Contacts of the strand formed by residues 174 - 180 (chain F) in PDB entry 3TKR
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 174 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42F ALA* 3.8 12.6 - - + -
43F LYS 3.7 30.5 - - - +
44F ILE* 3.4 7.8 - - + -
45F SER* 2.7 32.7 + - - -
46F LYS 2.9 17.2 + - - +
48F ALA* 3.9 11.4 - - + +
49F PRO* 5.2 2.9 - - + -
151F TYR* 5.4 0.9 - - + -
166F PHE* 3.7 23.3 - - + -
167F ILE 3.6 11.2 - - - +
168F ILE* 4.0 10.3 - - + +
172F GLY 3.8 2.2 + - - -
173F ILE* 1.3 70.9 - - - +
175F ARG* 1.3 58.3 + - - +
176F GLN 3.6 21.3 - - - +
177F ILE* 3.7 24.0 - - + -
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Residues in contact with ARG 175 (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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181D ASP* 2.9 60.3 + - - +
183D PRO* 3.7 16.8 - - - +
44F ILE* 4.0 5.6 - - - +
73F TYR* 3.3 14.1 + - + +
167F ILE* 2.8 15.8 + - + +
169F ASP* 3.2 35.2 + - + +
173F ILE* 3.4 21.9 - - - +
174F LEU* 1.3 77.6 - - - +
176F GLN* 1.3 60.3 + - + +
198F PHE* 3.3 40.3 - - + -
201F THR* 4.7 1.0 + - - -
202F ASP* 2.9 28.3 + - - -
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Residues in contact with GLN 176 (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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178D THR* 3.6 12.1 - - - +
179D LEU 3.4 6.9 + - - +
180D ASN* 3.0 29.5 + - - +
44F ILE* 4.2 1.7 - - - +
165F LEU* 4.2 4.7 - - - +
166F PHE* 3.4 5.2 - - - -
167F ILE* 3.0 46.8 + - + +
174F LEU* 3.6 6.0 - - - +
175F ARG* 1.3 80.5 - - - +
177F ILE* 1.3 84.2 + - - +
178F THR* 2.7 30.0 + - - -
194F LEU* 3.8 22.9 - - + +
198F PHE* 3.9 18.2 - - + -
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Residues in contact with ILE 177 (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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177D ILE 3.8 1.3 - - - +
178D THR* 3.6 1.2 - - - -
179D LEU* 2.9 57.2 + - + -
42F ALA* 4.2 14.8 - - + +
44F ILE* 4.0 17.3 - - + +
165F LEU 3.5 2.5 - - - +
166F PHE* 3.8 26.5 - - + -
174F LEU* 3.7 22.4 - - + -
176F GLN* 1.3 82.0 + - - +
178F THR* 1.3 63.8 + - - +
179F LEU* 3.6 33.7 - - + -
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Residues in contact with THR 178 (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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176D GLN* 3.6 19.3 - - - +
177D ILE 3.6 2.2 - - - -
178D THR* 4.7 4.6 - - + +
194D LEU* 6.0 1.1 - - + -
163F ARG 3.4 2.6 - - - +
164F GLY* 3.3 1.7 - - - -
165F LEU* 2.7 53.2 + - + +
176F GLN* 2.7 31.7 + - - -
177F ILE* 1.3 72.1 - - - +
179F LEU* 1.3 63.4 + - - +
180F ASN* 3.9 8.5 - - - +
186F ARG* 4.7 13.2 - - + -
194F LEU* 4.8 4.3 - - - +
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Residues in contact with LEU 179 (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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44D ILE* 3.3 19.0 - - + +
176D GLN* 3.3 6.1 + - - -
177D ILE* 2.8 65.4 + - + +
179D LEU* 6.0 0.9 - - + -
38F HIS* 6.2 4.9 - - + -
151F TYR 5.5 0.2 - - - +
152F GLY 5.3 7.4 - - - +
153F VAL* 4.0 16.8 - - + -
162F LEU* 4.3 9.6 - - + -
163F ARG 3.5 2.5 - - - -
164F GLY* 3.7 16.8 - - - -
166F PHE* 4.3 4.3 - - + -
177F ILE* 3.6 26.7 - - + -
178F THR* 1.3 79.0 - - - +
180F ASN* 1.3 63.5 + - - +
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Residues in contact with ASN 180 (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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44D ILE* 4.4 3.8 - - - -
175D ARG 4.1 2.7 - - - -
176D GLN* 3.0 32.2 + - - +
194D LEU* 3.7 16.7 - - - +
198D PHE* 4.8 2.0 - - + -
162F LEU* 3.7 5.4 - - - +
163F ARG* 2.9 38.8 + - + +
178F THR* 3.9 6.4 - - - +
179F LEU* 1.3 73.8 - - - +
181F ASP* 1.3 64.7 + - - +
184F VAL* 3.0 30.3 + - - +
185F GLY 3.4 18.2 + - - -
186F ARG* 3.8 12.6 - - - +
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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