Contacts of the helix formed by residues 187 - 192 (chain C) in PDB entry 1TYE
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 GLY 187 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166C TYR* 2.9 36.7 - - - +
167C CYS 2.9 7.5 + - - -
168C GLU* 4.8 1.5 - - - +
186C PRO* 1.3 77.7 - - - +
188C GLY* 1.3 65.7 + - - +
189C TYR 3.6 0.7 + - - -
190C TYR 3.7 2.6 + - - -
191C PHE* 3.0 32.1 + - - -
262D LEU* 4.7 5.3 - - - +
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Residues in contact with GLY 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163C ASP 4.7 0.2 - - - -
167C CYS* 3.4 14.7 - - - +
185C ALA 2.9 16.2 + - - -
186C PRO 3.2 0.6 - - - -
187C GLY* 1.3 77.1 - - - +
189C TYR* 1.3 69.5 + - - +
192C LEU 3.0 4.2 + - - -
193C GLY* 2.6 27.5 + - - -
194C LEU* 3.7 18.2 - - - -
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Residues in contact with TYR 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C PHE 5.7 1.3 - - - -
162C TRP* 4.0 17.3 - + - -
163C ASP* 3.0 36.2 + - - +
164C LYS* 3.4 32.3 + - + +
188C GLY* 1.3 73.8 - - - +
190C TYR* 1.3 69.2 + - - +
191C PHE 3.4 0.2 + - - -
192C LEU* 3.5 19.2 - - + +
193C GLY 4.3 4.3 - - - -
194C LEU* 3.7 28.9 - - + +
221C LEU* 4.7 2.8 - - - +
222C SER 2.6 23.5 + - - -
223C PHE* 3.3 34.0 - - - -
224C ASP* 3.6 37.6 - - + +
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Residues in contact with TYR 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C PHE* 3.6 42.6 - + + +
163C ASP* 3.3 29.1 + - + +
166C TYR* 3.4 27.2 - + - -
187C GLY 3.7 2.0 + - - -
188C GLY 3.4 0.2 - - - -
189C TYR* 1.3 76.8 - - - +
191C PHE* 1.3 85.3 + + - +
192C LEU* 3.7 7.1 + - + +
232C ASP* 4.7 3.4 + - - +
166D TYR* 4.1 7.6 + - - -
216D ARG* 2.7 42.9 + - + +
217D ASP* 4.7 3.1 - - - -
218D ALA 5.4 1.6 - - - -
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Residues in contact with PHE 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166C TYR* 4.0 26.5 - + + -
168C GLU* 5.6 0.2 - - - -
186C PRO 3.7 4.7 - - - +
187C GLY* 3.0 25.8 + - - -
190C TYR* 1.3 100.4 - + - +
192C LEU* 1.3 64.5 + - - +
193C GLY 3.3 0.9 - - - -
232C ASP* 3.2 34.9 - - - +
233C GLY 3.5 2.9 + - - -
234C TYR* 3.5 15.1 + + + -
163D PRO* 3.9 41.1 - - + -
164D TYR* 5.9 1.6 - + - -
216D ARG* 4.1 16.4 - - + -
217D ASP* 3.9 29.8 - - + -
262D LEU* 4.1 18.8 - - + -
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Residues in contact with LEU 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C PRO 3.8 0.9 - - - -
188C GLY 3.0 5.8 + - - +
189C TYR* 3.5 17.3 - - + +
190C TYR* 4.0 7.2 - - + +
191C PHE* 1.3 80.5 - - - +
193C GLY* 1.3 65.1 + - - +
223C PHE 5.7 1.1 - - - +
224C ASP* 3.6 15.0 - - - +
225C SER* 3.6 32.8 - - - +
230C TYR* 3.5 39.4 - - + +
231C PHE* 3.8 29.8 - - + -
233C GLY 4.0 0.7 - - - -
234C TYR 3.4 3.6 + - - -
235C TRP* 2.8 29.3 + - - +
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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