Contacts of the helix formed by residues 272 - 283 (chain A) in PDB entry 3APO
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 THR 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A CYS 3.3 3.9 + - - -
271A LEU* 1.3 75.7 - - - +
273A SER* 1.3 59.9 + - - +
274A GLN* 3.2 12.3 - - + +
275A THR* 3.1 37.5 + - - +
276A ARG* 3.0 29.7 + - - +
334A LEU* 5.4 1.6 + - - +
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Residues in contact with SER 273 (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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271A LEU 4.0 0.2 + - - -
272A THR* 1.3 73.3 + - - +
274A GLN* 1.3 65.2 + - - +
276A ARG* 3.6 35.1 + - - +
277A LEU* 3.3 25.3 + - - +
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Residues in contact with GLN 274 (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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223A GLU 5.7 1.0 + - - -
226A VAL* 4.1 16.6 - - - +
227A ALA* 5.1 8.1 - - - +
230A MET* 3.8 26.7 - - + +
272A THR* 3.2 10.2 - - + +
273A SER* 1.3 75.7 - - - +
275A THR* 1.3 61.5 + - - +
277A LEU* 3.4 9.0 + - + +
278A ARG* 2.8 36.3 + - - +
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Residues in contact with THR 275 (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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271A LEU* 4.4 12.1 - - + -
272A THR* 3.1 29.7 + - - +
274A GLN* 1.3 74.9 - - - +
276A ARG* 1.3 58.6 + - - +
278A ARG* 2.9 12.9 + - - +
279A LEU* 2.8 36.9 + - + +
334A LEU 3.7 24.4 + - - +
335A ASP 4.7 0.2 - - - -
336A ALA* 4.0 24.2 + - + +
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Residues in contact with ARG 276 (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 VAL* 3.5 28.3 - - + +
262A THR* 4.0 22.2 - - + +
264A CYS* 5.7 1.4 - - - -
271A LEU* 4.3 18.3 + - + -
272A THR 3.0 20.3 + - - +
273A SER* 3.6 36.7 + - - +
275A THR* 1.3 75.7 - - - +
277A LEU* 1.3 59.3 + - - +
279A LEU* 3.6 11.2 - - - +
280A SER* 2.9 28.1 + - - -
289A VAL* 3.6 17.8 - - + +
290A GLY 4.8 1.8 - - - -
291A TRP* 3.8 46.4 - - - +
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Residues in contact with LEU 277 (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 MET* 4.9 15.5 - - + +
233A VAL* 5.5 0.7 - - - +
235A SER* 3.6 29.6 - - - +
237A VAL* 3.7 28.0 - - + +
273A SER* 3.3 22.0 + - - +
274A GLN* 3.4 9.6 - - + +
276A ARG* 1.3 76.4 - - - +
278A ARG* 1.3 66.3 + - - +
280A SER* 3.1 5.2 - - - -
281A GLY* 3.0 18.0 + - - -
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Residues in contact with ARG 278 (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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174A GLU* 2.4 56.1 + - - +
175A VAL* 4.4 3.0 - - - +
178A LEU* 3.6 31.0 - - + +
226A VAL* 4.1 21.6 - - - +
230A MET* 3.8 18.5 - - + +
274A GLN* 2.8 25.0 + - - +
275A THR* 2.9 12.2 + - - +
277A LEU* 1.3 73.2 - - - +
279A LEU* 1.3 56.4 + - - +
281A GLY* 3.2 2.3 + - - +
282A MET* 2.9 42.0 + - - +
336A ALA* 4.1 17.9 - - + +
337A LYS* 4.1 8.0 - - - +
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Residues in contact with LEU 279 (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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260A LEU* 3.9 23.8 - - + -
271A LEU* 3.8 28.9 - - + -
275A THR* 2.8 23.3 + - + +
276A ARG* 3.6 11.2 - - + +
277A LEU 3.3 0.2 - - - -
278A ARG* 1.3 69.1 - - - +
280A SER* 1.3 59.6 + - - +
282A MET* 3.3 3.7 + - - +
283A LEU* 2.9 39.5 + - + +
289A VAL* 4.2 5.3 - - + +
336A ALA* 3.4 31.9 - - + +
339A ILE* 4.0 17.9 - - + -
340A TYR* 3.8 22.0 - - + +
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Residues in contact with SER 280 (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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234A ARG 4.2 0.7 - - - +
235A SER* 3.0 8.6 - - - -
236A THR 2.8 41.8 + - - -
237A VAL* 3.9 5.8 - - - -
276A ARG 2.9 14.8 + - - -
277A LEU 3.1 14.4 - - - -
279A LEU* 1.3 75.9 - - - +
281A GLY* 1.3 54.3 + - - +
283A LEU 3.6 1.4 - - - -
284A ASP* 2.9 30.5 + - - +
287A VAL 5.5 0.6 - - - +
289A VAL* 3.6 14.1 - - - +
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Residues in contact with GLY 281 (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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178A LEU* 4.0 10.2 - - - +
233A VAL* 3.6 29.9 - - - +
234A ARG 3.9 7.2 - - - -
235A SER* 4.2 0.2 - - - -
277A LEU 3.0 12.9 + - - -
278A ARG 3.2 3.8 + - - -
280A SER* 1.3 73.5 + - - +
282A MET* 1.3 64.2 + - - +
283A LEU 3.2 0.9 + - - -
284A ASP* 3.3 15.1 + - - +
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Residues in contact with MET 282 (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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175A VAL* 5.5 0.4 - - - -
176A ASP 3.3 26.7 - - - +
177A GLY 3.5 20.9 - - - +
178A LEU* 3.8 17.2 - - + +
278A ARG* 2.9 30.2 + - + +
279A LEU* 3.8 6.3 - - - +
281A GLY* 1.3 77.2 - - - +
283A LEU* 1.3 59.6 + - - +
284A ASP 3.5 0.7 + - - +
336A ALA* 4.4 20.9 - - - +
337A LYS* 4.5 10.8 - - + -
340A TYR* 3.3 52.5 - - + -
386A LYS* 2.8 30.8 + - - +
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Residues in contact with LEU 283 (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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260A LEU* 3.9 24.9 - - + -
279A LEU* 2.9 25.1 + - + +
280A SER* 3.6 3.4 - - - -
282A MET* 1.3 76.2 - - - +
284A ASP* 1.3 66.3 + - - +
285A GLY 3.2 0.7 + - - -
286A LEU* 2.9 24.2 + - + -
287A VAL* 3.1 33.0 + - + +
289A VAL* 5.2 1.3 - - + -
340A TYR* 3.6 28.7 - - + -
343A ILE* 3.8 36.3 - - + -
344A ILE* 3.7 17.5 - - + -
347A LEU* 4.6 0.7 - - + -
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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