Contacts of the strand formed by residues 184 - 190 (chain B) in PDB entry 1ZR3
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 184 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B GLY 4.7 2.8 + - - -
183B PHE* 1.3 81.4 + - - +
185B VAL* 1.3 67.5 + - - +
186B LEU* 3.7 18.7 + - + -
200B VAL* 3.1 5.9 - - - +
201B GLN* 2.8 48.7 + - - +
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Residues in contact with VAL 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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183B PHE* 3.5 24.7 + - + -
184B THR* 1.3 78.4 - - - +
186B LEU* 1.3 63.9 + - - +
187B SER* 3.9 10.3 - - - +
188B THR* 3.6 24.0 - - - +
198B GLN* 3.4 30.1 - - - +
199B VAL 3.8 3.6 - - - +
200B VAL* 3.9 3.1 - - + -
247C LYS* 4.0 18.8 - - + +
248C LYS* 3.7 15.8 - - + +
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Residues in contact with LEU 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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184B THR* 3.9 23.3 - - + +
185B VAL* 1.3 77.8 - - - +
187B SER* 1.3 61.0 + - - +
199B VAL* 2.7 27.3 + - + +
200B VAL 4.4 1.1 - - - -
201B GLN* 3.8 31.6 - - + +
356B ILE* 3.5 45.8 - - + -
360B VAL* 5.8 0.2 - - + -
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Residues in contact with SER 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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185B VAL* 3.7 2.1 - - - +
186B LEU* 1.3 83.7 - - - +
188B THR* 1.3 69.6 + - - +
197B LEU 3.8 0.2 - - - +
198B GLN* 3.1 5.2 - - - +
199B VAL* 2.8 29.7 + - - +
360B VAL* 3.5 35.7 - - - +
363B MET* 3.5 15.5 - - - +
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Residues in contact with THR 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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185B VAL* 3.6 8.3 - - - +
187B SER* 1.3 81.6 + - - +
189B LYS* 1.3 66.1 + - - +
190B SER* 4.0 18.4 - - - +
196B LYS* 4.1 14.4 - - + -
197B LEU 3.2 3.8 - - - +
198B GLN* 3.0 36.5 + - + +
363B MET* 4.3 4.0 - - - +
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Residues in contact with LYS 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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188B THR* 1.3 75.8 - - - +
190B SER* 1.3 73.6 + - - +
191B LEU* 3.6 21.1 + - + +
196B LYS* 3.5 0.5 - - - -
197B LEU* 2.7 45.5 + - + +
363B MET* 3.3 43.2 - - + +
364B ALA* 4.0 14.8 + - - +
366B LEU* 2.8 27.5 + - + +
367B ASP* 2.9 18.5 + - - +
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Residues in contact with SER 190 (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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188B THR* 4.0 14.3 + - - +
189B LYS* 1.3 84.5 + - - +
191B LEU* 1.3 65.7 + - - +
192B PHE* 3.9 7.6 + - - -
195B GLN 3.6 5.8 - - - -
196B LYS* 4.2 10.8 - - - +
367B ASP* 5.1 1.2 - - - +
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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