Contacts of the helix formed by residues 230 - 242 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A TYR* 3.8 19.2 + - - -
228A GLY 3.2 10.6 + - - +
229A ASP* 1.3 73.2 + - - +
231A SER* 1.3 62.8 + - - +
233A LEU* 3.1 8.7 + - + +
234A ALA* 3.0 21.6 + - - +
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Residues in contact with SER 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A ASP* 2.6 31.5 + - - -
230A ASP* 1.3 76.7 - - - +
232A TYR* 1.3 62.0 + - - +
234A ALA* 3.2 9.8 - - - +
235A LYS* 2.8 28.3 + - - +
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Residues in contact with TYR 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LYS* 3.5 28.7 + - + +
186A TYR* 4.2 18.5 - + - -
187A THR* 5.4 1.9 + - - -
220A ALA* 3.6 27.2 - - + +
223A LEU* 3.7 38.1 - - + +
224A TYR* 3.8 6.1 - - - +
227A THR* 3.6 31.4 - - + -
229A ASP* 3.1 29.0 + - + +
230A ASP 3.1 0.6 - - - -
231A SER* 1.3 78.6 + - - +
233A LEU* 1.3 59.4 + - - +
235A LYS* 3.0 8.5 + - + +
236A ALA* 2.8 29.3 + - - +
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Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A TYR* 5.1 2.9 - - + +
224A TYR* 3.7 54.7 - - + +
230A ASP* 3.1 12.7 + - + +
232A TYR* 1.3 77.5 - - - +
234A ALA* 1.3 63.2 + - - +
236A ALA* 3.2 6.4 + - + +
237A GLU* 3.0 41.1 + - + +
271A LEU* 4.2 23.8 - - + -
274A GLU* 4.3 13.7 - - + -
275A THR* 4.6 9.0 - - + -
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Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A ASP 3.0 11.5 + - - +
231A SER* 3.2 13.9 - - - +
233A LEU* 1.3 79.0 - - - +
235A LYS* 1.3 56.8 + - - +
237A GLU* 3.4 7.5 + - - +
238A TYR* 3.0 30.4 + - - +
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Residues in contact with LYS 235 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A TYR* 3.4 32.8 - - + +
190A ASP* 2.8 39.4 + - - -
193A ARG* 4.0 1.4 - - - +
220A ALA* 3.9 5.6 - - + -
231A SER 2.8 13.6 + - - +
232A TYR* 3.0 15.5 + - + +
234A ALA* 1.3 76.7 - - - +
236A ALA* 1.3 61.7 + - - +
238A TYR* 3.3 11.2 + - + +
239A GLU* 2.8 51.5 + - + +
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Residues in contact with ALA 236 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A VAL* 3.7 27.8 - - + +
220A ALA* 3.9 17.0 - - + +
221A TYR* 4.1 12.1 - - + +
232A TYR 2.8 12.1 + - - +
233A LEU* 3.2 11.6 + - + +
235A LYS* 1.3 76.9 - - - +
237A GLU* 1.3 58.9 + - - +
238A TYR 3.2 0.2 + - - -
239A GLU* 3.3 1.6 + - - -
240A TYR* 2.9 30.0 + - - +
271A LEU* 4.6 11.0 - - + -
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Residues in contact with GLU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A LEU* 3.0 40.5 + - + +
234A ALA* 3.9 6.4 - - - +
236A ALA* 1.3 74.8 - - - +
238A TYR* 1.3 61.0 + - - +
240A TYR* 3.6 10.6 - - - +
241A ASP* 3.4 15.1 - - - +
271A LEU* 4.7 6.7 - - + -
275A THR* 3.6 16.8 - - - +
277A LYS* 2.8 37.2 + - - +
279A LYS* 4.6 2.9 + - - -
280A TYR* 2.8 30.9 + - + +
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Residues in contact with TYR 238 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A ALA 3.0 17.1 + - - +
235A LYS* 3.6 11.2 - - + +
236A ALA 3.1 0.2 - - - -
237A GLU* 1.3 76.3 - - - +
239A GLU* 1.3 86.4 + - + +
240A TYR 3.2 0.7 + - - -
241A ASP* 3.5 16.9 + - - +
242A PHE* 3.6 41.8 - + - -
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Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A TYR* 5.0 0.4 - - - +
190A ASP* 4.1 0.2 - - - +
193A ARG* 3.4 16.9 + - - -
213A GLN* 3.0 39.3 + - - +
216A LEU* 4.4 15.2 - - + +
217A VAL* 3.7 20.3 - - + +
235A LYS* 2.8 58.2 + - + +
236A ALA 4.0 0.4 - - - +
238A TYR* 1.3 85.4 - - + +
240A TYR* 1.3 64.8 + - - +
242A PHE* 3.0 25.6 + - - -
243A LEU 4.0 1.4 + - - -
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Residues in contact with TYR 240 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A VAL* 3.7 11.0 - - + +
236A ALA 2.9 16.1 + - - +
237A GLU* 3.6 13.9 - - - +
238A TYR 3.1 0.6 - - - -
239A GLU* 1.3 77.0 - - - +
241A ASP* 1.3 61.3 + - - +
242A PHE 3.2 1.2 + - - -
243A LEU* 3.2 30.7 + - + +
252A ARG* 3.6 30.4 + - - -
267A THR* 3.8 17.5 - - - -
268A TYR* 3.2 26.2 - + - -
271A LEU* 3.4 20.6 - - + -
279A LYS* 4.0 14.1 - - + -
280A TYR* 3.5 36.2 - + + -
283A ASP* 2.7 23.8 + - - +
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Residues in contact with ASP 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A GLU 3.4 13.0 - - - +
238A TYR* 3.6 10.9 - - - +
239A GLU 3.1 1.8 + - - -
240A TYR* 1.3 76.2 - - - +
242A PHE* 1.3 69.1 + - + +
243A LEU 3.4 3.0 + - - +
252A ARG* 4.2 16.0 + - - +
279A LYS* 2.7 38.2 + - - -
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Residues in contact with PHE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A GLN* 3.5 30.0 - - + +
238A TYR* 3.6 50.7 - + - -
239A GLU* 3.0 24.4 + - - -
241A ASP* 1.3 84.3 - - + +
243A LEU* 1.3 66.0 + - - +
244A SER* 3.7 1.2 + - - -
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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