Contacts of the strand formed by residues 192 - 196 (chain H) in PDB entry 2PGW
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 ARG 192 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174E GLU* 5.7 1.1 - - - +
2500E GOL 4.2 22.5 - - - +
164H ARG* 3.7 21.4 + - - +
165H VAL* 3.6 18.9 - - - +
166H PHE* 3.0 31.3 + - - -
185H ARG* 4.8 0.2 - - - +
190H ASP 5.3 1.1 - - - +
191H ALA* 1.3 73.4 - - - +
193H LEU* 1.3 60.4 + - - +
194H ARG* 3.0 25.0 - - - +
219H GLU* 3.1 26.5 + - + +
321H ASP* 4.4 0.2 + - - -
322H ASP* 2.7 44.9 + - - -
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Residues in contact with LEU 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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166H PHE* 3.6 17.0 - - + +
168H LEU* 4.2 14.1 - - + -
181H THR* 4.2 21.5 - - + +
184H VAL* 3.9 31.0 - - + -
185H ARG* 3.5 27.5 - - + +
188H ILE* 4.1 7.4 - - + -
191H ALA 3.5 1.0 + - - -
192H ARG* 1.3 72.9 - - - +
194H ARG* 1.3 71.0 + - - +
195H LEU* 4.1 8.1 - - + -
216H TYR 4.5 2.9 - - - +
217H ASP 4.3 2.5 + - - +
218H ILE* 3.6 24.3 - - + +
219H GLU* 2.9 29.0 + - - +
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Residues in contact with ARG 194 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E HIS* 4.5 1.0 + - - -
140H PHE* 5.7 0.2 - - - -
165H VAL* 3.3 22.2 - - + +
166H PHE 2.8 12.2 + - - +
167H TYR* 3.5 17.6 - - + -
168H LEU* 2.9 26.9 + - - +
192H ARG* 3.0 14.1 - - - +
193H LEU* 1.3 75.2 - - - +
195H LEU* 1.3 65.1 + - - +
219H GLU* 2.8 45.5 + - + +
220H PHE* 3.2 51.3 - - + -
267H MSE 4.1 1.2 - - - +
296H CYS* 4.3 2.2 - - - -
321H ASP* 2.7 42.2 + - - -
322H ASP* 4.1 0.2 + - - -
323H GLY* 3.4 16.9 + - - +
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Residues in contact with LEU 195 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167H TYR* 5.2 2.0 - - - -
168H LEU* 3.2 33.0 - - + +
170H VAL* 4.1 15.7 - - + -
181H THR* 4.2 4.7 - - - +
193H LEU* 4.1 13.2 - - + -
194H ARG* 1.3 82.8 - - - +
196H ASP* 1.3 54.1 + - - +
197H ALA 3.9 0.6 + - - -
213H LEU* 3.6 37.5 - - + -
218H ILE* 3.7 33.9 - - + -
220H PHE* 3.0 8.6 + - - +
221H ILE* 3.2 14.7 - - + -
222H GLU* 2.7 34.4 + - - +
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Residues in contact with ASP 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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167H TYR* 3.3 42.4 + - + +
168H LEU 2.8 12.8 + - - +
169H LYS* 3.3 27.5 - - - +
170H VAL* 2.8 28.5 + - - -
194H ARG 4.2 0.2 + - - -
195H LEU* 1.3 71.2 - - - +
197H ALA* 1.3 57.1 + - - +
198H ASN* 2.8 31.3 + - - +
222H GLU* 3.6 15.2 - - - +
223H GLN* 5.0 1.4 - - - +
247H ASP* 5.0 4.1 - - - +
248H GLN* 5.2 0.9 + - - +
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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