Contacts of the helix formed by residues 225 - 237 (chain B) in PDB entry 4KAL
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 225 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B LEU* 3.9 2.2 - - - -
223B THR* 2.9 18.5 + - - +
224B ASP* 1.3 79.8 + - - +
226B PHE* 1.3 63.9 + - - +
227B GLU* 3.1 22.7 + - - +
228B GLU* 3.1 24.4 + - + +
229B ALA 3.0 17.5 + - - -
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Residues in contact with PHE 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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214B ARG* 3.4 68.2 - - + +
217B ALA* 4.5 5.6 - - + -
218B LEU* 3.7 14.1 - - + +
224B ASP 3.4 6.1 + - - -
225B ASP* 1.3 72.6 + - - +
227B GLU* 1.3 66.1 + - + +
229B ALA* 3.2 5.9 + - + +
230B LEU* 2.9 63.4 + - + +
242B VAL* 3.8 18.8 - - + -
244B MSE 3.6 35.0 - - + -
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Residues in contact with GLU 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 ASP* 3.1 10.7 + - - +
226B PHE* 1.3 81.8 - - + +
228B GLU* 1.3 65.0 + - - +
230B LEU* 3.4 14.0 + - - +
231B ASN* 3.1 34.0 + - - +
257B ARG* 3.1 30.8 + - - -
259B TYR* 4.7 4.3 + - - -
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Residues in contact with GLU 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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221B TYR 4.4 1.4 - - - +
223B THR* 3.1 29.6 + - - +
225B ASP* 3.1 27.2 + - - +
227B GLU* 1.3 74.6 - - - +
229B ALA* 1.3 57.9 + - - +
231B ASN* 3.2 9.9 + - - +
232B ARG* 2.8 68.1 + - + +
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Residues in contact with ALA 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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217B ALA* 3.8 36.8 - - + +
218B LEU* 4.3 2.7 - - + -
221B TYR* 3.8 12.6 - - + -
223B THR* 4.2 10.3 - - + +
225B ASP 3.0 12.7 + - - +
226B PHE* 3.4 14.4 - - + +
228B GLU* 1.3 77.4 - - - +
230B LEU* 1.3 57.5 + - - +
233B ILE* 2.9 33.8 + - - +
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Residues in contact with LEU 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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217B ALA* 5.8 0.9 - - + -
226B PHE* 2.9 56.8 + - + +
227B GLU* 3.7 13.5 - - - +
228B GLU 3.3 0.2 - - - -
229B ALA* 1.3 76.9 - - - +
231B ASN* 1.3 62.6 + - - +
233B ILE* 3.3 6.3 - - + +
234B ALA* 3.1 24.9 + - - +
242B VAL* 4.0 20.2 - - + -
250B VAL* 3.9 25.8 - - + -
252B LEU* 3.6 11.9 - - + +
257B ARG* 3.7 31.2 - - - +
259B TYR* 4.3 6.5 - - + +
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Residues in contact with ASN 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 GLU* 3.1 22.4 + - - +
228B GLU* 3.2 9.3 + - + +
230B LEU* 1.3 75.4 - - - +
232B ARG* 1.3 64.7 + - + +
234B ALA* 3.5 7.1 + - - +
235B ALA* 3.2 21.8 + - - +
257B ARG* 2.8 25.2 + - - +
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Residues in contact with ARG 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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199B LEU* 5.7 2.6 - - - +
203B ARG* 4.2 15.6 - - - +
221B TYR* 3.2 57.4 + - + +
228B GLU* 2.8 51.1 + - + +
231B ASN* 1.3 77.0 - - + +
233B ILE* 1.3 64.8 + - - +
235B ALA* 3.0 8.4 + - - +
236B ASP* 3.0 27.0 + - - +
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Residues in contact with ILE 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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185B LEU* 4.6 1.1 - - + -
202B MSE 3.6 18.4 - - + -
210B VAL* 4.5 13.2 - - + +
212B ALA* 4.2 25.4 - - + -
217B ALA* 4.9 7.0 - - + -
220B LEU* 4.4 14.4 - - + -
221B TYR* 3.3 14.0 + - + +
229B ALA 2.9 16.9 + - - +
230B LEU* 3.3 16.6 - - + +
232B ARG* 1.3 76.4 - - - +
234B ALA* 1.3 66.0 + - - +
236B ASP* 3.1 9.5 + - - -
237B CYS* 3.2 20.9 + - - -
240B ALA* 4.0 23.8 - - + -
242B VAL* 4.3 13.9 - - + -
252B LEU* 4.4 3.4 - - + -
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Residues in contact with ALA 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 LEU 3.1 18.1 + - - +
231B ASN* 3.7 7.2 - - - +
232B ARG 3.3 0.2 - - - -
233B ILE* 1.3 77.3 - - - +
235B ALA* 1.3 57.5 + - - +
237B CYS 3.1 19.5 - - - +
240B ALA* 5.2 1.6 - - - -
252B LEU* 3.9 26.5 - - + -
254B GLY* 3.8 32.5 + - - +
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Residues in contact with ALA 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 ASN 3.2 12.6 + - - +
232B ARG* 3.0 12.6 + - - +
234B ALA* 1.3 76.3 - - - +
236B ASP* 1.3 67.0 + - - +
237B CYS 3.6 0.6 + - - -
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Residues in contact with ASP 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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199B LEU* 3.7 3.5 - - + +
202B MSE 3.2 52.9 - - + +
203B ARG* 2.9 45.2 + - + +
221B TYR* 2.6 32.3 + - - +
232B ARG* 3.0 12.7 + - - +
233B ILE 3.1 0.6 + - - +
235B ALA* 1.3 86.0 - - - +
237B CYS* 1.3 58.5 + - - +
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Residues in contact with CYS 237 (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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202B MSE 3.7 12.8 - - + -
207B VAL 4.7 4.7 - - - +
208B ASP 4.5 3.1 - - - +
210B VAL* 3.7 29.2 - - + -
233B ILE 3.2 14.6 + - - -
234B ALA* 3.1 19.1 - - - +
235B ALA 3.6 0.4 - - - -
236B ASP* 1.3 79.8 - - - +
238B LYS* 1.3 64.1 + - - +
239B ILE* 3.2 23.2 - - - +
240B ALA* 3.6 16.4 - - - -
252B LEU 5.6 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