Contacts of the helix formed by residues 221 - 234 (chain B) in PDB entry 2IKS
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 GLU 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219B SER* 2.9 34.2 + - - +
220B TYR* 1.3 80.1 - - - +
222B ARG* 1.3 66.9 + - - +
223B GLU* 4.6 3.5 - - + +
224B ALA* 3.3 11.1 + - + +
225B ALA* 3.0 24.0 + - - +
248B ALA* 4.2 5.6 - - - -
249B LEU* 3.9 2.9 - - - +
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Residues in contact with ARG 222 (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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277A GLU* 4.0 21.5 + - - +
280A ASP* 4.3 18.4 + - - +
281A PHE* 3.4 23.0 - - - -
221B GLU* 1.3 71.0 - - - +
223B GLU* 1.3 59.0 + - - +
225B ALA* 3.3 0.9 + - - -
226B ALA* 2.9 26.9 + - - +
248B ALA* 3.3 23.7 + - + +
251B GLN* 3.7 29.5 - - + +
252B GLY* 3.3 11.4 - - - +
255B ASP* 2.6 43.3 + - - +
259B ARG* 4.1 11.7 - - - +
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Residues in contact with GLU 223 (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 GLU* 3.4 4.0 - - + +
222B ARG* 1.3 79.1 - - - +
224B ALA* 1.3 62.6 + - - +
226B ALA* 3.3 7.2 + - + +
227B GLN* 3.0 50.4 + - + +
255B ASP* 5.7 0.4 - - - -
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Residues in contact with ALA 224 (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* 4.5 7.1 - - + +
218B ASN* 3.5 27.6 - - - +
219B SER* 3.7 18.4 - - - +
221B GLU* 3.3 14.4 + - + +
223B GLU* 1.3 77.5 - - - +
225B ALA* 1.3 62.9 + - - +
227B GLN* 3.3 7.9 + - - +
228B LEU* 3.1 24.8 + - - +
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Residues in contact with ALA 225 (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* 4.2 10.5 - - + +
217B ALA* 4.5 8.6 - - - +
221B GLU 3.0 16.6 + - - +
222B ARG 3.7 4.3 - - - +
224B ALA* 1.3 76.6 - - - +
226B ALA* 1.3 56.3 + - - +
228B LEU* 3.4 2.5 + - - +
229B PHE* 2.9 35.0 + - - +
249B LEU* 3.5 44.9 - - + +
252B GLY* 4.2 2.2 - - - -
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Residues in contact with ALA 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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222B ARG 2.9 17.2 + - - +
223B GLU* 3.6 8.1 - - + +
225B ALA* 1.3 75.8 - - - +
227B GLN* 1.3 60.4 + - + +
230B GLU* 2.9 28.6 + - - +
252B GLY* 3.6 24.1 - - - +
255B ASP* 4.4 10.8 - - + +
256B VAL* 3.2 18.5 - - + +
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Residues in contact with GLN 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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223B GLU* 3.0 40.3 + - + +
224B ALA* 3.7 7.1 - - - +
226B ALA* 1.3 77.6 - - + +
228B LEU* 1.3 61.2 + - - +
230B GLU* 3.6 5.9 + - - +
231B LYS* 3.2 22.7 + - - +
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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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185B LEU* 4.5 4.5 - - + -
215B LEU* 3.8 32.8 - - + -
216B TYR 3.2 36.8 - - - +
217B ALA* 3.5 12.8 - - + +
224B ALA 3.1 16.4 + - - +
225B ALA* 4.0 3.1 - - - +
227B GLN* 1.3 74.6 - - - +
229B PHE* 1.3 61.3 + - - +
231B LYS* 3.3 11.7 + - + +
232B TRP* 2.9 26.5 + - - +
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Residues in contact with PHE 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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183B LEU* 3.7 32.1 - - + -
185B LEU* 5.2 2.9 - - + +
215B LEU* 4.5 6.5 - - + +
225B ALA 2.9 19.3 + - - +
226B ALA* 4.0 3.1 - - - +
228B LEU* 1.3 75.9 - - - +
230B GLU* 1.3 65.3 + - - +
232B TRP* 3.1 22.2 + + - +
233B LEU* 3.0 43.2 + - + +
238B MSE 3.7 24.5 - - - -
239B PRO* 4.2 5.4 - - + -
242B LEU* 5.6 0.2 - - + -
253B VAL* 3.7 34.8 - - + -
256B VAL* 3.8 19.3 - - + -
257B THR* 3.7 20.6 - - - -
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Residues in contact with GLU 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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226B ALA 2.9 18.8 + - - +
227B GLN* 3.7 6.3 - - - +
229B PHE* 1.3 78.3 - - - +
231B LYS* 1.3 62.3 + - - +
233B LEU* 3.4 12.8 + - - +
234B GLU* 3.6 15.3 + - + +
256B VAL* 4.2 24.6 - - + +
260B ARG* 3.4 34.1 + - - +
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Residues in contact with LYS 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 GLN 3.2 15.3 + - - +
228B LEU* 3.6 15.5 - - + +
230B GLU* 1.3 74.4 - - - +
232B TRP* 1.3 63.2 + - - +
234B GLU* 3.1 57.5 + - - +
235B THR* 4.3 2.6 + - - -
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Residues in contact with TRP 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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181B THR* 4.2 9.6 - - + -
183B LEU* 3.8 35.1 - - + +
213B HIS* 3.9 20.8 - + + +
214B PHE 5.6 1.2 + - - -
215B LEU* 3.7 33.6 - - + +
228B LEU 2.9 16.8 + - - +
229B PHE* 3.1 19.5 + + - +
231B LYS* 1.3 76.0 - - - +
233B LEU* 1.3 66.8 + - + +
235B THR* 3.2 3.8 + - - -
236B HIS* 3.0 77.1 + + + +
237B PRO 3.2 28.7 - - - -
239B PRO* 3.9 17.9 - - + -
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Residues in contact with LEU 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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229B PHE* 3.0 46.4 + - + +
230B GLU* 3.6 8.7 - - - +
231B LYS 3.3 0.2 - - - -
232B TRP* 1.3 76.9 - - + +
234B GLU* 1.3 64.8 + - - +
235B THR 3.1 3.0 + - - -
236B HIS 3.2 24.8 - - - +
238B MSE 3.8 44.6 - - + +
256B VAL* 3.9 19.5 - - + -
260B ARG* 4.1 22.8 + - - +
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Residues in contact with GLU 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 GLU* 3.6 10.1 + - + +
231B LYS* 3.1 52.2 + - - +
233B LEU* 1.3 78.1 - - - +
235B THR* 1.3 68.0 + - + +
260B ARG* 5.7 4.7 - - - +
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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