Contacts of the helix formed by residues 142 - 146 (chain B) in PDB entry 4TR8
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 142 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B LEU 2.9 16.4 + - - +
139B ILE 3.1 0.4 + - - -
140B ASP 3.2 0.2 - - - -
141B ARG* 1.4 84.5 - - - +
143B SER* 1.3 65.5 + - - +
144B PHE* 3.2 5.8 - - - -
145B ALA* 3.1 16.7 + - - +
158B MET* 3.1 20.5 - - - +
169B SER* 3.4 22.5 + - - +
171B ALA* 3.3 15.3 - - - +
178B ALA* 3.6 13.5 - - - +
179B MET* 3.7 34.8 - - - +
180B CYS* 3.7 4.3 - - + +
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Residues in contact with SER 143 (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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139B ILE* 2.8 25.7 + - - +
140B ASP* 4.4 11.6 + - - -
142B THR* 1.3 72.2 + - - +
144B PHE* 1.3 62.1 + - - +
145B ALA 3.2 0.9 + - - -
146B MET* 3.3 28.2 + - - +
158B MET* 3.6 17.3 - - - -
198B ARG* 5.0 1.7 + - - -
202B LEU* 3.6 30.9 - - - +
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Residues in contact with PHE 144 (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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140B ASP 4.9 1.3 + - - -
141B ARG 3.6 12.1 - - - -
142B THR* 4.2 4.7 - - - -
143B SER* 1.3 79.2 + - - +
145B ALA* 1.4 66.1 + - + +
146B MET 3.4 4.8 + - - +
176B ARG* 3.4 33.3 + - + -
177B LEU 5.4 1.6 - - - -
178B ALA* 3.9 8.1 - - + -
327B ASP* 3.4 38.8 - - + +
328B VAL* 4.1 18.8 - - + -
331B VAL* 3.5 37.2 - - + -
360B TYR* 3.7 24.0 - + - -
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Residues in contact with ALA 145 (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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142B THR 3.1 12.3 + - - +
144B PHE* 1.4 80.8 - - + +
146B MET* 1.3 62.7 + - - +
171B ALA* 3.4 20.4 - - - +
172B THR 3.0 25.6 - - - -
173B ASP* 3.1 7.1 + - - +
176B ARG* 3.8 23.6 - - - +
177B LEU* 4.2 2.0 - - - -
178B ALA* 3.7 18.6 - - + +
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Residues in contact with MET 146 (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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143B SER* 3.3 24.3 + - - +
144B PHE 4.1 5.2 - - - +
145B ALA* 1.3 78.9 - - - +
147B ALA* 1.3 65.1 + - - +
148B GLN* 5.1 0.7 - - - +
155B LEU 4.0 3.4 - - - +
157B GLY* 3.3 37.9 - - - +
158B MET* 3.8 6.1 - - + -
171B ALA* 3.6 17.2 - - + +
172B THR 4.3 2.0 - - - +
173B ASP* 4.3 3.7 - - - +
176B ARG* 5.5 1.0 + - - -
198B ARG* 3.6 38.0 + - + +
201B ILE* 3.6 28.5 - - + -
202B LEU* 3.9 21.8 - - + -
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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