Contacts of the helix formed by residues 236 - 246 (chain B) in PDB entry 1K0Y
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 PRO 236 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232B LEU 3.4 12.5 - - - +
233B VAL 3.5 15.0 - - - +
234B VAL 3.4 8.1 - - - +
235B TYR* 1.3 85.5 - - - +
237B TRP* 1.4 62.7 + - + +
238B THR 3.1 0.7 - - - -
239B GLN* 3.0 40.9 + - - +
488C ALA 6.1 0.2 - - - -
492C ARG* 4.1 8.7 + - - +
540C TYR 4.2 7.9 - - - +
541C ARG* 3.8 26.9 - - + -
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Residues in contact with TRP 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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235B TYR* 3.0 41.1 + + + -
236B PRO* 1.4 83.2 - - + +
238B THR* 1.4 61.6 + - + +
239B GLN 3.1 0.9 - - - -
240B ARG* 3.0 58.2 + - - +
305B LEU* 3.9 10.1 - - + +
488C ALA 5.2 2.7 - - - +
492C ARG* 3.5 32.4 - - + +
494C ASP* 3.0 29.4 + - - -
495C PRO* 3.7 15.9 - - + +
540C TYR* 3.5 34.7 + + + +
541C ARG* 4.2 9.6 - - - -
801D CNO 3.8 46.0 - + + -
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Residues in contact with THR 238 (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 LEU* 3.4 32.3 + - + +
232B LEU* 3.2 22.1 - - - +
235B TYR* 2.7 28.9 + - + +
237B TRP* 1.4 75.4 - - + +
239B GLN* 1.4 59.8 + - - +
240B ARG* 3.1 9.8 + - - +
241B PHE* 3.4 13.5 - - - -
242B PHE* 3.4 17.2 - - - -
302B ASN* 3.3 27.1 - - - +
305B LEU* 4.1 8.1 - - + -
348B HEM 4.1 5.6 - - - -
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Residues in contact with GLN 239 (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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232B LEU* 2.9 46.9 + - + +
233B VAL* 5.0 0.6 - - - +
236B PRO* 3.0 26.4 + - - +
238B THR* 1.4 77.9 + - - +
240B ARG* 1.4 63.4 + - - +
241B PHE 3.2 0.7 - - - -
242B PHE* 3.0 20.2 + - - +
243B GLU* 3.9 7.6 + - - +
248B LEU* 3.9 44.8 + - + +
254B VAL* 4.6 5.3 - - - +
492C ARG* 3.6 22.1 + - - +
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Residues in contact with ARG 240 (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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237B TRP* 3.0 44.4 + - - +
238B THR 3.1 1.6 - - - -
239B GLN* 1.4 76.9 - - - +
241B PHE* 1.4 90.0 + - + +
242B PHE 3.7 0.2 + - - -
243B GLU* 3.7 21.2 - - - +
297B HIS 5.4 0.4 + - - -
299B ASP* 3.7 4.0 - - - +
302B ASN* 3.3 34.9 + - - +
442C TYR* 3.0 36.7 + - - -
490C LYS 5.0 2.2 - - - +
491C LEU 4.1 8.5 - - - +
492C ARG* 2.8 50.3 + - + +
494C ASP* 3.9 6.3 - - - +
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Residues in contact with PHE 241 (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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238B THR* 3.4 15.3 - - - -
239B GLN 3.2 0.8 - - - -
240B ARG* 1.4 116.2 - - + +
242B PHE* 1.4 68.9 + - + +
243B GLU 3.7 1.8 + - - -
244B SER* 5.2 3.1 + - - -
245B PHE* 5.6 0.9 - - - -
296B LEU 4.2 8.3 - - - -
297B HIS* 3.4 21.8 - - + -
298B VAL* 3.8 23.3 - - + -
302B ASN* 3.5 22.7 - - - -
348B HEM 3.6 46.5 - - + +
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Residues in contact with PHE 242 (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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228B LEU* 4.8 8.3 - - + -
232B LEU* 3.7 24.7 - - + -
238B THR 3.4 24.7 - - - -
239B GLN* 3.0 9.8 + - - +
241B PHE* 1.4 85.4 - - + +
243B GLU* 1.4 58.2 + - - +
244B SER* 3.1 4.0 - - - +
245B PHE* 2.9 63.7 + + + +
246B GLY 4.3 0.2 + - - -
248B LEU* 3.9 18.1 - - + +
263B HIS* 3.6 29.6 - + - -
348B HEM 3.8 48.9 - + + -
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Residues in contact with GLU 243 (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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239B GLN 3.9 6.4 + - - +
240B ARG* 3.7 21.1 - - - +
241B PHE 3.7 2.4 - - - -
242B PHE* 1.4 72.6 - - - +
244B SER* 1.4 59.7 + - - +
245B PHE 3.3 0.7 + - - -
246B GLY* 3.6 13.3 + - - +
248B LEU* 5.3 3.1 - - - -
492C ARG* 4.6 14.1 + - - +
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Residues in contact with SER 244 (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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241B PHE 5.2 2.6 + - - -
242B PHE* 4.8 1.6 - - - -
243B GLU* 1.4 73.9 - - - +
245B PHE* 1.4 75.1 + - - +
246B GLY* 3.2 7.7 + - - -
259B LYS* 3.8 19.1 + - - +
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Residues in contact with PHE 245 (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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228B LEU* 5.4 1.6 - - + -
232B LEU* 6.1 0.2 - - + -
241B PHE 5.6 0.4 - - - -
242B PHE* 2.9 52.8 + + + +
244B SER* 1.4 90.8 - - - +
246B GLY* 1.4 58.0 + - - +
248B LEU* 4.7 6.1 - - + -
257B ASN* 2.9 29.7 + - - +
259B LYS* 3.3 59.6 - - + +
260B VAL* 3.7 14.4 - - + -
263B HIS* 3.7 23.1 - + + -
348B HEM 5.3 13.0 - - + -
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Residues in contact with GLY 246 (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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242B PHE 4.3 0.2 + - - -
243B GLU* 3.6 10.2 + - - +
244B SER 3.2 6.3 - - - -
245B PHE* 1.4 78.5 - - - +
247B ASP* 1.4 63.1 + - - -
248B LEU* 3.3 13.0 + - - +
257B ASN* 4.3 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