Contacts of the strand formed by residues 163 - 168 (chain J) 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 ARG 163 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80J PRO* 3.4 18.2 - - + +
84J THR* 5.4 0.4 + - - -
86J VAL* 3.4 24.1 - - - +
87J CYS* 3.3 36.0 - - - +
90J GLU* 3.0 29.9 + - - -
162J LEU* 1.3 78.6 - - - +
164J GLY* 1.3 55.4 + - - +
178J THR 3.5 4.7 - - - +
180J ASN* 2.9 37.7 + - + +
181J ASP 4.1 2.5 - - - +
182J LEU* 2.7 33.3 + - - +
184J VAL 3.3 23.5 + - - -
186J ARG* 3.2 28.8 + - - +
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Residues in contact with GLY 164 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77J PHE* 3.4 1.2 - - - -
78J PHE* 2.7 39.2 + - - +
153J VAL* 4.2 7.4 - - - -
162J LEU* 3.1 13.3 + - - -
163J ARG* 1.3 71.4 - - - +
165J LEU* 1.3 58.8 + - - -
166J PHE* 3.8 5.4 - - - -
178J THR 3.4 5.8 - - - -
179J LEU* 3.6 17.0 - - - -
186J ARG* 3.1 6.5 + - - +
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Residues in contact with LEU 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75J VAL* 3.9 14.6 - - + -
76J PHE 3.8 2.5 - - - -
77J PHE* 3.8 15.7 - - + -
94J PHE* 3.7 21.3 - - + -
164J GLY* 1.3 73.1 - - - -
166J PHE* 1.3 70.7 + - - +
167J ILE* 3.8 26.9 - - + -
176J GLN* 4.3 8.5 - - - +
177J ILE* 3.5 4.7 - - - +
178J THR* 2.7 46.6 + - + +
186J ARG* 3.6 22.0 - - + +
191J THR* 3.6 24.7 - - + +
194J LEU* 6.2 0.4 - - + -
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Residues in contact with PHE 166 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42J ALA* 4.0 9.6 - - + -
74J LEU 3.5 2.4 - - - +
75J VAL* 3.5 3.1 - - - -
76J PHE* 2.8 49.5 + + + +
78J PHE* 3.6 24.9 - + - -
151J TYR* 3.3 52.3 - + + -
153J VAL* 3.6 15.5 - - + -
164J GLY 3.8 9.9 - - - -
165J LEU* 1.3 79.5 - - - +
167J ILE* 1.3 62.2 + - - +
168J ILE* 3.9 7.2 - - + -
174J LEU* 3.8 24.5 - - + -
176J GLN 3.5 2.0 - - - -
177J ILE* 3.8 24.7 - - + -
179J LEU* 4.2 8.5 - - + -
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Residues in contact with ILE 167 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73J TYR* 4.0 28.5 - - + -
74J LEU 3.6 4.7 - - - +
75J VAL* 4.6 8.7 - - + -
165J LEU* 3.8 16.6 - - + -
166J PHE* 1.3 74.4 - - - +
168J ILE* 1.3 62.5 + - - +
174J LEU* 3.5 2.9 - - - +
175J ARG* 2.8 31.6 + - + +
176J GLN* 3.0 36.6 + - + +
191J THR* 4.2 6.3 - - + +
194J LEU* 3.7 33.4 - - + -
195J VAL* 4.1 21.8 - - + +
198J PHE* 4.9 3.1 - - + -
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Residues in contact with ILE 168 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48J ALA* 3.6 25.6 - - + -
66J LEU* 4.1 21.1 - - + -
73J TYR* 3.4 6.9 - - - -
74J LEU* 2.7 49.1 + - + +
76J PHE* 4.1 23.6 - - + -
151J TYR* 4.0 12.1 - - + +
166J PHE* 4.5 5.6 - - + +
167J ILE* 1.3 79.9 - - - +
169J ASP* 1.3 67.8 + - - +
172J GLY* 3.6 30.7 - - - +
173J ILE 3.6 4.5 - - - +
174J LEU* 4.0 9.4 - - + -
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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