Contacts of the helix formed by residues 272 - 281 (chain O) in PDB entry 2I2X
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 GLU 272 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218O THR* 3.8 1.9 - - - -
219O ASP* 2.8 33.6 + - - +
247O ARG* 3.1 33.9 + - + +
250O SER* 3.3 25.6 - - - +
251O ALA* 4.1 16.8 - - + +
254O SER* 2.8 26.4 + - - +
269O CYS 4.3 0.2 - - - +
270O GLY* 3.4 12.5 - - - -
271O TYR* 1.3 75.5 + - - +
273O ASN* 1.3 63.8 + - - +
274O ILE 2.9 8.1 + - - -
275O ILE* 2.9 25.2 + - + +
276O VAL* 3.2 9.9 + - + +
370O LEU* 4.8 0.9 - - - -
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Residues in contact with ASN 273 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217O ASP 4.6 5.9 - - - +
254O SER* 5.2 3.6 - - - -
258O TYR* 4.6 2.8 + - - -
266O GLY* 3.6 15.7 - - - -
267O LYS 2.7 27.7 + - - -
270O GLY* 2.8 25.8 + - - +
271O TYR 3.0 0.2 - - - -
272O GLU* 1.3 82.5 - - - +
274O ILE* 1.3 56.7 + - - +
275O ILE 3.3 0.2 - - - -
276O VAL* 3.5 11.0 - - - +
277O LYS* 2.8 31.5 + - - +
284O MET* 3.5 25.4 - - + +
285O THR 3.1 15.0 + - - -
286O MET* 3.6 12.3 - - - -
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Residues in contact with ILE 274 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17O MET* 3.9 9.6 - - + -
271O TYR 3.6 17.5 + - - +
272O GLU 2.9 1.3 + - - +
273O ASN* 1.3 77.6 - - - +
275O ILE* 1.3 65.3 + - - +
277O LYS* 3.4 5.3 + - + +
278O ALA* 3.2 20.6 + - - +
284O MET* 6.0 0.2 - - - -
286O MET* 4.3 13.4 - - + +
305O GLN* 3.6 23.8 - - + +
306O CYS* 3.7 38.1 - - + +
370O LEU* 3.6 30.5 - - + +
372O TYR* 4.1 6.1 - - + -
375O ALA* 3.7 19.7 - - + -
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Residues in contact with ILE 275 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247O ARG* 5.0 0.9 - - + +
248O ALA* 4.8 5.4 - - - -
251O ALA* 3.6 31.0 - - + -
272O GLU* 2.9 13.5 + - + +
274O ILE* 1.3 76.3 - - + +
276O VAL* 1.3 63.2 + - - +
278O ALA* 3.4 4.8 + - - +
279O ILE* 3.2 23.0 + - + +
369O MET* 4.0 26.2 - - + -
370O LEU* 4.1 11.4 - - + -
375O ALA* 3.7 30.3 - - + +
378O VAL* 4.3 9.4 - - + -
379O GLY* 3.9 24.0 - - - +
382O ILE* 3.9 12.1 - - + -
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Residues in contact with VAL 276 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251O ALA* 3.8 26.0 - - - +
254O SER* 4.4 11.2 - - - -
255O LEU* 4.1 12.6 - - + +
258O TYR* 3.7 24.2 - - + -
272O GLU 3.2 12.0 + - - +
273O ASN* 3.1 16.4 + - - +
275O ILE* 1.3 76.6 - - - +
277O LYS* 1.3 52.8 + - - +
279O ILE* 3.1 8.3 + - + +
280O THR* 2.7 46.4 + - + +
284O MET* 3.7 21.1 - - + -
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Residues in contact with LYS 277 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11O TYR* 3.4 21.7 - - + -
17O MET* 4.0 11.9 - - + -
18O THR 3.2 12.0 + - - +
21O VAL 2.9 27.8 + - - -
22O SER* 3.8 6.1 - - - -
273O ASN 2.8 16.8 + - - +
274O ILE* 3.7 7.2 - - + +
276O VAL* 1.3 75.1 - - - +
278O ALA* 1.3 61.7 + - - +
280O THR* 3.9 5.8 - - - -
281O GLY 2.8 26.3 + - - -
282O MET 3.5 17.5 - - - +
284O MET* 3.9 10.1 - - + +
306O CYS* 2.8 28.2 + - + +
307O CYS 4.6 0.4 - - - -
308O ASP* 2.8 29.9 + - - +
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Residues in contact with ALA 278 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9O MET* 3.8 24.2 - - + +
10O ALA 3.5 12.8 + - - -
11O TYR* 3.5 13.1 + - - +
17O MET* 3.6 28.5 - - - +
274O ILE 3.2 12.4 + - - +
275O ILE* 3.5 11.0 - - - +
277O LYS* 1.3 76.2 - - - +
279O ILE* 1.3 63.1 + - - +
375O ALA 4.6 0.4 - - - +
376O TYR* 3.9 17.3 - - + +
379O GLY* 5.4 0.2 - - - -
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Residues in contact with ILE 279 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6O TYR* 3.7 38.1 - - + -
8O SER 3.9 2.7 - - - +
9O MET* 3.8 11.0 - - - -
10O ALA* 3.0 24.8 + - - +
251O ALA 5.7 0.9 - - - +
255O LEU* 3.8 29.4 - - + -
275O ILE* 3.2 16.8 + - + +
276O VAL* 3.1 8.5 + - - +
278O ALA* 1.3 76.4 - - - +
280O THR* 1.3 59.8 + - - +
379O GLY* 3.9 30.3 - - - +
382O ILE* 4.0 24.2 - - + -
383O VAL* 3.9 11.2 - - + -
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Residues in contact with THR 280 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6O TYR* 3.6 34.9 + - + +
10O ALA* 3.6 3.7 - - - +
24O TYR* 3.3 20.6 - - - -
255O LEU* 3.6 27.8 - - + -
258O TYR* 4.2 9.0 - - + -
276O VAL* 2.7 38.0 + - + +
277O LYS* 3.9 1.2 - - - -
279O ILE* 1.3 72.4 - - - +
281O GLY* 1.3 61.1 + - - +
282O MET* 3.2 29.2 + - - +
284O MET* 4.2 0.3 - - - +
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Residues in contact with GLY 281 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10O ALA* 3.4 17.1 - - - +
11O TYR* 3.7 11.9 - - - -
22O SER* 3.3 5.9 - - - -
23O LYS* 3.1 15.7 + - - -
24O TYR* 3.0 28.0 + - - -
277O LYS 2.8 22.3 + - - -
280O THR* 1.3 72.0 - - - +
282O MET* 1.3 57.8 + - - +
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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