Contacts of the strand formed by residues 184 - 189 (chain B) in PDB entry 1TAR
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 SER 184 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123B PHE* 4.7 0.2 - - - -
126B SER* 4.1 16.2 + - - -
130B ASP* 4.4 2.2 + - - +
134B TYR* 4.0 13.0 - - - -
180B ILE* 3.5 19.6 - - - +
181B PRO* 2.9 36.1 + - - +
182B GLU 3.2 1.5 + - - -
183B LYS* 1.3 80.8 - - - +
185B ILE* 1.3 63.9 + - - +
217B LEU* 3.7 8.0 - - - +
218B LEU* 3.0 23.7 + - - +
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Residues in contact with ILE 185 (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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119B LEU* 4.3 22.4 - - + -
123B PHE* 3.5 38.4 - - + -
126B SER 4.0 10.1 - - - +
129B ARG 5.2 0.9 - - - -
130B ASP 3.1 20.9 + - - +
133B VAL* 3.6 26.0 - - + -
134B TYR* 2.8 31.3 + - - +
152B LEU* 5.3 2.9 - - + -
180B ILE* 6.0 0.2 - - - -
184B SER* 1.3 76.4 - - - +
186B ILE* 1.3 69.2 + - - +
187B LEU* 5.5 0.2 - - - -
217B LEU* 5.8 0.2 - - - -
218B LEU* 3.6 23.3 - - + +
220B TYR* 4.4 15.3 - - + -
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Residues in contact with ILE 186 (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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134B TYR* 3.8 4.7 - - + +
158B TYR* 3.6 35.9 - - + +
177B ILE* 3.8 32.8 - - + -
180B ILE* 4.0 10.3 - - + -
184B SER 3.9 0.6 + - - -
185B ILE* 1.3 77.3 - - - +
187B LEU* 1.3 60.3 + - - +
188B LEU* 3.8 14.9 + - + +
212B VAL* 4.6 7.0 - - + -
217B LEU* 4.0 23.3 - - + -
218B LEU 3.0 15.0 + - - +
219B ALA* 3.5 14.3 - - + -
220B TYR 2.9 26.5 + - - -
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Residues in contact with LEU 187 (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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112B LEU* 4.5 9.0 - - + -
133B VAL* 4.6 5.4 - - + -
134B TYR 2.9 19.5 + - - +
135B LEU* 3.7 15.5 - - + -
136B PRO* 3.9 6.8 - - + +
143B HIS* 3.7 35.2 - - + +
147B PHE* 3.6 37.0 - - + -
158B TYR* 3.0 20.1 + - - -
185B ILE* 4.2 1.2 - - - +
186B ILE* 1.3 69.9 - - - +
188B LEU* 1.3 65.1 + - - +
189B HIS* 3.9 17.3 - - + +
220B TYR* 3.4 19.3 - - + +
222B ASP* 4.8 4.5 - - + -
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Residues in contact with LEU 188 (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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158B TYR* 3.5 24.5 - - + +
160B TYR* 6.1 3.4 - - + -
177B ILE* 5.9 2.7 - - + -
186B ILE* 4.2 19.5 - - + +
187B LEU* 1.3 78.3 - - - +
189B HIS* 1.4 60.7 + - - +
190B ALA 3.7 0.2 + - - -
205B TRP* 4.6 13.7 - - + -
208B LEU* 5.8 7.2 - - + -
212B VAL* 5.0 4.0 - - + -
219B ALA* 4.0 16.4 - - + -
220B TYR 2.8 11.7 + - - +
221B PHE* 3.2 26.1 - - + -
222B ASP 2.7 32.2 + - - -
243B PHE* 3.7 32.5 - - + -
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Residues in contact with HIS 189 (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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136B PRO* 3.9 8.7 - - + +
139B SER* 2.9 24.7 + - - -
140B TRP 4.3 0.2 - - - -
143B HIS* 3.8 17.5 - + - -
160B TYR* 5.5 3.2 + - - +
187B LEU* 3.9 12.1 - - + -
188B LEU* 1.4 73.5 - - - +
190B ALA* 1.3 64.5 + - - +
191B CYS* 3.4 6.1 + - - +
192B ALA 5.0 0.8 + - - -
193B HIS* 3.5 35.1 + + + -
194B ASN 3.0 42.2 + - - -
199B ASP* 5.4 1.6 - - - +
200B PRO* 5.6 0.7 - - - +
205B TRP* 3.7 18.4 - - - -
221B PHE* 4.7 1.6 - - - -
222B ASP* 3.7 11.0 - - + +
411B PLP 4.0 13.3 - - + +
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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