Contacts of the helix formed by residues 192 - 197 (chain B) in PDB entry 2YZ5
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 192 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B VAL 4.8 2.9 - - - +
191B ASN* 1.3 68.9 - - - +
193B ALA* 1.3 63.8 + - - +
194B GLY 2.9 2.5 - - - -
195B LEU* 2.9 24.1 + - - +
196B ARG* 3.7 10.6 + - - -
202B VAL* 4.5 7.9 - - + -
221B LEU* 6.0 1.6 - - + -
222B GLY 3.0 10.2 + - - +
223B SER* 3.3 19.2 - - - -
233B PHE* 2.9 34.1 + - - +
234B ALA 4.5 0.2 - - - +
235B PHE* 4.1 11.4 - - + -
238B VAL* 3.5 33.2 - - + -
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Residues in contact with ALA 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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191B ASN* 2.9 20.3 + - - +
192B THR* 1.3 79.4 + - - +
194B GLY* 1.3 57.5 + - - +
196B ARG* 2.9 49.8 + - - +
197B ARG* 3.2 29.4 + - - +
203B TYR* 3.9 6.7 - - + -
223B SER 3.5 1.2 + - - -
224B ASP* 3.5 12.6 - - + +
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Residues in contact with GLY 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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191B ASN 3.5 2.0 + - - -
192B THR 2.9 1.8 - - - -
193B ALA* 1.3 78.9 - - - +
195B LEU* 1.3 57.9 + - - +
197B ARG* 3.5 5.8 + - - +
199B ALA* 3.7 4.4 - - - +
200B LYS 3.0 12.8 + - - -
201B GLU 3.0 35.9 + - - +
203B TYR* 3.2 32.2 - - - -
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Residues in contact with LEU 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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192B THR* 2.9 13.6 + - - +
194B GLY* 1.3 77.8 - - - +
196B ARG* 1.3 60.1 + - - +
197B ARG 3.3 5.1 + - - +
200B LYS* 3.9 16.0 - - - +
201B GLU* 3.8 22.9 - - - +
202B VAL* 3.8 27.1 - - + +
233B PHE* 3.9 11.4 - - + -
234B ALA* 3.6 28.9 - - + -
237B GLU* 5.5 3.6 - - + -
238B VAL* 4.2 7.2 - - + -
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Residues in contact with ARG 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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192B THR* 3.8 0.6 + - - +
193B ALA* 2.9 30.5 + - - +
195B LEU* 1.3 78.0 - - - +
197B ARG* 1.3 85.2 + - - +
198B PRO* 4.9 0.2 - - - +
223B SER* 2.8 30.9 + - - -
224B ASP 3.2 19.2 + - - -
225B ALA 4.1 0.2 - - - +
230B GLU* 3.6 35.0 + - - -
233B PHE* 3.4 57.5 - - + +
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Residues in contact with ARG 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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160B LYS* 3.4 39.4 - - + +
161B PHE* 6.0 0.7 - - - -
193B ALA* 3.2 26.3 + - - +
194B GLY 3.5 3.8 + - - +
195B LEU 3.3 0.7 - - - +
196B ARG* 1.3 125.2 + - - +
198B PRO* 1.3 67.9 - - + +
199B ALA* 2.8 4.4 + - + +
200B LYS* 2.7 33.6 + - - +
203B TYR* 4.0 17.0 + - - +
224B ASP 4.9 3.6 + - - -
226B HIS* 5.0 7.5 + - - -
230B GLU* 5.4 4.0 + - - -
2002B PO4 5.2 7.3 + - - -
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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