Contacts of the strand formed by residues 198 - 203 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A HIS 3.4 3.5 + - - +
174A LYS* 3.4 27.9 - - + +
175A VAL 2.9 25.2 + - - +
197A ALA* 1.3 92.7 - - + +
199A VAL* 1.3 66.3 + - - +
218A ASP* 3.2 28.2 - - + +
219A LEU* 4.0 22.6 - - + +
238A GLN 5.4 1.4 + - - -
239A LEU* 3.9 17.3 - - + +
312B SER* 4.4 9.7 - - - -
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Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A VAL* 3.3 11.9 - - + +
177A VAL* 3.8 24.0 - - + -
188A LEU* 3.4 28.5 - - + -
191A ALA* 3.9 15.3 - - + -
192A LYS* 3.9 16.4 - - + -
196A ALA* 3.8 21.8 - - + -
198A GLN* 1.3 79.9 - - - +
200A VAL* 1.3 61.9 + - - +
201A VAL* 4.1 6.0 + - + -
217A ALA* 4.0 1.0 - - - -
218A ASP* 2.8 31.9 + - - +
219A LEU 3.2 8.0 + - - +
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Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A VAL 2.8 10.8 + - - +
176A LEU* 3.4 17.9 - - + +
177A VAL* 2.7 33.3 + - - +
199A VAL* 1.3 75.0 - - - +
201A VAL* 1.3 63.8 + - - +
202A THR* 4.9 0.7 - - + -
219A LEU* 3.3 24.2 - - + +
220A VAL* 4.6 1.3 - - - +
221A LEU* 4.8 4.9 - - + -
235A VAL* 4.7 5.6 - - + -
238A GLN* 3.4 24.7 - - - +
239A LEU* 3.4 45.1 - - + -
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Residues in contact with VAL 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A VAL* 3.3 15.7 - - + +
179A GLY 3.8 13.9 - - - +
180A ALA* 3.9 16.2 - - + -
185A MET* 4.0 7.9 - - + -
188A LEU* 4.3 14.1 - - + -
199A VAL* 4.1 14.8 - - + -
200A VAL* 1.3 79.0 - - - +
202A THR* 1.3 72.1 + - - +
209A LEU* 3.5 10.4 - - + +
212A ALA* 4.4 4.7 - - + -
217A ALA* 3.8 21.8 - - + -
219A LEU 3.0 7.9 + - - +
220A VAL* 3.1 5.5 - - + -
221A LEU 2.9 23.0 + - - -
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Residues in contact with THR 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LEU* 3.7 25.6 - - + -
177A VAL 2.9 5.9 + - - -
178A CYS* 3.2 24.9 - - - +
179A GLY* 2.8 25.8 + - - -
180A ALA 3.5 0.3 + - - -
200A VAL* 4.9 1.3 - - + -
201A VAL* 1.3 78.0 - - - +
203A ASP* 1.3 66.4 + - - +
209A LEU* 3.8 1.1 - - - -
221A LEU* 3.2 30.3 - - + -
223A ILE* 3.9 16.4 - - + -
231A ILE* 5.0 4.0 - - + -
235A VAL* 4.7 3.4 - - + -
255A SER* 5.1 0.2 + - - -
400A NAD 3.8 6.4 - - - -
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Residues in contact with ASP 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A ALA* 2.6 28.2 + - + -
202A THR* 1.3 77.9 - - - +
204A LEU* 1.3 74.5 + - - +
205A SER* 2.8 18.8 + - - +
208A ARG* 4.3 3.4 - - - -
209A LEU* 3.6 22.3 - - + +
221A LEU 3.2 4.2 + - - -
222A GLN* 3.3 9.0 - - - -
223A ILE* 2.8 22.8 + - - +
400A NAD 2.5 54.7 + - - -
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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