Contacts of the helix formed by residues 187 - 194 (chain B) in PDB entry 1KEK
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 187 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B GLY* 2.8 39.6 + - - +
3B LYS 4.8 1.8 - - - +
4B LYS* 4.6 19.7 + - - +
16B HIS* 5.5 0.7 - - - -
186B LEU* 1.4 78.5 - - - +
188B TYR* 1.3 65.5 + - - +
189B ALA* 4.2 8.5 - - + +
190B ASP* 3.1 23.4 + - - +
191B MET* 3.4 10.0 + - - +
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Residues in contact with TYR 188 (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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16B HIS* 2.8 50.7 + + - -
19B TYR* 3.7 19.9 - + - +
20B ALA* 3.6 29.8 - - + -
48B ARG* 3.1 31.0 + - + -
49B LYS 3.3 26.7 - - - -
50B ASN* 4.5 2.9 - - - -
51B ILE* 3.6 9.9 - - + +
187B ASP* 1.3 74.0 - - - +
189B ALA* 1.3 56.0 + - - +
191B MET* 3.2 17.0 + - + +
192B ALA* 2.9 28.8 + - - +
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Residues in contact with ALA 189 (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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187B ASP* 3.2 6.7 + - + +
188B TYR* 1.3 76.8 - - - +
190B ASP* 1.3 62.0 + - - +
192B ALA* 3.4 8.7 + - - +
193B SER* 3.1 22.9 + - - -
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Residues in contact with ASP 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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2B GLY* 2.7 47.2 + - - +
186B LEU* 4.3 14.8 - - + -
187B ASP* 3.1 11.5 + - - +
189B ALA* 1.3 77.7 - - - +
191B MET* 1.3 65.3 + - - +
193B SER* 2.7 24.6 + - - -
194B LEU* 3.6 12.0 + - - +
253B LEU* 4.0 24.4 - - + +
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Residues in contact with MET 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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16B HIS* 3.5 23.3 - - + +
17B VAL* 3.8 31.2 - - + -
20B ALA* 3.7 23.1 - - - -
21B MET* 3.8 17.2 - - - +
51B ILE* 4.6 1.3 - - + -
150B HIS* 4.2 5.8 - - - +
154B LEU* 4.0 18.8 - - + -
158B LEU* 4.3 3.3 - - - +
186B LEU* 3.4 29.4 - - + +
187B ASP 3.7 7.2 - - - +
188B TYR* 3.2 14.0 + - + +
190B ASP* 1.3 77.1 - - - +
192B ALA* 1.3 62.6 + - - +
194B LEU* 3.1 26.8 + - - +
195B VAL* 3.8 8.1 + - - +
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Residues in contact with ALA 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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51B ILE* 3.8 30.8 - - + +
188B TYR 2.9 19.1 + - - +
189B ALA* 3.4 9.6 + - - +
191B MET* 1.3 72.6 - - - +
193B SER* 1.3 60.8 + - - +
194B LEU 3.2 1.0 + - - -
195B VAL* 3.2 23.4 + - - +
197B GLN* 4.1 11.6 + - - +
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Residues in contact with SER 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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189B ALA 3.1 13.3 + - - -
190B ASP* 2.7 22.8 + - - -
192B ALA* 1.3 75.1 - - - +
194B LEU* 1.3 67.9 + - - +
195B VAL 3.5 3.3 - - - +
253B LEU* 4.7 4.0 - - - +
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Residues in contact with LEU 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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154B LEU* 4.1 11.0 - - + -
158B LEU* 3.7 28.7 - - + -
190B ASP 3.6 13.5 - - - +
191B MET* 3.1 11.0 + - - +
193B SER* 1.3 87.5 + - - +
195B VAL* 1.3 64.8 + - - +
196B ASN 3.6 0.3 + - - -
246B TYR* 3.5 22.6 + - + -
249B LYS* 4.3 32.8 + - + +
250B VAL* 4.0 15.5 - - + -
252B SER* 5.7 0.4 - - - +
253B LEU* 3.7 32.3 - - + -
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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