Contacts of the helix formed by residues 272 - 281 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E THR* 4.0 1.2 - - - +
219E ASP* 3.0 31.9 + - - +
247E ARG* 3.0 33.5 + - + +
250E SER* 3.2 28.5 + - - +
251E ALA* 4.1 11.2 - - + -
254E SER* 3.1 26.5 + - - +
270E GLY* 2.7 13.4 + - - -
271E TYR* 1.3 72.2 + - - +
273E ASN* 1.3 62.3 + - - +
274E ILE 3.3 1.6 - - - -
275E ILE* 3.2 16.7 + - + +
276E VAL* 2.9 25.4 + - - +
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Residues in contact with ASN 273 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217E ASP 4.8 5.4 - - - +
218E THR* 6.0 0.2 - - - -
254E SER* 5.3 2.4 - - - -
258E TYR* 4.9 2.6 + - - -
266E GLY* 3.6 1.0 - - - -
267E LYS 3.0 34.6 + - - +
270E GLY* 2.7 29.4 + - - +
272E GLU* 1.3 73.1 - - - +
274E ILE* 1.3 56.4 + - - +
276E VAL* 3.7 11.5 - - - +
277E LYS* 2.6 37.8 + - - +
284E MET* 3.5 37.2 - - + +
285E THR 3.4 12.1 + - - -
286E MET* 3.6 7.4 - - - -
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Residues in contact with ILE 274 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17E MET* 4.3 8.5 - - + +
271E TYR 3.7 16.8 + - - +
273E ASN* 1.3 77.5 - - - +
275E ILE* 1.3 66.0 + - - +
277E LYS* 3.4 3.8 + - + +
278E ALA* 3.3 18.7 + - - +
286E MET* 4.2 13.0 - - + +
302E LEU* 5.7 0.4 - - + -
303E VAL* 6.5 0.2 - - + -
305E GLN* 3.3 26.5 - - + +
306E CYS* 3.7 37.0 - - + +
370E LEU* 3.5 31.0 - - + +
372E TYR* 3.9 9.2 - - + -
375E ALA* 3.7 19.5 - - + +
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Residues in contact with ILE 275 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247E ARG 4.7 4.3 - - - +
248E ALA* 4.8 0.7 - - - -
251E ALA* 3.6 30.1 - - + -
272E GLU* 3.2 12.9 + - - +
274E ILE* 1.3 78.9 - - + +
276E VAL* 1.3 64.7 + - - +
278E ALA* 3.2 18.1 + - - +
279E ILE* 3.6 11.3 + - + +
369E MET* 3.8 30.5 - - + -
370E LEU* 3.9 11.7 - - + -
375E ALA* 4.0 26.0 - - + +
378E VAL* 4.0 12.3 - - + -
379E GLY* 4.0 23.3 - - - +
382E ILE* 4.1 6.3 - - + -
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Residues in contact with VAL 276 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251E ALA* 3.7 26.0 - - - +
254E SER* 4.2 10.1 - - - -
255E LEU* 4.2 12.8 - - + +
258E TYR* 3.7 22.2 - - + -
272E GLU* 2.9 24.6 + - + +
273E ASN* 3.2 11.4 + - - +
275E ILE* 1.3 75.3 - - - +
277E LYS* 1.3 55.2 + - - +
279E ILE* 3.1 12.6 + - + +
280E THR* 2.7 36.5 + - + +
284E MET* 3.7 23.6 - - + -
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Residues in contact with LYS 277 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E TYR* 3.3 19.5 - - + +
17E MET* 3.9 14.6 - - + -
18E THR 3.2 23.2 + - - +
21E VAL 3.4 6.9 + - - -
22E SER* 3.7 18.8 - - - -
273E ASN 2.6 22.5 + - - +
274E ILE* 3.8 6.3 - - + +
276E VAL* 1.3 73.4 - - - +
278E ALA* 1.3 56.7 + - - +
279E ILE 3.1 0.2 - - - -
280E THR* 3.5 7.0 - - - -
281E GLY 2.9 25.6 + - - -
282E MET 3.4 16.6 - - - +
284E MET* 4.0 9.8 - - + +
306E CYS* 2.8 34.0 + - + +
307E CYS 4.4 0.2 + - - -
308E ASP* 3.2 23.9 + - - +
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Residues in contact with ALA 278 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E MET* 3.2 30.6 - - + +
10E ALA 3.7 4.5 + - - -
11E TYR* 4.0 11.3 - - - -
17E MET* 3.7 28.1 - - - +
274E ILE 3.3 6.9 + - - +
275E ILE* 3.2 11.6 + - - +
277E LYS* 1.3 77.0 - - - +
279E ILE* 1.3 57.9 + - - +
375E ALA* 5.0 0.7 - - + +
376E TYR* 3.8 27.6 - - + +
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Residues in contact with ILE 279 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E TYR* 3.7 28.6 - - + -
8E SER 3.7 6.2 - - - +
9E MET* 4.0 7.4 - - - +
10E ALA* 3.0 22.9 + - - +
251E ALA* 6.1 1.3 - - + +
255E LEU* 3.8 28.5 - - + -
275E ILE* 3.7 16.2 - - + +
276E VAL* 3.1 8.0 + - + +
277E LYS 3.1 0.6 - - - -
278E ALA* 1.3 81.8 - - - +
280E THR* 1.3 61.9 + - - +
281E GLY 3.6 0.4 - - - -
379E GLY* 3.9 32.1 - - - +
382E ILE* 4.4 13.2 - - + -
383E VAL* 3.6 22.2 - - + -
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Residues in contact with THR 280 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E TYR* 3.8 27.7 + - + -
10E ALA* 3.6 3.6 - - - +
24E TYR* 3.4 19.6 - - - -
255E LEU* 3.5 30.3 - - + -
258E TYR* 4.2 5.2 - - + -
276E VAL* 2.7 34.2 + - + +
277E LYS* 3.5 3.6 - - - -
279E ILE* 1.3 76.3 - - - +
281E GLY* 1.3 59.7 + - - +
282E MET* 3.1 37.7 + - - +
284E MET* 4.2 0.3 - - - +
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Residues in contact with GLY 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E ALA* 3.7 9.5 - - - +
11E TYR* 3.8 16.6 - - - -
22E SER* 3.4 5.5 - - - -
23E LYS* 2.9 15.4 + - - -
24E TYR* 2.9 32.2 + - - -
277E LYS 2.9 14.8 + - - -
279E ILE 3.6 1.4 - - - -
280E THR* 1.3 76.6 - - - +
282E MET* 1.3 58.9 + - - +
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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