Contacts of the helix formed by residues 230 - 242 (chain B) in PDB entry 1TF4
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 230 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197A SER 4.0 5.7 - - - +
198A ASP* 3.0 41.1 + - - +
224B TYR* 3.8 19.1 + - - -
228B GLY 3.2 8.2 + - - +
229B ASP* 1.3 71.0 + - - +
231B SER* 1.3 62.7 + - - +
233B LEU* 3.1 8.5 + - + +
234B ALA* 3.0 21.9 + - - +
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Residues in contact with SER 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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198A ASP* 3.9 15.2 - - - -
229B ASP* 2.6 32.0 + - - -
230B ASP* 1.3 77.2 - - - +
232B TYR* 1.3 59.7 + - - +
234B ALA* 3.2 10.5 - - - +
235B LYS* 2.8 27.8 + - - +
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Residues in contact with TYR 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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183B LYS* 3.3 41.0 + - + +
186B TYR* 4.2 18.1 - + - -
187B THR* 5.4 1.9 + - - -
220B ALA* 3.6 25.6 - - + +
223B LEU* 3.7 35.9 - - + +
224B TYR 3.8 5.8 - - - +
227B THR* 3.5 25.1 - - + -
229B ASP* 3.1 30.1 + - + +
230B ASP 3.1 0.6 - - - -
231B SER* 1.3 79.1 + - - +
233B LEU* 1.3 60.5 + - - +
235B LYS* 3.0 9.0 + - + +
236B ALA* 2.8 29.1 + - - +
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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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221B TYR* 5.1 2.7 - - + +
224B TYR* 3.7 53.7 - - + +
230B ASP* 3.1 12.5 + - + +
232B TYR* 1.3 77.4 - - - +
234B ALA* 1.3 62.4 + - - +
236B ALA* 3.2 6.6 + - + +
237B GLU* 3.0 41.5 + - + +
271B LEU* 4.1 24.9 - - + -
274B GLU* 4.4 12.8 - - + -
275B THR* 4.6 9.2 - - + -
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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 ASP 3.0 10.9 + - - +
231B SER* 3.2 14.1 - - - +
233B LEU* 1.3 78.2 - - - +
235B LYS* 1.3 56.6 + - - +
237B GLU* 3.4 7.8 + - - +
238B TYR* 2.9 31.5 + - - +
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Residues in contact with LYS 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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186B TYR* 3.4 31.4 - - + +
190B ASP* 2.8 36.2 + - - -
193B ARG* 3.9 2.0 - - - +
216B LEU* 5.6 0.2 - - - -
220B ALA* 3.9 6.5 - - + -
231B SER 2.8 14.1 + - - +
232B TYR* 3.2 14.8 - - + +
234B ALA* 1.3 76.1 - - - +
236B ALA* 1.3 56.9 + - - +
238B TYR* 3.4 10.4 + - + +
239B GLU* 2.8 64.8 + - + +
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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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217B VAL* 3.7 27.9 - - + +
220B ALA* 3.9 15.7 - - + -
221B TYR* 4.1 11.9 - - + +
232B TYR 2.8 12.5 + - - +
233B LEU* 3.5 11.4 - - - +
235B LYS* 1.3 75.9 - - - +
237B GLU* 1.3 58.4 + - - +
239B GLU 3.3 1.4 + - - -
240B TYR* 2.9 29.7 + - - +
271B LEU* 4.6 12.1 - - + -
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Residues in contact with GLU 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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233B LEU* 3.0 39.7 + - + +
234B ALA* 3.9 6.1 - - - +
236B ALA* 1.3 75.5 - - - +
238B TYR* 1.3 63.1 + - - +
240B TYR* 3.5 14.5 - - - +
241B ASP* 3.6 11.4 - - - +
271B LEU* 4.7 6.3 - - + -
275B THR* 3.7 13.5 - - - +
277B LYS* 2.8 35.8 + - - +
279B LYS* 4.6 4.2 + - - -
280B TYR* 2.7 32.9 + - + +
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Residues in contact with TYR 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 ALA 2.9 17.3 + - - +
235B LYS* 3.7 11.7 - - + +
236B ALA 3.2 0.4 - - - -
237B GLU* 1.3 78.8 - - - +
239B GLU* 1.3 83.9 + - + +
240B TYR 3.2 1.2 + - - -
241B ASP* 3.4 16.0 + - - +
242B PHE* 3.6 40.9 - + - -
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Residues in contact with GLU 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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190B ASP* 4.1 0.2 - - - +
193B ARG* 3.4 18.5 + - - -
213B GLN* 3.0 39.8 + - - +
216B LEU* 4.5 12.6 - - + +
217B VAL* 3.8 19.5 - - + +
235B LYS* 2.8 59.8 + - + +
236B ALA 3.9 0.9 - - - +
238B TYR* 1.3 88.0 - - + +
240B TYR* 1.3 65.5 + - - +
241B ASP 3.2 0.2 - - - -
242B PHE* 3.0 25.9 + - - +
243B LEU 4.0 1.0 + - - -
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Residues in contact with TYR 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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217B VAL* 4.0 10.1 - - + -
236B ALA 2.9 17.2 + - - +
237B GLU* 3.5 14.4 - - - +
238B TYR 3.1 0.2 - - - -
239B GLU* 1.3 74.8 - - - +
241B ASP* 1.3 61.9 + - - +
242B PHE 3.1 1.4 + - - -
243B LEU* 3.2 34.2 + - + +
252B ARG* 3.5 31.1 + - - -
267B THR* 3.9 13.0 - - - -
268B TYR* 3.2 26.0 - + - -
271B LEU* 3.5 21.1 - - + -
279B LYS* 3.9 13.0 - - + -
280B TYR* 3.5 35.7 - + + +
283B ASP* 2.7 24.1 + - - +
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Residues in contact with ASP 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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237B GLU 3.6 11.6 - - - +
238B TYR* 3.4 11.8 + - - +
239B GLU 3.1 1.6 + - - -
240B TYR* 1.3 74.9 - - - +
242B PHE* 1.3 68.0 + - + +
243B LEU 3.3 4.3 + - - +
252B ARG* 4.2 16.2 + - - +
279B LYS* 2.7 38.0 + - - -
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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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213B GLN* 3.4 26.8 - - - +
238B TYR* 3.6 50.7 - + - -
239B GLU* 3.0 27.5 + - - +
241B ASP* 1.3 84.3 - - + +
243B LEU* 1.3 64.9 + - - +
244B SER* 3.7 1.4 + - - -
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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