Contacts of the helix formed by residues 191 - 201 (chain B) in PDB entry 1GKU
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 191 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188B LEU 3.6 8.6 + - - -
189B LYS 3.5 7.1 + - - -
190B ALA* 1.3 68.8 - - - +
192B LYS* 1.3 61.2 + - - +
193B ASN 2.8 6.9 + - - -
194B VAL* 2.9 28.4 + - - +
195B ASP* 3.5 0.7 - - - +
232B LYS* 3.3 33.3 - - - +
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Residues in contact with LYS 192 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190B ALA* 2.6 9.0 + - + +
191B SER* 1.3 79.9 + - - +
193B ASN* 1.3 55.4 + - - +
194B VAL 3.3 0.4 - - - -
195B ASP* 3.3 33.2 + - + +
196B LYS* 3.0 49.5 + - + +
232B LYS* 5.2 5.9 - - - +
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Residues in contact with ASN 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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163B THR* 4.9 4.3 + - - +
166B LEU* 4.0 19.3 - - + +
167B SER* 3.2 35.8 + - - -
186B ALA 5.2 1.6 + - - -
187B ILE* 3.2 32.8 + - + +
190B ALA* 2.6 47.7 + - - +
192B LYS* 1.3 70.2 - - - +
194B VAL* 1.3 56.3 + - - +
196B LYS* 3.4 8.1 + - - +
197B LEU* 2.6 38.1 + - - +
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Residues in contact with VAL 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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187B ILE* 5.2 4.0 - - + +
188B LEU* 3.7 34.3 - - + -
191B SER* 2.9 18.6 + - - +
193B ASN* 1.3 78.2 - - - +
195B ASP* 1.3 58.1 + - - +
197B LEU* 3.4 8.0 + - - +
198B LEU* 2.9 34.0 + - + +
232B LYS* 3.9 24.0 - - + +
235B LEU* 4.1 17.0 - - + -
236B PHE* 3.9 28.0 - - + -
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Residues in contact with ASP 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 SER 3.5 8.7 - - - +
192B LYS* 3.3 38.3 + - + +
193B ASN 3.2 0.4 - - - -
194B VAL* 1.3 74.8 - - - +
196B LYS* 1.3 62.6 + - + +
198B LEU* 3.2 5.7 + - - +
199B HIS* 2.9 37.4 + - + +
212B TRP* 3.5 35.1 - - + -
232B LYS* 3.4 26.1 + - - +
235B LEU* 4.7 1.4 - - - +
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Residues in contact with LYS 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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166B LEU* 4.0 9.4 - - + +
167B SER* 2.7 48.1 + - - +
170B TYR* 3.2 54.5 - - + +
192B LYS* 3.0 38.4 + - + +
193B ASN* 3.1 11.0 + - - +
195B ASP* 1.3 75.2 - - + +
197B LEU* 1.3 64.7 + - - +
199B HIS* 3.4 9.8 + - + +
200B LEU* 3.1 23.9 + - - +
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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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105B ILE* 5.0 7.2 - - + -
166B LEU* 4.3 11.6 - - + +
179B ILE* 4.0 30.1 - - + -
181B VAL* 4.4 13.9 - - + -
187B ILE* 4.3 22.7 - - + -
193B ASN 2.6 18.8 + - - +
194B VAL* 3.5 8.7 - - - +
196B LYS* 1.3 73.4 - - - +
198B LEU* 1.3 65.8 + - + +
200B LEU* 3.0 19.7 + - + +
201B LEU* 3.4 13.8 + - + +
220B LEU* 3.9 30.3 - - + -
222B VAL* 6.5 0.2 - - + -
236B PHE* 4.7 12.8 - - + -
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Residues in contact with LEU 198 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194B VAL* 2.9 23.0 + - + +
195B ASP* 3.3 17.3 - - - +
197B LEU* 1.3 78.5 - - + +
199B HIS* 1.3 56.8 + - - +
201B LEU* 3.0 20.5 + - + +
203B PHE* 3.2 30.3 + - + +
212B TRP* 4.0 20.0 - - + -
235B LEU* 3.9 30.3 - - + +
236B PHE* 4.6 15.9 - - + -
239B LEU* 4.1 24.9 - - + -
240B LEU* 4.5 24.5 - - + -
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Residues in contact with HIS 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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170B TYR* 4.4 19.7 - + + +
171B ARG* 3.5 39.0 + - - -
174B GLY 4.9 0.3 - - - +
175B HIS* 3.4 17.4 - - - -
195B ASP* 2.9 22.5 + - + +
196B LYS* 3.5 13.0 - - - +
197B LEU 3.2 0.2 - - - -
198B LEU* 1.3 77.2 - - - +
200B LEU* 1.3 62.4 + - + +
202B GLY* 3.4 8.7 + - - -
203B PHE 3.3 14.7 + - - -
204B HIS* 3.6 30.5 - - + +
205B TYR 4.9 1.2 + - - -
212B TRP* 4.6 6.5 - + - -
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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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103B TYR* 3.5 37.7 - - + -
105B ILE* 5.8 0.2 - - + -
166B LEU* 3.8 11.7 - - + -
170B TYR* 3.0 33.0 - - + +
173B LEU* 3.7 12.6 - - + -
174B GLY 3.7 15.9 - - - +
175B HIS* 3.3 6.5 + - - +
176B PHE* 3.0 43.5 + - + +
179B ILE* 4.0 8.1 - - + -
196B LYS 3.1 16.2 - - - +
197B LEU* 3.0 8.9 + - + +
199B HIS* 1.3 80.7 - - + +
201B LEU* 1.3 61.4 + - - +
202B GLY 3.3 0.2 - - - -
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Residues in contact with LEU 201 (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 PHE 4.6 4.5 - - - +
179B ILE* 3.8 22.7 - - + -
197B LEU* 3.7 19.7 - - + +
198B LEU* 3.0 16.4 + - + +
200B LEU* 1.3 78.9 - - - +
202B GLY* 1.3 53.0 + - - +
203B PHE* 3.6 11.0 - - + -
216B ALA* 3.5 5.0 - - - -
217B ARG* 2.6 36.0 + - - +
218B GLY* 3.7 30.5 - - - +
219B CYS 4.1 10.5 - - - +
220B LEU* 4.1 10.8 - - + -
240B LEU* 3.4 35.9 - - + -
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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