Contacts of the helix formed by residues 232 - 243 (chain D) 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 ALA 232 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236C LYS* 6.0 2.5 - - - +
88D TYR* 4.8 9.8 + - + -
89D ASP* 4.1 20.0 - - - +
146D LEU* 3.9 22.3 - - + +
230D GLU* 3.1 18.6 - - + +
231D ALA* 1.3 77.5 - - - +
233D ASP* 1.3 61.0 + - - +
234D ALA 3.4 0.7 - - - -
235D PRO* 3.7 8.6 - - - +
236D LYS* 3.8 13.7 + - - +
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Residues in contact with ASP 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D GLY* 4.1 16.5 - - - -
229D GLU* 3.4 13.3 + - - +
230D GLU* 3.0 39.1 + - - +
231D ALA 2.9 1.2 - - - -
232D ALA* 1.3 83.1 - - - +
234D ALA* 1.3 59.0 + - - +
235D PRO 3.6 0.2 - - - -
236D LYS* 3.8 16.6 - - - +
237D ILE* 3.1 29.9 + - - +
255D PHE* 5.5 4.8 - - + -
258D HIS* 5.7 1.9 - - - -
500D B13 5.2 0.9 - - - -
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Residues in contact with ALA 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D VAL* 3.4 35.9 - - + +
147D LEU* 3.5 12.2 - - + +
177D MET* 4.2 2.4 - - - +
179D THR* 4.9 3.8 - - + -
208D ALA* 5.5 0.4 - - - -
230D GLU 4.2 1.2 + - - -
231D ALA 3.1 8.1 + - - +
233D ASP* 1.3 76.2 - - - +
235D PRO* 1.4 67.4 - - + +
237D ILE* 3.1 24.2 - - - +
238D ALA* 3.1 13.3 + - - +
500D B13 4.5 12.9 - - + +
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Residues in contact with PRO 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D LEU* 3.9 24.0 - - + -
147D LEU* 3.6 18.2 - - + -
150D ASN* 3.5 39.7 - - + +
152D TYR* 4.7 2.9 - - + -
231D ALA 3.5 9.6 - - - +
232D ALA* 3.7 9.9 - - - +
234D ALA* 1.4 94.6 - - + +
236D LYS* 1.3 59.5 + - - +
238D ALA* 3.6 4.5 - - + +
239D ASP* 3.0 38.5 + - - +
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Residues in contact with LYS 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D ALA 3.8 16.4 + - - +
233D ASP* 3.8 18.2 - - - +
234D ALA 3.3 0.6 - - - -
235D PRO* 1.3 82.3 - - - +
237D ILE* 1.3 57.7 + - - +
239D ASP* 3.8 10.5 + - - +
240D ALA* 3.8 10.2 + - - +
255D PHE* 3.7 28.8 - - + -
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Residues in contact with ILE 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D MET* 3.6 23.6 - - + -
206D PRO* 5.3 1.1 - - + -
208D ALA* 4.3 11.4 - - + -
226D VAL* 3.6 32.5 - - + -
233D ASP 3.1 15.8 + - - +
234D ALA* 3.1 23.1 - - - +
236D LYS* 1.3 74.1 - - - +
238D ALA* 1.3 64.3 + - - +
239D ASP 3.2 0.4 - - - -
240D ALA* 3.2 11.4 + - - +
241D ILE* 3.3 13.5 - - - +
251D LEU* 3.8 20.2 - - + -
255D PHE* 3.6 39.4 - - + -
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Residues in contact with ALA 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D VAL* 4.9 2.5 - - + -
147D LEU* 4.6 5.6 - - + -
152D TYR* 3.1 34.9 + - + +
176D ILE* 3.5 9.3 - - + +
177D MET* 3.8 19.3 - - - -
234D ALA 3.1 19.1 + - - +
235D PRO* 3.2 6.9 + - + +
237D ILE* 1.3 77.3 - - - +
239D ASP* 1.3 57.1 + - - +
241D ILE* 3.2 23.1 + - - +
242D ILE* 3.5 4.9 + - - +
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Residues in contact with ASP 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D LYS* 4.7 8.0 + - - +
150D ASN* 5.2 4.7 - - - +
152D TYR* 2.3 36.7 + - - -
235D PRO* 3.0 23.8 + - - +
236D LYS* 3.9 9.6 - - - +
237D ILE 3.2 0.2 - - - -
238D ALA* 1.3 74.0 - - - +
240D ALA* 1.3 54.7 + - - +
241D ILE 3.1 5.4 - - - -
242D ILE* 3.2 12.1 + - + +
243D ALA* 3.1 24.1 + - - +
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Residues in contact with ALA 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D LYS 3.8 2.1 + - - +
237D ILE 3.2 13.4 + - - +
239D ASP* 1.3 77.3 - - - +
241D ILE* 1.3 59.4 + - - +
243D ALA* 3.8 10.4 - - - +
244D GLY 3.6 2.1 + - - -
245D THR* 3.1 32.7 + - - +
251D LEU* 4.0 11.4 - - + -
255D PHE* 3.9 30.5 - - + -
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Residues in contact with ILE 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D ILE* 3.7 37.0 - - + +
177D MET* 3.6 15.5 - - + -
206D PRO* 3.5 26.2 - - + -
237D ILE 3.3 20.2 - - - +
238D ALA* 3.4 10.8 - - - +
239D ASP 3.1 0.4 - - - -
240D ALA* 1.3 79.1 - - - +
242D ILE* 1.3 63.7 + - - +
243D ALA 3.2 1.1 - - - -
244D GLY* 3.5 11.2 + - - +
245D THR 3.4 23.3 - - - +
246D THR* 5.0 8.3 - - + +
251D LEU* 4.1 9.2 - - + -
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Residues in contact with ILE 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D LYS* 3.4 47.1 - - + +
152D TYR* 3.6 17.3 - - + +
176D ILE* 4.5 7.9 - - + -
238D ALA 3.6 15.9 - - - +
239D ASP* 3.2 11.6 + - + +
241D ILE* 1.3 79.6 - - - +
243D ALA* 1.3 58.8 + - - +
244D GLY* 3.4 0.6 + - - -
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Residues in contact with ALA 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D ASP 3.1 14.6 + - - +
240D ALA* 3.9 13.0 - - + +
241D ILE 3.2 0.2 - - - -
242D ILE* 1.3 79.1 - - - +
244D GLY* 1.3 55.6 + - - +
245D THR* 3.7 5.6 + - - +
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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