Contacts of the helix formed by residues 189 - 197 (chain B) in PDB entry 1YLA
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 ASP 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165B LYS* 4.9 0.4 - - - +
183B LEU* 4.5 0.9 - - - +
186B LYS* 2.9 12.4 + - - +
187B SER* 4.4 2.9 - - - +
188B TRP* 1.3 74.8 - - - +
190B VAL* 1.3 66.1 + - - +
191B GLU* 3.6 9.7 + - - +
192B THR* 2.4 50.3 + - + +
193B ALA* 3.0 24.7 + - - +
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Residues in contact with VAL 190 (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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165B LYS* 3.9 40.4 - - + +
168B ASN* 6.5 0.7 - - + -
169B LEU* 4.3 12.3 - - + +
183B LEU* 4.4 9.4 - - + +
188B TRP 3.7 1.2 + - - -
189B ASP* 1.3 73.4 + - - +
191B GLU* 1.3 57.5 + - - +
193B ALA* 3.8 1.2 - - - +
194B THR* 2.6 46.5 + - - +
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Residues in contact with GLU 191 (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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189B ASP* 3.3 11.8 + - - +
190B VAL* 1.3 81.2 - - - +
192B THR* 1.3 65.2 + - + +
194B THR* 3.5 5.9 + - - -
195B GLU* 3.2 20.4 + - - +
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Residues in contact with THR 192 (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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186B LYS* 3.5 25.2 + - - +
189B ASP* 2.4 50.3 + - + +
191B GLU* 1.3 75.8 - - + +
193B ALA* 1.3 61.4 + - - +
195B GLU* 3.1 15.4 + - - +
196B LEU* 2.9 27.2 + - - +
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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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169B LEU* 4.6 3.1 - - + -
182B ALA* 3.7 29.5 - - + +
183B LEU* 3.8 18.8 - - + +
186B LYS* 3.7 11.2 - - + +
189B ASP 3.0 18.7 + - - +
190B VAL 3.8 2.2 - - - +
192B THR* 1.3 78.3 + - - +
194B THR* 1.3 57.9 - - - +
196B LEU* 3.2 4.9 + - - +
197B LEU* 2.9 33.7 + - - +
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Residues in contact with THR 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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169B LEU* 3.4 19.2 - - - +
172B MET* 4.4 20.3 - - + +
174B PHE* 4.4 6.5 - - + -
190B VAL* 2.6 30.1 + - - +
191B GLU* 3.8 7.4 - - - -
192B THR 3.2 0.2 - - - -
193B ALA* 1.3 76.3 - - - +
195B GLU* 1.3 59.6 + - - +
197B LEU* 3.7 12.5 + - - +
198B LEU* 3.2 31.1 - - + +
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Residues in contact with GLU 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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191B GLU 3.2 11.9 + - - +
192B THR* 3.1 17.0 + - - +
193B ALA 3.1 0.6 - - - -
194B THR* 1.3 74.8 - - - +
196B LEU* 1.3 60.6 + - - +
197B LEU 3.1 1.1 - - - -
198B LEU* 2.8 26.8 + - + +
199B SER* 3.3 11.9 + - - +
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Residues in contact with LEU 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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181B VAL* 5.5 0.9 - - + -
182B ALA* 3.9 27.1 - - + +
185B SER* 4.6 8.5 - - - -
186B LYS* 3.4 33.0 - - + +
192B THR 2.9 13.4 + - - +
193B ALA 3.2 8.7 + - - +
195B GLU* 1.3 77.0 - - - +
197B LEU* 1.3 58.0 + - + +
198B LEU 2.9 5.4 + - - -
199B SER* 3.1 27.5 + - - +
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Residues in contact with LEU 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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169B LEU* 3.6 31.9 - - + -
174B PHE* 3.1 57.8 - - + -
178B ALA* 3.3 42.4 - - + +
179B VAL* 3.9 5.6 - - + +
182B ALA* 3.8 7.6 - - + -
193B ALA 2.9 17.1 + - - +
194B THR* 3.8 7.6 - - - +
195B GLU 3.1 0.6 - - - -
196B LEU* 1.3 73.9 - - + +
198B LEU* 1.3 60.0 + - - +
199B SER 3.7 2.1 - - - +
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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