Contacts of the strand formed by residues 163 - 168 (chain B) in PDB entry 1KY9
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 163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B GLY 4.8 6.5 - - - -
162B ASP* 1.3 78.6 - - - +
164B THR* 1.3 62.8 + - - +
180B GLY 3.4 14.8 - - - +
181B ILE* 3.4 18.4 - - + -
182B VAL* 5.1 0.2 - - - +
216B ASN* 4.0 19.8 - - - +
217B LEU* 3.6 42.7 + - + -
222B ILE* 4.8 1.7 - - - +
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Residues in contact with THR 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B TYR* 1.3 74.0 + - - +
165B VAL* 1.3 62.6 + - - +
179B SER* 3.5 3.8 - - - -
180B GLY 2.8 33.5 + - - +
181B ILE* 3.9 11.0 - - - +
182B VAL* 3.8 12.1 - - - +
201B THR* 3.0 28.9 + - - +
203B ALA* 3.5 14.1 - - + -
214B LEU* 3.4 19.7 - - + +
215B VAL 3.8 3.6 - - - -
216B ASN* 5.6 0.2 - - - -
217B LEU* 5.6 3.0 - - - +
222B ILE* 3.5 23.6 - - - +
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Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 4.9 7.6 - - + -
18B MSE 3.2 18.4 - - + -
19B LEU* 4.3 11.7 - - + -
164B THR* 1.3 77.3 - - - +
166B ALA* 1.3 63.3 + - - +
167B ILE* 4.7 3.2 - - + +
177B VAL* 3.7 23.6 - - + -
178B THR 3.5 13.9 - - - +
179B SER* 4.7 6.7 - - - -
213B ALA 3.8 0.5 - - - +
214B LEU* 3.5 4.6 - - - +
215B VAL* 2.8 74.7 + - + +
216B ASN 4.1 1.8 - - - +
217B LEU* 5.5 3.4 - - + -
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Residues in contact with ALA 166 (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 VAL* 1.3 72.5 - - - +
167B ILE* 1.3 66.4 + - - +
168B GLY 4.3 0.2 - - - -
176B THR 3.9 0.7 - - - +
177B VAL* 3.2 4.7 - - - +
178B THR* 2.8 42.8 + - + +
203B ALA* 3.6 24.8 - - + +
204B ALA* 5.7 0.2 - - - -
213B ALA 3.2 9.4 - - - +
214B LEU* 4.1 5.8 - - + +
225B ASN* 3.9 13.9 - - - +
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Residues in contact with ILE 167 (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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19B LEU* 4.5 11.4 - - + -
22B VAL* 3.7 29.8 - - + -
23B MSE 4.0 27.6 - - + -
26B VAL* 4.0 30.0 - - + +
89B SER* 4.6 3.2 - - - -
165B VAL* 4.7 7.0 - - + +
166B ALA* 1.3 81.4 - - - +
168B GLY* 1.3 62.2 + - - +
175B GLU* 5.1 4.5 - - + +
176B THR 3.5 9.4 - - - +
177B VAL* 4.3 11.4 - - + -
212B GLY* 3.5 4.8 + - - -
213B ALA* 2.9 37.2 + - + +
215B VAL* 5.0 8.5 - - + -
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Residues in contact with GLY 168 (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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89B SER* 3.5 14.4 - - - -
167B ILE* 1.3 77.0 - - - +
169B ASN* 1.3 60.3 + - - -
170B PRO* 3.1 9.3 - - - +
175B GLU* 3.4 5.3 - - - -
176B THR 2.8 33.0 + - - -
211B GLY* 4.2 15.7 - - - -
212B GLY 4.2 0.2 - - - -
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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