Contacts of the strand formed by residues 190 - 197 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115F TYR* 3.1 24.1 + - - -
117F LEU* 3.7 22.4 - - + -
154F GLY* 4.5 0.7 - - - -
155F ALA 3.4 14.6 - - - -
188F PHE* 4.3 1.6 - - - -
189F GLY* 1.3 76.9 - - - +
191F LYS* 1.3 73.2 + - - +
192F HIS* 3.8 12.4 - - + +
224F ASP* 4.9 0.7 - - + -
225F ALA* 3.4 39.3 - - + +
228F GLN* 3.8 28.3 - - + -
229F ALA* 4.1 2.5 - - - +
236F ILE* 3.5 17.5 - - + +
275F VAL* 3.9 14.4 - - + -
280F HIS* 3.6 5.5 - - - +
281F TYR* 3.0 49.4 + - + +
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Residues in contact with LYS 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F LEU* 6.0 0.8 - - - +
154F GLY* 3.2 4.2 - - - -
155F ALA* 2.8 40.0 + - - +
185F LEU* 5.3 8.5 - - - +
188F PHE* 3.5 42.4 - - + -
190F TYR* 1.3 78.6 - - - +
192F HIS* 1.3 67.5 - - - +
193F VAL* 3.7 9.2 + - + +
210F GLN* 5.6 6.5 + - - -
279F ASN* 3.6 7.9 - - + +
280F HIS* 3.3 33.6 + - + +
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Residues in contact with HIS 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F TYR* 2.6 34.8 + + - -
190F TYR* 3.8 14.4 + - + +
191F LYS* 1.3 75.2 - - - +
193F VAL* 1.3 63.4 + - - +
194F LEU 3.6 16.2 - - - -
195F THR* 3.3 27.9 + - - -
235F LYS* 3.5 27.5 + - + -
236F ILE* 3.4 17.7 - - + +
275F VAL* 4.5 8.5 - - + -
279F ASN* 2.9 54.6 + - + +
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Residues in contact with VAL 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F PHE* 3.0 53.7 + - + +
154F GLY* 4.0 4.7 - - - -
155F ALA* 5.1 1.3 - - + +
191F LYS* 3.7 11.6 + - + +
192F HIS* 1.3 78.6 - - - +
194F LEU* 1.3 64.3 + - - +
195F THR 4.3 1.1 + - - -
206F GLU* 4.2 25.1 - - + +
210F GLN* 4.6 9.2 - - - +
279F ASN* 4.7 5.5 + - - +
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Residues in contact with LEU 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F TYR* 3.6 1.2 - - - -
151F ILE 4.3 3.8 - - - +
152F GLY* 3.3 6.6 - - - -
153F PHE* 3.0 48.1 + - + +
192F HIS* 3.6 10.6 - - - -
193F VAL* 1.3 79.7 - - - +
195F THR* 1.3 72.8 + - - +
197F THR* 4.6 7.0 - - + -
202F ARG* 3.7 35.4 - - - +
203F PHE* 3.7 47.6 - - + +
206F GLU* 3.7 19.3 - - + +
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Residues in contact with THR 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F ILE 3.6 5.5 - - - +
152F GLY* 4.2 0.4 - - - -
192F HIS* 3.3 20.9 + - - -
193F VAL 4.3 0.4 + - - -
194F LEU* 1.3 79.7 - - - +
196F LEU* 1.3 74.0 + - - +
197F THR* 3.1 13.7 + - - +
202F ARG* 5.5 0.7 + - - -
234F GLU 4.9 1.6 - - - +
235F LYS 3.5 11.4 + - - +
236F ILE 3.4 14.4 - - - +
237F GLY* 4.2 7.2 - - - -
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Residues in contact with LEU 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F ASP* 3.9 9.2 - - - +
114F ILE 3.3 35.9 - - - +
115F TYR* 4.2 6.1 - - + +
150F ARG* 4.0 24.8 + - + +
151F ILE* 3.6 10.1 - - - +
152F GLY* 3.5 11.0 - - - +
194F LEU 3.8 1.2 + - - -
195F THR* 1.3 78.4 - - - +
197F THR* 1.3 60.0 + - - +
236F ILE* 3.2 22.3 + - + +
237F GLY* 3.5 29.4 - - - +
238F TRP* 3.7 27.1 - - + +
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Residues in contact with THR 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150F ARG* 3.4 8.2 - - - +
151F ILE* 2.7 48.7 + - + +
194F LEU* 4.6 9.6 - - + -
195F THR* 3.7 11.4 - - - +
196F LEU* 1.3 75.0 - - - +
198F ASP* 1.3 71.4 + - - +
199F GLN* 2.9 49.2 + - + +
202F ARG* 4.4 10.5 - - - +
203F PHE* 5.9 0.2 - - + -
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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