Contacts of the helix formed by residues 225 - 236 (chain B) in PDB entry 1CK4
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 MET 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190B TYR* 3.4 14.4 - - + -
192B GLU* 3.8 35.8 - - - +
223B GLN* 3.5 13.8 + - + +
224B THR* 1.3 70.9 - - - +
226B THR* 1.3 65.0 + - - +
227B ALA 3.3 2.7 - - - -
228B LEU* 3.0 25.9 + - + -
229B GLY 3.1 9.9 + - - -
261B HIS* 3.7 26.5 - - - -
262B ASP* 2.9 44.0 - - + +
264B TYR* 4.9 7.4 - - - +
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Residues in contact with THR 226 (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 TYR* 2.9 31.4 + - + +
224B THR* 3.4 10.7 + - - +
225B MET* 1.3 72.9 - - - +
227B ALA* 1.3 63.4 + - - +
228B LEU 3.3 0.2 + - - -
229B GLY* 3.3 2.4 + - - -
230B ILE* 3.1 41.3 + - + +
254B ILE* 4.3 12.6 - - + -
256B THR* 4.2 10.4 + - + +
258B GLY 4.8 1.9 + - - -
260B SER* 3.4 23.9 + - - -
266B LEU* 5.3 2.9 - - + -
302B GLU* 5.5 0.7 - - - -
303B ILE* 6.0 1.7 - - + +
306B ILE* 4.9 11.7 - - + -
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Residues in contact with ALA 227 (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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225B MET 3.3 1.0 + - - -
226B THR* 1.3 78.2 - - - +
228B LEU* 1.3 55.2 + - - +
230B ILE* 4.6 3.6 - - - -
231B ASP* 3.1 31.2 + - - +
262B ASP* 3.2 32.0 - - + +
265B ARG* 3.8 22.1 + - + +
266B LEU* 3.9 22.8 - - + +
269B VAL* 3.7 10.7 - - + +
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Residues in contact with LEU 228 (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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192B GLU 3.8 22.0 - - - +
193B ASN* 4.2 6.7 - - - +
194B VAL* 3.4 22.7 - - + +
225B MET* 3.0 20.0 + - + +
227B ALA* 1.3 75.0 - - - +
229B GLY* 1.3 58.0 + - - +
231B ASP* 3.3 2.3 + - + +
232B THR* 2.5 49.1 + - - +
262B ASP* 3.3 13.7 + - - +
265B ARG* 3.7 21.1 - - - +
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Residues in contact with GLY 229 (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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152B VAL* 3.9 10.6 - - - +
188B VAL* 4.3 3.3 - - - +
190B TYR* 4.0 18.6 - - - +
194B VAL* 3.8 18.4 - - - +
225B MET 3.1 7.7 + - - -
226B THR 3.3 2.4 + - - -
228B LEU* 1.3 79.0 - - - +
230B ILE* 1.3 55.4 + - - +
232B THR* 3.4 1.7 + - - -
233B ALA* 2.8 30.1 + - - +
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Residues in contact with ILE 230 (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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152B VAL* 4.0 5.6 - - + +
226B THR* 3.1 37.2 + - + +
227B ALA* 4.0 5.6 - - - +
229B GLY* 1.3 72.0 - - - +
231B ASP* 1.3 62.4 + - - +
233B ALA* 3.2 3.3 + - - +
234B ARG* 2.9 28.2 + - - +
252B MET* 3.8 15.5 - - - +
254B ILE* 4.0 21.8 - - + -
266B LEU* 5.1 1.3 - - + -
269B VAL* 3.3 20.4 - - + -
270B ILE* 4.5 7.2 - - + -
273B CYS* 3.7 20.0 - - - -
280B ARG* 5.8 0.4 - - - -
306B ILE* 4.0 33.0 - - + -
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Residues in contact with ASP 231 (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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227B ALA 3.1 20.5 + - - +
228B LEU* 3.7 3.4 - - + +
230B ILE* 1.3 77.2 - - - +
232B THR* 1.3 58.7 + - - +
234B ARG* 2.3 45.3 + - - +
235B LYS* 2.8 54.2 + - - +
265B ARG* 3.8 20.1 + - - +
269B VAL* 3.8 21.1 - - + +
272B ASP* 4.7 0.9 - - - +
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Residues in contact with THR 232 (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 VAL* 3.5 36.4 - - + +
196B HIS* 4.4 6.4 - - + +
228B LEU* 2.5 32.4 + - - +
229B GLY 3.7 3.8 - - - -
231B ASP* 1.3 73.5 + - - +
233B ALA* 1.3 57.2 + - - +
235B LYS* 4.4 6.5 - - - +
236B GLU* 2.7 66.7 + - - +
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Residues in contact with ALA 233 (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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150B VAL* 4.0 14.6 - - + -
152B VAL* 3.8 24.2 - - + -
188B VAL* 4.3 9.3 - - + +
229B GLY 2.8 18.2 + - - +
230B ILE 3.5 4.5 - - - +
232B THR* 1.3 76.2 - - - +
234B ARG* 1.3 61.2 + - - +
237B ALA* 2.9 36.0 + - + +
238B PHE* 3.4 8.8 + - - -
252B MET* 4.1 5.6 - - + -
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Residues in contact with ARG 234 (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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230B ILE 2.9 16.3 + - - +
231B ASP* 2.3 33.7 + - - +
233B ALA* 1.3 76.9 - - - +
235B LYS* 1.3 95.1 + - - +
238B PHE* 4.1 24.6 + - - +
252B MET* 4.1 1.7 - - + +
269B VAL* 4.1 6.3 + - - +
272B ASP* 3.1 34.7 + - - +
273B CYS* 4.0 26.7 - - - +
276B GLU* 3.1 44.4 + - - +
278B ILE* 3.8 13.9 - - + -
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Residues in contact with LYS 235 (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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231B ASP* 2.8 35.1 + - - +
232B THR* 4.0 4.9 - - - +
234B ARG* 1.3 109.0 - - - +
236B GLU* 1.3 69.8 + - + +
238B PHE 5.2 0.6 - - - -
239B THR* 3.7 9.9 + - - -
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Residues in contact with GLU 236 (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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196B HIS* 3.0 28.2 + - - +
232B THR* 2.7 34.0 + - - +
235B LYS* 1.3 86.3 - - + +
237B ALA* 1.3 62.0 + - - +
238B PHE 3.3 2.0 - - - -
239B THR* 3.0 24.4 + - - -
242B ARG* 3.3 23.7 + - - +
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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