Contacts of the helix formed by residues 234 - 241 (chain B) in PDB entry 5T0I
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 234 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B LEU* 4.8 9.6 - - + -
193B GLN* 3.3 42.4 - - + +
194B ILE* 5.3 0.2 - - + -
197B ILE* 3.6 33.7 - - + -
224B LEU* 4.3 16.8 - - + +
230B THR 4.2 0.8 + - - -
231B GLY 3.9 2.7 + - - -
233B THR* 1.3 80.6 - - + +
235B LEU* 1.3 64.2 + - - +
236B ALA 3.0 2.0 - - - -
237B LYS* 3.1 35.1 + - + +
238B ALA* 3.6 3.6 + - - +
351B ILE* 3.5 34.3 - - + -
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Residues in contact with LEU 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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182B GLU* 5.4 10.3 - - + -
224B LEU* 5.0 3.1 - - - -
231B GLY 3.6 6.5 + - - +
232B LYS* 3.2 39.6 + - + +
234B LEU* 1.3 76.6 - - - +
236B ALA* 1.3 59.5 + - - +
237B LYS 3.1 0.2 - - - -
238B ALA* 2.9 27.6 + - + +
239B VAL* 3.1 19.5 + - + +
247B PHE* 5.7 3.6 - - + -
249B ARG* 5.3 9.2 - - - -
283B PHE* 3.5 37.0 - - + -
285B ASP* 5.5 2.5 - - - +
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Residues in contact with ALA 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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182B GLU* 4.9 2.8 - - + +
183B THR 5.3 4.3 - - - +
184B TYR* 5.6 5.0 + - - +
187B ILE* 3.5 47.1 - - + -
232B LYS 3.8 2.3 + - - +
233B THR 3.8 8.9 + - - +
234B LEU 3.0 0.6 - - - -
235B LEU* 1.3 81.4 - - - +
237B LYS* 1.3 56.8 + - - +
239B VAL* 3.1 14.5 - - + +
240B ALA* 3.0 24.1 + - - +
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Residues in contact with LYS 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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194B ILE* 2.4 56.5 + - + +
197B ILE* 3.2 24.1 - - + +
198B LYS* 3.0 50.6 - - + +
201B VAL* 4.8 10.5 - - + -
234B LEU* 3.1 19.8 + - + +
236B ALA* 1.3 78.9 - - + +
238B ALA* 1.3 58.5 + - - +
239B VAL 3.3 0.2 - - - -
240B ALA* 3.3 7.8 + - + +
241B ASN* 2.7 40.3 + - - +
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Residues in contact with ALA 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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234B LEU 3.6 2.3 + - - +
235B LEU* 2.9 22.1 + - + +
237B LYS* 1.3 79.3 - - - +
239B VAL* 1.3 57.4 + - - +
241B ASN* 3.1 24.3 + - - +
242B GLN* 3.4 13.7 + - - +
247B PHE* 3.6 35.2 - - + -
281B ILE* 5.0 4.9 - - + -
283B PHE* 5.4 5.4 - - + -
328B ILE* 5.3 7.6 - - + -
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Residues in contact with VAL 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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180B PRO* 3.8 19.5 - - + +
182B GLU* 3.2 60.3 - - + +
235B LEU* 3.1 12.1 + - + +
236B ALA* 3.1 29.8 - - + +
238B ALA* 1.3 73.0 - - - +
240B ALA* 1.3 59.7 + - - +
241B ASN 3.1 1.3 - - - -
242B GLN* 3.0 49.4 + - - +
243B THR 4.0 0.2 + - - -
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Residues in contact with ALA 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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180B PRO* 5.6 0.4 - - - -
182B GLU 5.6 0.7 - - - -
184B TYR* 5.9 7.6 - - + +
198B LYS* 4.3 17.4 + - - +
202B GLU* 5.3 1.6 - - - +
236B ALA 3.0 20.7 + - - +
237B LYS* 3.3 11.6 + - + +
239B VAL* 1.3 78.2 - - - +
241B ASN* 1.3 59.8 + - - +
242B GLN 3.2 0.9 - - - -
243B THR* 3.1 28.8 + - - +
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Residues in contact with ASN 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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198B LYS* 4.8 2.8 + - - -
201B VAL* 3.4 38.0 + - - +
202B GLU* 3.0 25.3 - - - +
237B LYS 2.7 26.5 + - - +
238B ALA* 3.4 13.4 - - - +
239B VAL 3.1 0.8 - - - -
240B ALA* 1.3 76.4 - - - +
242B GLN* 1.3 55.3 + - - +
243B THR* 3.3 1.8 - - - -
244B SER 2.6 25.9 - - - +
245B ALA* 4.9 0.2 - - - +
246B THR 4.6 9.5 + - - +
247B PHE* 5.1 0.9 - - + -
281B ILE* 4.5 27.1 - - + +
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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