Contacts of the strand formed by residues 163 - 168 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78E PHE 3.9 0.4 - - - -
80E PRO* 3.3 21.7 - - + +
84E THR* 5.2 1.2 + - - -
86E VAL* 3.4 24.3 - - - +
87E CYS* 3.2 37.4 - - - +
90E GLU* 3.0 29.9 + - - -
162E LEU* 1.3 79.0 - - - +
164E GLY* 1.3 55.7 + - - +
178E THR 3.4 2.9 - - - +
179E LEU* 3.4 1.7 - - - -
180E ASN* 2.8 43.2 + - + +
181E ASP 4.0 2.9 - - - +
182E LEU* 2.8 31.5 + - - +
184E VAL 3.5 22.7 - - - -
186E ARG* 3.3 28.7 + - - +
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Residues in contact with GLY 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E PHE* 3.5 0.9 - - - -
78E PHE* 2.8 36.5 + - - +
153E VAL* 4.0 10.8 - - - -
162E LEU 3.2 9.9 + - - -
163E ARG* 1.3 71.0 - - - +
165E LEU* 1.3 59.6 + - - -
166E PHE* 3.9 5.6 - - - -
178E THR 3.4 4.3 - - - -
179E LEU* 3.5 19.1 - - - -
186E ARG* 3.1 6.5 + - - +
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Residues in contact with LEU 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E VAL* 3.8 14.6 - - + -
76E PHE 3.8 2.5 - - - -
77E PHE* 3.9 13.0 - - + -
94E PHE* 3.8 21.1 - - + -
164E GLY* 1.3 74.7 - - - -
166E PHE* 1.3 70.4 + - - +
167E ILE* 3.9 27.8 - - + -
176E GLN* 4.2 9.4 - - - +
177E ILE* 3.5 4.7 - - - +
178E THR* 2.7 46.2 + - - +
179E LEU* 4.5 0.2 - - - +
186E ARG* 3.9 24.0 - - + +
191E THR* 3.7 22.9 - - + +
194E LEU* 6.2 0.7 - - + -
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Residues in contact with PHE 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42E ALA* 4.0 7.4 - - + -
74E LEU 3.4 2.3 - - - +
75E VAL* 3.5 3.1 - - - -
76E PHE* 2.8 52.5 + - + +
78E PHE* 3.6 29.8 - + - -
151E TYR* 3.4 51.1 - + + -
153E VAL* 3.6 13.7 - - + -
164E GLY 3.9 8.3 - - - -
165E LEU* 1.3 76.8 - - - +
167E ILE* 1.3 64.0 + - - +
168E ILE* 3.9 2.9 - - + -
174E LEU* 3.8 17.3 - - + -
176E GLN 3.4 2.0 - - - -
177E ILE* 3.7 35.2 - - + -
179E LEU* 4.1 8.1 - - + -
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Residues in contact with ILE 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73E TYR* 3.9 28.5 - - + -
74E LEU 3.6 4.5 - - - +
75E VAL* 4.7 9.9 - - + -
165E LEU* 3.9 16.2 - - + -
166E PHE* 1.3 74.7 - - - +
168E ILE* 1.3 62.3 + - - +
174E LEU* 3.5 2.1 - - - +
175E ARG* 2.8 33.7 + - + +
176E GLN* 3.0 34.7 + - + +
191E THR* 4.3 11.9 - - + +
194E LEU* 3.7 33.2 - - + -
195E VAL* 4.3 12.1 - - + -
198E PHE* 4.9 5.2 - - + -
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Residues in contact with ILE 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E ALA* 3.6 26.9 - - + -
66E LEU* 4.2 20.6 - - + -
73E TYR* 3.3 7.9 - - - -
74E LEU* 2.7 47.5 + - + +
76E PHE* 4.1 24.7 - - + -
151E TYR* 4.0 11.2 - - + +
166E PHE* 4.5 6.3 - - + +
167E ILE* 1.3 77.7 - - - +
169E ASP* 1.3 71.2 + - - +
172E GLY* 3.7 26.5 - - - +
173E ILE 3.5 4.5 - - - +
174E LEU* 4.0 10.1 - - + -
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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