Contacts of the helix formed by residues 272 - 281 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218I THR* 3.8 0.9 - - - -
219I ASP* 2.8 23.0 + - - +
247I ARG* 3.0 35.9 + - + +
250I SER* 3.3 24.5 - - - +
251I ALA* 3.9 21.5 - - + +
254I SER* 2.7 32.6 + - - +
269I CYS 4.5 0.2 - - - +
270I GLY* 3.4 12.3 - - - -
271I TYR* 1.3 71.8 + - - +
273I ASN* 1.3 56.0 + - - +
274I ILE* 3.0 5.2 - - - -
275I ILE* 2.7 35.9 + - + +
276I VAL* 3.1 9.5 + - + +
370I LEU* 4.9 0.2 - - - -
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Residues in contact with ASN 273 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217I ASP 4.7 6.2 - - - +
218I THR* 5.6 0.2 - - - -
254I SER* 5.2 3.5 - - - -
258I TYR* 4.8 2.8 + - - -
266I GLY* 3.6 15.4 - - - -
267I LYS 2.7 28.5 + - - +
270I GLY* 2.8 24.5 + - - +
272I GLU* 1.3 80.8 - - - +
274I ILE* 1.3 57.3 + - - +
276I VAL* 3.6 12.3 - - - +
277I LYS* 2.7 32.4 + - - +
284I MET* 3.6 25.3 - - + +
285I THR 3.2 12.9 + - - -
286I MET* 3.7 10.5 - - - -
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Residues in contact with ILE 274 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I MET* 3.8 13.7 - - + -
271I TYR 3.5 18.0 + - - +
272I GLU 2.9 1.2 + - - +
273I ASN* 1.3 79.4 - - - +
275I ILE* 1.3 65.1 + - + +
277I LYS* 3.7 4.0 - - + +
278I ALA* 3.2 21.3 + - - +
286I MET* 4.2 13.4 - - + +
302I LEU* 6.0 0.2 - - + -
305I GLN* 3.7 24.5 - - + +
306I CYS* 3.6 35.4 - - + +
370I LEU* 3.7 30.5 - - + +
372I TYR* 4.1 4.5 - - + -
375I ALA* 3.8 20.8 - - + +
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Residues in contact with ILE 275 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247I ARG 5.0 0.4 - - - +
248I ALA* 5.0 3.1 - - - -
251I ALA* 3.4 31.2 - - + -
272I GLU* 2.7 20.0 + - + +
274I ILE* 1.3 73.9 - - + +
276I VAL* 1.3 60.9 + - - +
278I ALA* 3.3 5.6 + - - +
279I ILE* 3.3 23.9 + - + +
369I MET* 4.0 29.8 - - + -
370I LEU* 4.3 10.8 - - + -
375I ALA* 3.6 37.5 - - + +
378I VAL* 4.1 9.6 - - + -
379I GLY* 4.2 6.0 - - - +
382I ILE* 3.8 19.1 - - + -
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Residues in contact with VAL 276 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251I ALA* 3.8 26.9 - - + +
254I SER* 4.3 13.9 - - - -
255I LEU* 4.2 7.4 - - + +
258I TYR* 3.6 35.4 - - + -
272I GLU 3.1 15.0 + - - +
273I ASN* 3.2 15.5 + - - +
275I ILE* 1.3 74.9 - - - +
277I LYS* 1.3 56.2 + - - +
279I ILE* 3.4 7.8 + - + +
280I THR* 2.7 44.0 + - + +
284I MET* 3.8 11.0 - - + -
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Residues in contact with LYS 277 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I TYR* 3.4 27.3 - - + +
17I MET* 4.2 7.4 - - + -
18I THR 3.2 12.0 + - - +
21I VAL 3.2 20.0 + - - -
22I SER* 3.8 8.3 - - - -
273I ASN 2.7 21.0 + - - +
274I ILE* 3.7 6.5 - - + +
276I VAL* 1.3 70.4 - - - +
278I ALA* 1.3 62.6 + - - +
280I THR* 3.7 5.8 - - - -
281I GLY* 2.7 29.8 + - - -
282I MET 3.5 16.2 - - - +
284I MET* 3.9 9.4 - - + +
306I CYS* 2.9 32.5 + - + +
307I CYS 4.5 0.2 + - - -
308I ASP* 2.7 31.6 + - - +
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Residues in contact with ALA 278 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I MET* 3.7 22.4 - - + +
10I ALA 3.6 8.5 + - - -
11I TYR* 3.5 16.9 + - - +
17I MET* 3.7 29.0 - - + +
274I ILE 3.2 10.6 + - - +
275I ILE* 3.4 11.7 - - - +
277I LYS* 1.3 81.0 - - - +
279I ILE* 1.3 60.8 + - - +
375I ALA* 4.8 0.7 - - + +
376I TYR* 3.9 15.9 - - + +
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Residues in contact with ILE 279 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I TYR* 3.6 40.3 - - + -
8I SER 4.0 3.6 - - - +
9I MET* 3.9 22.8 - - - -
10I ALA* 3.0 25.3 + - - +
251I ALA* 5.9 1.1 - - + +
255I LEU* 3.9 29.4 - - + -
275I ILE* 3.3 18.6 + - + +
276I VAL* 3.4 6.3 + - + +
277I LYS 3.2 0.6 - - - -
278I ALA* 1.3 77.1 - - - +
280I THR* 1.3 58.4 + - - +
379I GLY* 4.0 16.8 - - - -
382I ILE* 4.1 20.4 - - + -
383I VAL* 3.8 11.4 - - + -
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Residues in contact with THR 280 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I TYR* 3.6 34.0 + - + +
10I ALA* 3.6 3.4 - - - +
24I TYR* 3.3 22.3 - - - -
255I LEU* 3.6 22.0 - - + -
258I TYR* 4.0 13.0 - - + -
276I VAL* 2.7 36.4 + - + +
277I LYS* 3.7 1.9 - - - -
279I ILE* 1.3 76.2 - - - +
281I GLY* 1.3 62.9 + - - +
282I MET* 3.1 29.9 + - - +
284I MET* 4.1 0.5 - - - +
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Residues in contact with GLY 281 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I ALA* 3.5 11.2 - - - +
11I TYR* 3.7 17.9 - - - -
22I SER* 3.4 4.3 - - - -
23I LYS* 2.9 17.9 + - - -
24I TYR* 2.9 27.7 + - - -
277I LYS* 2.7 23.0 + - - -
280I THR* 1.3 71.3 - - - +
282I MET* 1.3 58.5 + - - +
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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