Contacts of the helix formed by residues 153 - 160 (chain B) in PDB entry 1T6S
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 THR 153 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B GLY* 2.6 26.5 + - - +
134B LEU 3.2 6.3 + - - -
135B ILE* 3.4 33.0 - - - +
136B GLU* 3.6 26.5 - - + +
152B THR* 1.3 74.2 - - - +
154B GLU* 1.3 58.9 + - - +
155B VAL* 2.9 9.2 - - + +
156B PHE* 2.9 28.9 + - - +
157B LEU* 3.0 19.2 + - - +
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Residues in contact with GLU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LEU* 6.2 0.3 - - - -
136B GLU* 5.4 0.2 + - - -
153B THR* 1.3 73.3 - - - +
155B VAL* 1.3 58.8 + - + +
157B LEU* 3.7 25.2 - - - +
158B ASP* 2.8 55.2 + - - +
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ARG 4.9 5.6 - - - +
133B GLY* 3.5 17.9 - - - +
134B LEU* 5.0 4.5 - - + -
153B THR* 3.3 16.8 - - - +
154B GLU* 1.3 81.9 - - + +
156B PHE* 1.3 62.0 + - - +
158B ASP* 4.0 4.6 - - - +
159B LEU* 3.1 28.8 + - + +
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Residues in contact with PHE 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A SER* 3.5 18.2 - - - -
97A LEU* 4.1 20.2 - - + -
408A NO3 3.4 20.6 - - - -
100B LEU* 4.1 24.9 - - + -
134B LEU* 3.6 36.5 - - + +
152B THR* 3.7 22.2 - - + -
153B THR* 2.9 13.3 + - - +
155B VAL* 1.3 74.1 - - - +
157B LEU* 1.3 77.9 + - + +
159B LEU* 3.3 2.3 + - - +
160B PHE* 3.0 64.9 + + + +
162B LEU* 4.5 2.5 - - + -
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Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LEU 4.3 6.5 - - - +
89A GLN* 3.4 37.2 - - - +
408A NO3 3.9 5.8 - - - +
152B THR* 5.0 2.5 - - - +
153B THR 3.0 17.0 + - - +
154B GLU* 3.8 32.8 - - - +
156B PHE* 1.3 95.1 - - + +
158B ASP* 1.3 62.5 + - - +
160B PHE 3.4 0.5 + - - -
161B HIS* 3.0 3.6 + - - -
162B LEU* 3.0 61.2 + - + +
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Residues in contact with ASP 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B GLU* 2.8 44.7 + - - +
155B VAL* 4.0 5.8 - - - +
157B LEU* 1.3 72.9 - - - +
159B LEU* 1.3 63.3 + - - +
161B HIS* 3.1 22.8 + - - +
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ARG* 5.6 1.7 - - - +
159A LEU* 3.4 55.7 - - + +
160A PHE* 5.5 2.0 - - + -
134B LEU* 4.5 18.6 - - + -
155B VAL* 3.1 22.4 + - + +
156B PHE* 3.7 3.8 - - - +
158B ASP* 1.3 78.2 - - - +
160B PHE* 1.3 67.0 + - + +
161B HIS* 3.3 15.5 + - - -
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Residues in contact with PHE 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A MET* 3.3 27.6 - - + +
97A LEU* 3.8 24.7 - - + -
100A LEU* 4.1 8.7 - - + -
132A ARG* 2.7 29.6 + - - +
134A LEU* 3.9 21.3 - - + -
159A LEU* 5.5 1.8 - - + -
160A PHE* 3.5 39.5 - + - -
134B LEU* 5.4 1.6 - - + -
156B PHE* 3.0 43.5 + + + +
159B LEU* 1.3 89.4 - - + +
161B HIS* 1.3 63.0 + - - +
162B LEU* 3.2 24.7 + - + +
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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