Contacts of the strand formed by residues 190 - 197 (chain B) 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 TYR 190 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B TYR* 2.8 25.9 + + - -
117B LEU* 3.9 21.1 - - + -
155B ALA 3.2 17.7 - - - -
188B PHE* 4.1 2.2 - - - -
189B GLY* 1.3 78.1 - - - +
191B LYS* 1.3 76.1 + - - +
192B HIS* 3.7 12.1 - - + +
224B ASP* 5.1 1.1 - - + -
225B ALA* 3.6 35.2 - - + +
228B GLN* 3.8 27.8 - - + -
229B ALA* 4.2 2.1 - - - +
236B ILE* 3.6 17.0 - - + +
275B VAL* 3.9 15.7 - - + -
280B HIS* 3.5 6.6 - - - +
281B TYR* 3.1 46.6 + - + +
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Residues in contact with LYS 191 (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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154B GLY* 3.4 2.3 - - - -
155B ALA* 2.8 38.4 + - - +
185B LEU* 5.9 8.1 - - - +
188B PHE* 3.7 42.4 - - + +
190B TYR* 1.3 80.9 - - - +
192B HIS* 1.3 69.2 + - - +
193B VAL* 3.5 10.4 + - + +
210B GLN* 5.7 4.3 - - - -
278B ASP 5.5 0.2 - - - +
279B ASN* 3.3 7.4 - - + +
280B HIS* 3.1 33.1 + - + +
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Residues in contact with HIS 192 (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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115B TYR* 2.7 34.3 + + - -
190B TYR* 3.7 15.3 - - + +
191B LYS* 1.3 74.4 - - - +
193B VAL* 1.3 61.0 + - - +
194B LEU 3.4 28.3 - - - -
195B THR* 3.1 30.4 + - - -
235B LYS* 3.4 26.2 + - + -
236B ILE* 3.9 10.6 - - + +
275B VAL* 4.5 8.1 - - + -
279B ASN* 2.9 57.7 + - + +
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Residues in contact with VAL 193 (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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153B PHE* 3.4 54.4 + - + +
154B GLY* 3.6 13.2 - - - -
155B ALA* 4.3 5.4 - - + +
191B LYS* 4.2 14.1 - - + +
192B HIS* 1.3 76.8 - - - +
194B LEU* 1.3 61.4 + - - +
195B THR 4.2 0.7 + - - -
206B GLU* 4.0 19.0 - - + +
210B GLN* 4.2 12.6 - - - +
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Residues in contact with LEU 194 (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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115B TYR* 3.9 0.7 - - - -
152B GLY* 3.4 2.7 - - - -
153B PHE* 3.0 50.3 + - + -
192B HIS* 3.4 10.0 - - - -
193B VAL* 1.3 77.2 - - + +
195B THR* 1.3 76.6 + - - +
196B LEU 3.7 0.2 + - - -
197B THR* 4.4 11.0 - - + -
202B ARG* 3.6 41.7 - - - +
203B PHE* 3.6 48.2 - - + +
206B GLU* 4.7 8.1 - - + -
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Residues in contact with THR 195 (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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151B ILE 3.8 1.0 - - - +
192B HIS* 3.1 23.0 + - - -
193B VAL 4.2 0.6 + - - -
194B LEU* 1.3 83.1 - - - +
196B LEU* 1.3 76.4 + - - +
197B THR* 3.2 16.3 + - - +
234B GLU 4.9 2.2 - - - +
235B LYS 3.3 19.7 + - - +
236B ILE 3.4 6.7 - - - +
237B GLY* 4.3 6.1 - - - -
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Residues in contact with LEU 196 (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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113B ASP* 3.4 15.7 - - - +
114B ILE 3.2 29.8 - - - +
115B TYR* 4.3 6.3 - - + -
150B ARG* 3.3 25.7 - - + +
151B ILE 3.3 2.2 - - - -
152B GLY* 3.4 12.3 - - - +
194B LEU 3.7 0.8 + - - -
195B THR* 1.3 78.3 - - - +
197B THR* 1.3 60.2 + - - +
236B ILE* 3.0 25.6 + - + +
237B GLY* 3.3 36.4 - - - +
238B TRP* 3.5 19.7 - - + +
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Residues in contact with THR 197 (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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150B ARG* 3.7 10.1 - - - +
151B ILE* 2.8 39.2 + - - +
194B LEU* 4.4 11.9 - - + -
195B THR 3.6 12.1 - - - +
196B LEU* 1.3 76.7 - - - +
198B ASP* 1.3 72.2 + - - +
199B GLN* 2.9 46.0 + - + +
200B VAL* 5.7 0.2 - - - +
202B ARG* 4.2 12.3 - - - +
203B PHE* 5.7 0.7 - - + -
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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