Contacts of the helix formed by residues 247 - 254 (chain B) in PDB entry 1JKT
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 LEU 247 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245B SER* 2.9 6.3 + - - -
246B ALA* 1.3 84.1 - - + +
248B ALA* 1.3 52.6 + - - +
250B ASP* 2.5 11.7 + - + +
251B PHE* 2.3 38.1 + - - +
272B HIS* 4.2 11.8 - - + -
273B PRO* 3.9 31.4 - - + +
274B TRP* 3.5 21.1 - - + +
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Residues in contact with ALA 248 (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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113B GLU* 4.0 0.2 - - - +
207B THR* 5.9 0.7 - - + -
211B LEU* 3.7 7.9 - - + -
244B THR* 3.6 15.0 - - + -
245B SER* 3.0 14.8 + - - +
247B LEU* 1.3 73.2 - - - +
249B LYS* 1.3 58.3 + - - +
250B ASP 2.6 12.0 + - - -
251B PHE* 2.8 11.9 + - - +
252B ILE* 3.0 19.6 + - + +
274B TRP* 2.8 48.4 - - + +
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Residues in contact with LYS 249 (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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211B LEU* 5.6 0.2 - - - +
236B PHE* 3.5 56.5 - - + +
241B PHE* 4.0 22.2 + - + -
242B SER* 4.9 6.6 - - - +
244B THR* 3.2 33.2 - - + +
245B SER 3.2 12.8 - - - +
246B ALA* 3.7 13.7 - - + +
248B ALA* 1.3 77.9 - - - +
250B ASP* 1.3 60.3 + - - +
252B ILE* 4.1 1.3 - - - +
253B ARG* 3.7 14.7 + - - +
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Residues in contact with ASP 250 (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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246B ALA 3.0 15.8 + - - +
247B LEU* 2.5 25.8 + - + +
249B LYS* 1.3 70.3 - - - +
251B PHE* 1.3 53.8 + - - +
252B ILE 2.9 1.8 - - - -
253B ARG* 2.3 50.9 + - - +
254B ARG* 3.1 36.3 + - - +
272B HIS* 4.4 7.0 + - + +
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Residues in contact with PHE 251 (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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120B LEU* 5.3 1.8 - - + -
124B LEU* 4.7 7.0 - - + -
203B ILE* 4.6 5.6 - - + -
204B GLY* 5.9 0.2 - - - -
207B THR* 4.3 22.9 - - + -
247B LEU 2.3 25.7 + - - +
248B ALA* 2.8 15.1 + - - +
250B ASP* 1.3 65.6 - - - +
252B ILE* 1.3 64.8 + - - +
254B ARG* 3.2 15.6 + - - +
255B LEU* 3.6 32.4 - - + +
264B MET* 3.9 3.3 - - + +
269B SER* 4.2 29.8 - - - -
272B HIS* 4.0 19.6 + + + -
274B TRP* 3.8 29.6 - + + -
275B ILE* 3.2 37.5 - - + -
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Residues in contact with ILE 252 (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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204B GLY* 4.2 13.2 - - - +
207B THR* 4.5 22.2 - - + -
208B TYR* 4.7 17.5 - - + -
211B LEU* 5.5 3.1 - - + -
234B TYR* 5.0 6.5 - - + -
236B PHE* 3.2 37.2 - - + -
241B PHE* 5.4 4.5 - - + -
248B ALA* 3.3 15.9 - - + +
249B LYS* 4.1 4.0 - - - +
250B ASP 2.7 3.6 + - - -
251B PHE* 1.3 73.6 - - + +
253B ARG* 1.3 56.9 + - - +
254B ARG 2.9 1.6 - - - -
255B LEU* 2.6 30.0 + - - +
256B LEU* 3.1 42.9 + - + -
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Residues in contact with ARG 253 (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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234B TYR* 3.1 35.1 + - + +
236B PHE* 5.2 13.2 - - + -
249B LYS 3.7 13.7 + - - +
250B ASP* 2.3 39.1 + - - +
252B ILE* 1.3 71.9 - - - +
254B ARG* 1.3 55.5 + - + +
255B LEU 3.1 4.7 + - - -
256B LEU 4.1 5.4 - - - +
257B VAL* 3.6 13.7 - - - +
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Residues in contact with ARG 254 (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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250B ASP* 3.1 30.4 + - - +
251B PHE* 3.6 3.4 - - - +
252B ILE 2.8 1.6 + - - -
253B ARG* 1.3 76.4 - - + +
255B LEU* 1.3 73.4 + - - +
257B VAL* 4.1 5.2 - - - -
262B LYS 5.2 1.7 - - - +
263B ARG* 4.3 1.1 - - - +
264B MET* 2.8 55.9 + - + +
268B ASP 5.3 0.2 - - - -
272B HIS* 3.7 27.2 + - - -
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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