Contacts of the helix formed by residues 272 - 281 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A THR* 3.9 1.4 - - - +
219A ASP* 2.9 21.2 + - - +
247A ARG* 3.2 32.0 + - + +
250A SER* 3.2 26.9 - - - +
251A ALA* 4.0 18.6 - - + -
254A SER* 2.7 32.2 + - - +
269A CYS 4.4 0.2 - - - +
270A GLY* 3.3 11.7 - - - -
271A TYR* 1.3 77.4 + - - +
273A ASN* 1.3 66.0 + - - +
274A ILE 3.0 3.1 - - - -
275A ILE* 2.9 24.6 + - + +
276A VAL* 3.2 10.0 + - + +
370A LEU* 4.7 1.3 - - - -
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Residues in contact with ASN 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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217A ASP 4.6 5.9 - - - +
254A SER* 5.2 3.1 - - - -
258A TYR* 4.6 5.0 + - - -
266A GLY* 3.7 12.7 - - - -
267A LYS 2.8 29.3 + - - +
270A GLY* 2.7 23.9 + - - +
271A TYR 3.0 0.2 - - - -
272A GLU* 1.3 81.0 - - - +
274A ILE* 1.3 57.5 + - - +
276A VAL* 3.5 13.7 - - - +
277A LYS* 2.8 32.4 + - - +
284A MET* 3.6 31.7 - - + +
285A THR 3.3 12.3 + - - -
286A MET* 3.7 7.0 - - - -
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Residues in contact with ILE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A MET* 4.0 10.5 - - + -
271A TYR 3.5 17.3 + - - +
272A GLU 4.4 0.2 - - - +
273A ASN* 1.3 78.7 - - - +
275A ILE* 1.3 65.4 + - - +
277A LYS* 3.4 4.2 + - + +
278A ALA* 3.1 22.0 + - - +
286A MET* 4.3 13.2 - - + +
305A GLN* 3.6 24.9 - - + +
306A CYS* 3.8 35.9 - - + -
370A LEU* 3.6 33.2 - - + +
372A TYR* 4.0 5.8 - - + -
375A ALA* 3.6 17.9 - - + +
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Residues in contact with ILE 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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248A ALA* 4.8 2.2 - - - -
251A ALA* 3.6 31.9 - - + -
272A GLU* 2.9 14.8 + - + +
274A ILE* 1.3 77.0 - - + +
276A VAL* 1.3 62.7 + - - +
278A ALA* 3.2 6.3 + - - +
279A ILE* 3.2 22.7 + - + +
369A MET* 3.9 30.3 - - + -
370A LEU* 4.4 6.7 - - + -
375A ALA* 3.7 28.0 - - + +
378A VAL* 4.0 9.4 - - + -
379A GLY* 3.8 23.8 - - - +
382A ILE* 3.9 12.3 - - + -
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Residues in contact with VAL 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A ALA* 3.8 25.1 - - - +
254A SER* 4.4 10.1 - - - -
255A LEU* 4.2 13.5 - - + +
258A TYR* 3.6 33.9 - - + -
272A GLU 3.2 13.4 + - - +
273A ASN* 3.1 15.8 + - - +
275A ILE* 1.3 75.6 - - + +
277A LYS* 1.3 49.9 + - - +
279A ILE* 3.3 7.7 + - + +
280A THR* 2.8 46.6 + - + +
284A MET* 3.7 14.4 - - + -
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Residues in contact with LYS 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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11A TYR* 3.5 18.2 - - + -
17A MET* 3.8 14.1 - - + -
18A THR 3.2 11.7 + - - +
21A VAL 3.1 26.8 + - - -
22A SER* 3.8 7.9 - - - -
273A ASN 2.8 19.9 + - - +
274A ILE* 3.7 6.7 - - + +
276A VAL* 1.3 69.8 - - - +
278A ALA* 1.3 61.5 + - - +
280A THR* 3.9 5.6 - - - -
281A GLY* 2.7 28.9 + - - -
282A MET 3.3 17.5 - - - +
284A MET* 4.0 9.8 - - + +
306A CYS* 2.8 28.8 + - + +
307A CYS 4.4 0.4 + - - -
308A ASP* 2.7 29.4 + - - +
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Residues in contact with ALA 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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9A MET* 3.3 26.9 - - + +
10A ALA 3.7 9.4 + - - -
11A TYR* 3.8 13.0 + - - +
17A MET* 3.4 29.7 - - + +
274A ILE 3.1 8.3 + - - +
275A ILE* 3.2 11.0 + - - +
277A LYS* 1.3 79.3 - - - +
279A ILE* 1.3 61.3 + - - +
375A ALA 4.8 0.4 - - - +
376A TYR* 3.9 18.6 - - + +
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Residues in contact with ILE 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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6A TYR* 3.6 40.2 - - + -
8A SER 4.0 3.1 - - - +
9A MET* 3.9 7.7 - - - -
10A ALA* 2.9 24.1 + - - +
251A ALA 5.9 0.9 - - - +
255A LEU* 3.9 28.0 - - + -
275A ILE* 3.2 17.8 + - + +
276A VAL* 3.7 7.2 - - + +
277A LYS 3.2 0.2 - - - -
278A ALA* 1.3 75.7 - - - +
280A THR* 1.3 59.4 + - - +
379A GLY* 4.0 24.9 - - - +
382A ILE* 4.0 29.8 - - + -
383A VAL* 3.9 11.4 - - + -
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Residues in contact with THR 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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6A TYR* 3.8 29.0 + - + +
10A ALA* 3.5 3.1 - - - +
24A TYR* 3.3 20.6 - - - -
255A LEU* 3.5 28.7 - - + -
258A TYR* 4.0 13.0 - - + -
276A VAL* 2.8 35.1 + - + +
277A LYS* 3.9 0.9 - - - -
279A ILE* 1.3 73.9 - - - +
281A GLY* 1.3 59.6 + - - +
282A MET* 3.1 35.1 + - - +
284A MET* 4.1 2.6 - - - +
27I LYS* 5.1 0.2 + - - -
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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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10A ALA* 3.4 15.8 - - - +
11A TYR* 3.7 13.5 - - - -
22A SER* 3.4 5.4 - - - -
23A LYS* 3.1 10.5 + - - -
24A TYR* 3.0 32.4 + - - -
277A LYS* 2.7 21.1 + - - -
280A THR* 1.3 72.7 - - - +
282A MET* 1.3 59.4 + - - +
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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