Contacts of the strand formed by residues 112 - 119 (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 VAL 112 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110F TYR 3.7 11.0 - - - +
111F PRO* 1.3 81.9 - - - +
113F ASP* 1.3 64.0 + - - +
114F ILE* 4.0 18.8 - - + -
142F MET* 3.4 36.3 - - + -
146F THR* 4.1 2.2 - - + -
148F ASN 3.0 8.4 + - - +
149F LEU* 3.2 11.5 - - + +
150F ARG 3.1 24.6 + - - -
239F ARG* 3.7 4.9 + - - +
243F SER* 3.5 15.3 - - - +
245F LEU* 4.1 12.6 - - + -
348F TYR* 4.0 17.0 - - + -
351F ILE* 4.4 2.2 - - + -
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Residues in contact with ASP 113 (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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112F VAL* 1.3 70.7 - - - +
114F ILE* 1.3 58.5 + - - +
150F ARG* 3.4 19.9 - - - +
196F LEU* 3.9 14.3 - - + +
238F TRP* 3.5 21.2 - - + -
239F ARG* 2.8 49.4 + - - +
242F ALA* 3.9 0.2 - - - +
243F SER 2.7 15.4 + - - +
244F HIS* 3.1 19.5 + - + -
245F LEU* 2.6 37.1 + - - +
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Residues in contact with ILE 114 (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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112F VAL* 4.0 7.0 - - + -
113F ASP* 1.3 76.8 - - - +
115F TYR* 1.3 64.5 + - - +
116F TYR* 4.7 1.1 - - - +
138F LEU* 4.2 29.4 - - + +
139F ALA* 6.3 0.4 - - - -
142F MET* 3.5 33.9 - - + -
149F LEU* 4.3 5.4 - - + -
150F ARG 3.3 8.7 + - - +
151F ILE* 3.2 38.3 - - + +
152F GLY 3.3 8.0 + - - -
196F LEU* 3.3 6.2 - - - +
245F LEU* 3.3 26.7 - - + +
247F VAL* 4.2 14.1 - - + -
344F ILE* 4.4 9.4 - - + -
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Residues in contact with TYR 115 (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 4.2 0.8 - - - -
114F ILE* 1.3 75.3 - - - +
116F TYR* 1.3 60.6 + - - +
117F LEU* 3.7 19.1 - - + -
152F GLY* 3.3 12.6 - - - -
153F PHE 3.1 31.1 + - - -
154F GLY* 3.4 7.2 + - - -
190F TYR* 3.1 18.3 + - - -
192F HIS* 2.6 33.3 + + - -
194F LEU 3.6 10.3 - - - -
196F LEU* 4.4 5.6 - - + -
229F ALA* 4.0 8.5 - - + -
236F ILE* 3.5 24.5 - - + -
238F TRP* 3.6 22.9 - - + -
245F LEU 2.9 5.9 + - - -
246F LEU* 3.2 22.8 - - + +
247F VAL 3.1 23.7 + - - -
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Residues in contact with TYR 116 (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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114F ILE* 4.0 2.8 + - + -
115F TYR* 1.3 73.6 - - - +
117F LEU* 1.3 67.7 + - - +
118F MET* 3.6 35.4 - - + -
131F ILE* 2.9 38.0 + - - +
134F LEU* 3.4 23.5 - - + +
135F GLY* 3.7 18.6 - - - -
138F LEU* 4.1 16.4 - - + -
151F ILE* 5.8 0.2 - - + -
152F GLY 2.9 8.9 + - - +
153F PHE* 3.2 15.7 - + + +
154F GLY 2.9 27.2 + - - +
203F PHE* 4.6 11.7 - + + -
207F VAL* 5.1 2.2 - - + -
247F VAL* 3.8 32.3 - - + -
249F THR* 3.7 15.1 - - + +
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Residues in contact with LEU 117 (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* 3.7 20.2 - - + -
116F TYR* 1.3 73.1 - - - +
118F MET* 1.3 61.7 + - - +
154F GLY 3.7 8.5 - - - +
156F PHE* 4.2 6.0 - - + -
190F TYR* 3.7 29.4 - - + -
225F ALA* 3.9 11.2 - - + +
226F ILE* 3.7 36.6 - - + +
229F ALA* 4.5 1.6 - - + -
246F LEU* 4.1 17.0 - - + -
247F VAL 2.8 17.5 + - - +
248F PHE* 4.0 20.9 - - + -
249F THR* 2.9 29.6 + - - +
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Residues in contact with MET 118 (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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116F TYR* 3.6 30.5 - - + -
117F LEU* 1.3 71.2 - - - +
119F ASP* 1.3 60.8 + - - +
120F LEU* 3.7 12.6 - - + -
128F LEU* 4.7 0.9 - - + -
131F ILE* 3.5 34.1 - - + +
132F GLN* 4.5 4.5 - - + -
153F PHE* 3.5 34.3 - - - -
154F GLY 2.9 14.2 + - - +
155F ALA* 3.1 4.8 - - + +
156F PHE* 2.9 32.1 + - - -
207F VAL* 4.1 29.4 - - + +
210F GLN* 4.2 14.4 - - + -
249F THR* 3.5 3.6 - - - +
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Residues in contact with ASP 119 (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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118F MET* 1.3 69.6 - - - +
120F LEU* 1.3 64.3 + - - +
121F SER* 2.6 30.8 + - - -
124F MET* 3.0 43.4 - - + +
131F ILE* 4.0 1.9 - - - +
156F PHE* 3.6 21.9 - - + +
157F VAL* 5.0 0.2 - - - -
220F GLU* 3.9 10.4 - - - +
249F THR* 3.1 25.5 + - - +
250F THR* 2.8 26.2 + - - -
251F ASP* 4.1 2.4 + - - +
1415F MG 4.2 1.6 - - - -
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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