Contacts of the strand formed by residues 192 - 196 (chain H) in PDB entry 1PQB
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 TYR 192 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183H ILE* 3.6 24.1 - - + +
187H LEU* 3.2 26.5 - - + +
188H GLU* 3.8 11.0 - - + -
191H GLY* 1.3 75.0 - - - +
193H THR* 1.3 64.6 + - - +
203H LEU* 3.8 27.1 - - + -
204H SER 3.2 15.5 - - - +
206H TRP* 3.7 4.9 - - - +
218H LYS* 3.6 2.4 - - - +
219H TYR* 2.7 69.7 + + + +
221H SER* 2.7 34.4 + - - -
235H ASP* 4.1 2.3 - - - +
239H VAL* 4.1 14.5 - - + +
254H PRO* 3.6 14.4 - - - +
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Residues in contact with THR 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192H TYR* 1.3 75.5 - - - +
194H VAL* 1.3 73.0 + - - +
195H ASP* 5.9 0.7 - - + -
203H LEU* 3.3 6.1 - - - +
204H SER* 2.8 37.0 + - - +
206H TRP* 3.7 9.2 - - + -
211H HIS* 3.6 34.5 - - + +
216H LEU* 3.4 30.7 - - + +
217H THR 2.8 24.6 + - - -
219H TYR* 4.1 5.1 - - - -
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Residues in contact with VAL 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192H TYR* 4.9 1.3 - - + -
193H THR* 1.3 91.6 + - - +
195H ASP* 1.3 61.2 + - - +
196H VAL* 4.4 5.9 + - + +
201H THR* 4.0 14.4 - - + -
202H PHE 3.0 6.7 - - - +
203H LEU* 3.9 18.2 - - + -
216H LEU* 3.8 11.6 - - - +
217H THR 5.7 0.2 + - - -
219H TYR* 4.5 16.4 - - + +
239H VAL* 3.2 50.5 - - + +
240H THR* 5.2 0.4 - - - +
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Residues in contact with ASP 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52H ASN* 2.7 33.9 + - - +
193H THR* 5.4 1.1 - - + +
194H VAL* 1.3 75.6 - - - +
196H VAL* 1.3 68.0 + - - +
197H LYS* 3.3 29.4 + - + +
201H THR* 4.3 0.9 - - - -
202H PHE* 2.7 45.3 + - + +
214H LYS* 5.6 2.3 - - - +
216H LEU* 3.7 21.6 - - + +
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Residues in contact with VAL 196 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194H VAL* 5.5 5.4 - - + +
195H ASP* 1.3 79.6 + - - +
197H LYS* 1.3 72.9 + - - +
199H LYS 6.2 0.4 - - - -
200H ARG 3.5 8.7 - - - +
201H THR* 3.4 23.3 - - + +
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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