Contacts of the strand formed by residues 192 - 197 (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 HIS 192 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B SER* 4.3 22.2 + - - -
126B LEU* 5.0 6.3 - - + +
160B LEU 4.0 0.9 - - - +
161B GLU* 3.4 4.5 - - - +
162B VAL* 3.0 46.7 + - + +
188B SER* 6.0 0.2 - - - -
190B ASP 3.5 4.7 + - - +
191B ARG* 1.3 76.3 - - - +
193B GLN* 1.3 69.8 + - - +
194B VAL* 3.7 24.7 - - + +
219B LEU* 3.9 27.1 - - + +
220B GLY 4.1 14.0 + - - -
221B GLN* 5.8 1.6 - - - -
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Residues in contact with GLN 193 (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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159B LEU* 3.7 26.8 - - + +
160B LEU 3.6 3.6 - - - -
161B GLU* 2.8 28.9 + - + +
191B ARG* 3.5 39.2 + - - +
192B HIS* 1.3 87.4 + - - +
194B VAL* 1.3 69.4 + - - +
195B ILE* 5.9 0.4 - - + -
241B LYS* 5.5 2.3 - - - +
242B PHE* 4.6 17.4 + - - +
243B PRO 5.8 0.8 + - - -
245B TYR* 4.5 4.8 - - - -
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Residues in contact with VAL 194 (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 MET 3.6 0.5 - - - +
159B LEU* 3.4 4.6 - - - +
160B LEU* 2.9 54.5 + - + +
192B HIS* 3.7 23.6 - - + +
193B GLN* 1.3 81.2 - - - +
195B ILE* 1.4 63.3 + - - +
196B VAL* 4.5 7.4 - - + -
219B LEU* 3.9 26.7 - - + -
220B GLY 4.3 3.4 - - - +
224B ILE* 4.8 1.3 - - + -
237B LEU* 3.7 37.7 - - + -
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Residues in contact with ILE 195 (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 TYR* 3.7 33.9 - - + +
157B GLY* 4.2 2.9 - - - -
158B MET 3.4 21.5 - - - +
159B LEU* 4.3 4.3 - - + -
193B GLN* 5.9 0.4 - - + -
194B VAL* 1.4 76.7 - - - +
196B VAL* 1.3 62.5 + - - +
237B LEU* 3.4 9.7 - - - +
238B VAL* 2.9 55.3 + - + +
240B GLY 3.3 30.7 - - - +
242B PHE* 3.7 34.1 - - + +
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Residues in contact with VAL 196 (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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157B GLY* 3.1 1.9 - - - -
158B MET* 2.8 34.0 + - - +
160B LEU* 3.5 24.9 - - + -
194B VAL* 4.5 2.7 - - + -
195B ILE* 1.3 73.7 - - - +
197B PRO* 1.4 75.7 - - + +
200B GLY 4.2 1.8 - - - -
201B ILE* 3.7 40.9 - - + +
204B LEU* 5.8 0.2 - - + -
224B ILE* 4.0 32.1 - - + -
233B PHE* 5.4 2.0 - - + -
235B SER* 3.9 13.0 - - - +
237B LEU* 4.2 6.3 - - + -
238B VAL* 4.2 0.7 - - - -
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Residues in contact with PRO 197 (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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50B GLU* 3.6 41.3 - - + +
156B ASN 3.8 4.0 - - - +
195B ILE 4.0 0.9 - - - +
196B VAL* 1.4 87.8 - - + +
198B ARG* 1.3 67.3 + - - +
199B LYS 4.6 1.6 - - - +
200B GLY* 3.1 5.9 + - - +
201B ILE* 3.0 20.1 + - - +
235B SER* 3.8 4.0 - - - +
236B LYS* 3.0 30.3 - - + +
237B LEU 4.7 0.7 - - - -
238B VAL* 3.7 26.8 - - + +
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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