.3 66.6 + - - +
214D ARG* 5.5 0.2 - - - +
215D TYR* 2.9 38.6 + - + +
216D HIS 3.4 2.8 + - - -
217D ARG* 3.0 27.7 - - + +
218D TYR* 3.8 14.7 - - + +
219D HIS 5.0 0.2 + - - -
222D SER* 4.5 3.5 + - - -
223D ALA* 4.7 1.0 - - - -
273D LEU 4.2 1.6 - - - +
275D PRO* 3.6 24.8 - - + +
278D ARG* 2.8 45.9 + - - -
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Residues in contact with TRP 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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199D THR 3.5 27.1 - - - -
200D ASP* 3.8 3.1 - - - -
201D PHE* 3.4 55.1 - + + -
205D ARG* 4.4 14.9 - - - +
208D SER* 3.5 25.4 - - - -
209D PRO* 3.1 20.4 + - + +
211D GLU* 1.3 83.1 - - - +
213D ILE* 1.3 66.3 + - + +
216D HIS* 2.8 81.8 + + - -
217D ARG 3.9 4.7 - - - +
218D TYR* 3.6 24.2 - + + -
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Residues in contact with ILE 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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205D ARG* 3.8 35.8 + - + +
208D SER* 3.6 19.7 - - - +
209D PRO 3.4 13.5 - - - +
210D PRO* 3.1 9.7 + - + +
212D TRP* 1.3 79.7 - - + +
214D ARG* 1.3 59.1 + - - +
216D HIS* 4.3 8.0 + - - -
245D ASP* 3.8 30.3 - - + +
248D ILE* 4.1 25.4 - - + -
249D ILE* 3.7 24.9 - - + +
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Residues in contact with ARG 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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210D PRO* 3.0 20.7 + - - +
213D ILE* 1.3 76.3 - - - +
215D TYR* 1.3 106.0 + - + +
216D HIS* 3.8 1.6 - - - -
249D ILE* 3.3 55.8 + - + +
273D LEU* 5.9 2.6 - - - +
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Residues in contact with TYR 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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211D GLU* 2.9 25.9 + - + +
214D ARG* 1.3 129.8 + - + +
216D HIS* 1.3 75.0 + - - +
217D ARG* 3.2 26.4 + - + +
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Residues in contact with HIS 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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199D THR* 3.4 27.6 + - - +
205D ARG* 4.4 13.7 + - - -
212D TRP* 2.8 66.3 + + + -
213D ILE* 4.3 9.7 + - - -
214D ARG 5.3 1.3 - - - -
215D TYR* 1.3 80.0 - - - +
217D ARG* 1.3 59.6 + - - +
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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