Contacts of the strand formed by residues 198 - 203 (chain B) in PDB entry 1PL8
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 GLN 198 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A SER* 4.7 6.7 - - - -
173B HIS 3.4 3.6 + - - +
174B LYS* 3.3 27.6 - - + +
175B VAL 2.8 25.8 + - - +
197B ALA* 1.3 87.6 - - + +
199B VAL* 1.3 64.8 + - - +
200B VAL 4.2 0.4 - - - -
218B ASP* 3.2 17.5 - - + +
219B LEU* 3.8 17.6 - - + +
238B GLN 5.2 1.2 + - - -
239B LEU* 3.9 37.1 + - + +
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Residues in contact with VAL 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B VAL* 3.2 11.2 - - + +
177B VAL* 3.8 24.0 - - + -
188B LEU* 3.4 28.3 - - + -
191B ALA* 3.8 25.4 - - + -
192B LYS* 4.0 17.3 - - + -
196B ALA* 3.9 13.0 - - + -
198B GLN* 1.3 77.0 - - - +
200B VAL* 1.3 63.9 + - - +
201B VAL* 4.0 6.3 - - + -
217B ALA* 4.0 1.0 - - - -
218B ASP* 2.8 32.0 + - - +
219B LEU 3.2 7.4 + - - +
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Residues in contact with VAL 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B VAL 2.8 9.6 + - - +
176B LEU* 3.4 16.0 - - + +
177B VAL* 2.7 33.1 + - - +
199B VAL* 1.3 73.6 - - - +
201B VAL* 1.3 63.1 + - - +
202B THR* 5.1 0.9 - - + -
219B LEU* 3.2 30.7 - - + +
220B VAL* 4.5 3.1 - - - +
221B LEU* 4.9 7.0 - - + -
235B VAL* 4.7 10.8 - - + +
238B GLN* 4.5 11.4 - - + +
239B LEU* 3.2 47.3 - - + -
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B VAL* 3.2 12.8 - - + +
179B GLY 3.7 17.7 - - - +
180B ALA* 3.9 15.0 - - + -
185B MET* 4.0 7.6 - - + -
188B LEU* 4.4 13.0 - - + -
199B VAL* 4.0 14.8 - - + -
200B VAL* 1.3 78.6 - - - +
202B THR* 1.3 74.8 - - - +
209B LEU* 3.6 9.6 - - + +
212B ALA* 4.4 5.2 - - + -
217B ALA* 3.9 22.2 - - + -
219B LEU 2.9 9.7 + - - +
220B VAL* 3.1 4.8 - - + -
221B LEU 2.8 23.4 + - - -
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Residues in contact with THR 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B LEU* 3.8 23.1 - - + -
177B VAL 3.0 4.4 + - - -
178B CYS* 3.2 24.9 - - - +
179B GLY* 2.8 27.5 + - - -
200B VAL* 5.1 1.1 - - + -
201B VAL* 1.3 77.6 - - - +
203B ASP* 1.3 66.1 + - - +
209B LEU* 3.8 1.3 - - - -
221B LEU* 3.2 30.3 - - + -
223B ILE* 3.9 16.4 - - + -
231B ILE* 4.9 4.7 - - + -
235B VAL* 4.7 5.4 - - + -
400B NAD 3.9 6.8 - - - -
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Residues in contact with ASP 203 (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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180B ALA* 2.5 28.8 + - + +
202B THR* 1.3 77.0 - - - +
204B LEU* 1.3 69.8 + - - +
205B SER* 2.7 20.8 + - - +
208B ARG* 4.3 2.0 - - - -
209B LEU* 3.5 22.1 - - + +
221B LEU 3.2 4.0 + - - -
222B GLN* 3.2 8.5 - - - -
223B ILE* 2.7 27.5 + - - +
400B NAD 2.5 53.1 + - - -
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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