Contacts of the strand formed by residues 149 - 156 (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 LEU 149 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112F VAL* 3.2 42.4 - - + +
114F ILE* 4.3 10.1 - - + -
139F ALA* 4.3 20.4 - - + +
142F MET* 3.6 30.1 - - + -
143F ARG* 4.3 17.9 - - - +
146F THR* 4.2 12.3 - - + +
147F SER 3.2 6.9 + - - +
148F ASN* 1.3 77.1 + - - +
150F ARG* 1.3 87.7 + - - +
151F ILE* 5.0 7.2 - - + -
198F ASP* 3.8 14.9 - - - +
200F VAL* 5.3 5.4 - - + -
239F ARG* 4.3 0.4 - - - +
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Residues in contact with ARG 150 (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 3.1 6.4 + - - +
113F ASP* 3.4 15.0 - - - +
114F ILE 3.3 21.5 + - - -
148F ASN* 5.5 4.2 + - - -
149F LEU* 1.3 88.6 + - - +
151F ILE* 1.3 64.7 + - - +
196F LEU* 4.0 23.2 + - + +
197F THR* 3.4 6.5 - - - +
198F ASP* 3.6 34.8 + - - +
239F ARG* 3.3 40.0 - - - +
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Residues in contact with ILE 151 (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* 3.2 37.9 - - + +
116F TYR* 5.5 0.9 - - + +
135F GLY 4.7 1.3 - - - +
138F LEU* 5.2 3.8 - - + -
139F ALA* 4.1 24.9 - - + +
149F LEU* 5.0 8.5 - - + -
150F ARG* 1.3 77.5 - - - +
152F GLY* 1.3 59.0 + - - +
194F LEU* 4.3 2.9 - - - +
195F THR 3.6 1.7 - - - +
196F LEU* 3.7 5.6 - - - -
197F THR* 2.7 41.1 + - - +
199F GLN 5.4 0.4 - - - +
200F VAL* 4.9 17.3 - - + +
203F PHE* 3.6 50.3 - - + -
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Residues in contact with GLY 152 (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 3.3 4.5 + - - +
115F TYR* 3.3 9.3 - - - -
116F TYR* 2.9 23.0 + - - +
151F ILE* 1.3 77.9 - - - +
153F PHE* 1.3 61.5 + - - +
194F LEU* 3.3 20.6 - - - -
195F THR 4.0 6.7 - - - -
196F LEU* 3.5 5.7 - - - +
203F PHE* 3.9 9.5 - - - -
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Residues in contact with PHE 153 (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* 3.1 15.3 + - - -
116F TYR* 3.2 26.5 - - + +
118F MET* 3.5 32.3 - - - -
152F GLY* 1.3 76.1 - - - +
154F GLY* 1.3 65.5 + - - +
155F ALA* 5.4 2.0 - - + -
193F VAL* 3.0 26.6 + - + +
194F LEU* 3.0 39.4 + - + +
203F PHE* 4.1 8.3 - + + -
206F GLU* 3.6 26.7 - - + -
207F VAL* 3.8 28.7 - - + -
210F GLN* 3.5 29.2 - - + -
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Residues in contact with GLY 154 (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* 3.4 12.9 + - - -
116F TYR 2.9 9.0 + - - +
117F LEU* 3.5 8.9 - - - -
118F MET* 2.9 23.9 + - - +
153F PHE* 1.3 81.0 - - - +
155F ALA* 1.3 60.9 + - - +
190F TYR* 4.5 0.7 - - - -
191F LYS 3.2 14.4 - - - -
193F VAL* 4.0 6.5 - - - -
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Residues in contact with ALA 155 (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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117F LEU* 5.4 0.2 - - - -
118F MET* 3.1 17.3 - - + +
120F LEU* 3.4 34.5 - - + -
153F PHE* 5.5 2.0 - - + -
154F GLY* 1.3 75.6 - - - +
156F PHE* 1.3 65.2 + - - +
188F PHE* 3.7 9.2 - - + -
190F TYR* 3.4 5.0 - - - -
191F LYS* 2.8 36.0 + - - +
193F VAL* 5.1 1.8 - - + +
210F GLN* 5.0 2.7 - - - +
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Residues in contact with PHE 156 (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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117F LEU* 4.2 10.1 - - + -
118F MET 2.9 33.6 + - - -
119F ASP* 3.6 31.6 - - + -
120F LEU* 2.9 25.8 + - - -
155F ALA* 1.3 78.1 - - - +
157F VAL* 1.3 72.7 + - - +
188F PHE* 3.6 4.5 - - - -
189F GLY 3.0 20.2 - - - +
190F TYR* 4.2 0.2 - - - -
220F GLU* 4.0 11.4 - - + -
221F GLY 4.0 1.6 - - - +
222F GLY* 3.5 30.7 - - - -
225F ALA* 3.9 27.6 - - + -
248F PHE* 3.7 23.8 - + - -
249F THR 3.6 9.2 - - - -
250F THR* 4.6 2.0 - - - -
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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