Contacts of the helix formed by residues 189 - 200 (chain B) in PDB entry 4KIS
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 SER 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184B PHE* 3.4 8.1 - - - -
187B GLU* 4.0 6.8 - - - +
188B GLN* 1.3 77.7 - - - +
190B ILE* 1.3 63.8 + - - +
191B THR* 3.4 4.9 + - - -
192B PHE* 3.1 35.1 + - - +
193B LEU* 3.0 19.4 + - - +
254B MET* 5.6 0.9 - - - -
261B ASN* 3.4 15.6 - - - +
37G G 4.3 1.6 + - - -
38G T 3.0 17.0 + - - -
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Residues in contact with ILE 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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184B PHE* 3.8 17.3 - - + -
189B SER* 1.3 71.2 - - - +
191B THR* 1.3 58.0 + - - +
193B LEU* 3.1 9.8 - - + +
194B GLN* 2.9 29.8 + - + +
207B TYR* 3.4 50.2 + - + +
210B TYR* 3.7 26.5 - - + +
211B ASN* 3.6 40.8 - - + +
214B LEU* 4.2 6.3 - - + -
251B PHE* 4.2 8.3 - - + -
254B MET* 5.6 2.5 - - + +
38G T 4.0 3.6 + - - -
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Residues in contact with THR 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 SER* 3.1 4.6 - - - -
190B ILE* 1.3 74.7 - - - +
192B PHE* 1.3 62.3 + - + +
193B LEU 2.9 1.3 - - - -
194B GLN* 2.7 37.2 + - + +
195B LYS* 2.8 26.0 + - + +
207B TYR* 4.4 6.6 - - - -
37G G 3.2 38.2 - - - +
38G T 2.5 25.6 + - - +
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Residues in contact with PHE 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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187B GLU* 3.8 33.4 - - + -
189B SER* 3.1 27.0 + - - +
191B THR* 1.3 80.7 - - + +
193B LEU* 1.3 56.9 + - - +
195B LYS* 3.6 20.6 - - + +
196B ARG* 2.9 43.7 + - + +
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Residues in contact with LEU 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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180B ILE* 3.6 30.3 - - + -
183B ILE* 3.6 35.4 - - + -
184B PHE* 4.1 10.5 - - + -
187B GLU* 5.0 0.4 - - + +
189B SER 3.0 12.2 + - - +
190B ILE* 3.1 12.8 - - - +
191B THR 2.9 0.6 - - - -
192B PHE* 1.3 75.1 - - - +
194B GLN* 1.3 55.6 + - - +
196B ARG* 3.2 1.4 + - - -
197B LEU* 2.8 67.5 + - + +
210B TYR* 4.0 14.8 - - + -
214B LEU* 4.0 18.4 - - + -
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Residues in contact with GLN 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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190B ILE* 2.9 16.6 + - - +
191B THR* 2.7 24.0 + - + +
193B LEU* 1.3 69.1 - - - +
195B LYS* 1.3 67.5 + - - +
197B LEU* 3.5 5.3 + - - +
198B LYS* 3.1 21.0 + - - +
204B VAL* 3.9 18.8 - - + +
205B ARG 2.8 27.3 + - - -
206B THR* 3.7 0.6 - - - +
207B TYR* 3.0 42.5 - - - +
210B TYR* 3.9 17.8 - - + -
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Residues in contact with LYS 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 THR* 2.8 22.0 + - + +
192B PHE* 3.6 29.2 - - + +
194B GLN* 1.3 80.6 - - - +
196B ARG* 1.3 66.0 + - + +
198B LYS* 3.0 22.0 + - + +
199B LYS* 3.1 7.6 + - - +
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Residues in contact with ARG 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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183B ILE* 4.7 18.8 - - + +
186B GLU* 5.1 5.5 + - - -
187B GLU* 4.2 29.5 + - - -
192B PHE* 2.9 32.4 + - + +
193B LEU* 3.6 4.7 - - - +
195B LYS* 1.3 75.1 - - + +
197B LEU* 1.3 67.6 + - - +
199B LYS* 2.8 17.8 + - - +
200B LEU* 2.9 28.7 - - + +
164D ASP* 2.4 43.2 + - - -
166D LYS* 4.9 1.8 - - - +
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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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176B GLN* 6.1 0.9 - - - +
179B LEU* 4.1 16.8 - - + -
180B ILE* 4.1 11.2 - - + -
183B ILE* 3.9 16.6 - - + -
193B LEU* 2.8 44.5 + - + +
194B GLN* 3.9 5.2 - - - +
196B ARG* 1.3 71.9 - - - +
198B LYS* 1.3 62.2 + - - +
200B LEU* 3.1 11.9 + - + +
201B GLY 3.1 0.2 + - - -
202B PHE* 3.1 44.5 + - + +
203B LYS 5.4 0.4 - - - +
204B VAL* 5.0 4.9 - - + -
210B TYR* 3.2 44.6 - - + +
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Residues in contact with LYS 198 (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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194B GLN 3.1 12.0 + - - +
195B LYS* 3.0 17.9 + - + +
196B ARG 3.0 0.4 - - - -
197B LEU* 1.3 76.5 - - - +
199B LYS* 1.3 53.9 + - - +
201B GLY* 2.7 25.9 + - - +
202B PHE 4.5 8.9 - - - +
204B VAL* 4.9 15.8 - - + +
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Residues in contact with LYS 199 (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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195B LYS 3.1 6.9 + - - +
196B ARG* 2.8 15.3 + - - +
198B LYS* 1.3 78.1 - - - +
200B LEU* 1.3 66.2 + - + +
201B GLY* 3.1 1.3 + - - -
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Residues in contact with LEU 200 (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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179B LEU* 4.3 11.9 - - + -
183B ILE* 4.6 7.4 - - + -
196B ARG* 2.9 37.1 + - - +
197B LEU* 3.5 8.5 - - - +
198B LYS 3.1 0.2 - - - -
199B LYS* 1.3 83.8 - - + +
201B GLY* 1.3 61.3 + - - +
202B PHE* 3.7 28.8 - - + -
163D ILE* 4.3 6.1 - - + -
164D ASP* 3.6 40.4 - - + +
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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