Contacts of the helix formed by residues 230 - 243 (chain A) in PDB entry 2ILU
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 SER 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A MET* 3.9 0.4 - - - +
229A GLY* 1.3 73.9 - - - -
231A VAL* 1.3 67.5 + - - +
232A SER* 3.6 11.2 + - - -
233A ALA* 3.1 12.8 + - - +
234A GLY 3.1 16.6 + - - -
252A LEU* 3.7 4.8 - - - +
383A GLU* 4.1 16.6 - - - -
385A PHE* 6.1 2.9 - - - -
482A NDP 2.5 39.9 + - - -
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Residues in contact with VAL 231 (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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230A SER* 1.3 71.6 - - - +
232A SER* 1.3 68.8 + - - +
234A GLY* 3.1 2.3 + - - -
235A GLU* 2.9 34.3 + - + +
252A LEU* 3.5 25.4 - - + +
383A GLU* 4.1 10.9 + - - +
409A TYR* 3.4 32.1 - - + +
454A LYS* 4.4 31.2 - - + +
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Residues in contact with SER 232 (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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230A SER* 3.1 10.0 + - - -
231A VAL* 1.3 86.1 - - - +
233A ALA* 1.3 62.2 + - - +
235A GLU* 3.2 19.4 + - - +
236A LYS* 3.0 38.4 + - - +
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Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A MET* 3.7 14.8 - - + -
230A SER* 3.1 3.0 + - - +
232A SER* 1.3 75.7 - - - +
234A GLY* 1.3 60.5 + - - +
236A LYS* 3.1 9.0 + - - +
237A ILE* 2.8 36.3 + - + +
482A NDP 3.2 56.1 - - + +
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Residues in contact with GLY 234 (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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227A MET* 4.3 7.1 - - - -
230A SER 3.1 10.3 + - - -
231A VAL 3.1 4.0 + - - -
233A ALA* 1.3 75.3 - - - +
235A GLU* 1.3 58.1 - - - +
237A ILE* 3.8 2.4 - - - -
238A MET* 2.9 32.9 + - - +
250A LEU* 3.8 13.4 - - - +
252A LEU* 4.0 24.9 - - - -
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Residues in contact with GLU 235 (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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231A VAL* 2.9 19.3 + - + +
232A SER* 3.3 15.0 - - - +
233A ALA 3.1 0.2 - - - -
234A GLY* 1.3 78.7 - - - +
236A LYS* 1.3 59.0 + - + +
238A MET* 4.2 3.6 - - - +
239A ALA* 3.0 30.9 + - + +
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Residues in contact with LYS 236 (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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214A GLN* 3.7 7.0 + - - +
232A SER* 3.0 33.4 + - - +
233A ALA* 3.1 7.4 + - - +
235A GLU* 1.3 75.0 - - + +
237A ILE* 1.3 64.2 + - - +
239A ALA* 3.9 4.6 - - - +
240A THR* 3.0 29.8 + - - -
482A NDP 3.2 32.1 - - - +
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Residues in contact with ILE 237 (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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149A ILE* 3.6 13.9 - - + -
214A GLN* 4.5 3.6 - - - +
217A ALA* 3.9 19.4 - - + +
225A VAL* 3.9 21.3 - - + -
227A MET* 3.1 40.8 - - + -
233A ALA 2.8 20.8 + - - +
234A GLY* 3.8 4.9 - - - +
236A LYS* 1.3 74.6 - - - +
238A MET* 1.3 61.2 + - - +
240A THR* 3.3 2.9 + - - -
241A ALA* 2.9 26.5 + - - +
248A VAL* 4.8 0.2 - - + -
250A LEU* 4.3 12.8 - - + -
482A NDP 3.4 28.5 - - + +
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Residues in contact with MET 238 (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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234A GLY 2.9 21.6 + - - +
235A GLU* 4.2 3.8 - - - +
237A ILE* 1.3 74.1 - - - +
239A ALA* 1.3 64.2 + - - +
241A ALA* 3.3 6.6 + - + +
242A ALA* 3.0 23.5 + - + +
248A VAL* 4.2 17.9 - - + -
250A LEU* 4.2 9.8 - - + +
457A ILE* 3.4 33.4 - - + -
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Residues in contact with ALA 239 (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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235A GLU* 3.0 22.9 + - + +
236A LYS* 3.9 5.8 - - - +
238A MET* 1.3 76.9 - - - +
240A THR* 1.3 57.5 + - - +
242A ALA* 3.1 24.4 - - - +
243A LYS* 3.9 12.9 + - - +
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Residues in contact with THR 240 (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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214A GLN* 2.5 36.0 + - + +
217A ALA* 4.0 2.9 - - - -
218A GLY* 3.3 35.2 - - - +
236A LYS 3.0 15.7 + - - -
237A ILE 3.8 2.9 - - - -
239A ALA* 1.3 71.5 - - - +
241A ALA* 1.3 67.4 + - - +
242A ALA 3.0 1.8 - - - -
243A LYS* 3.2 39.8 + - + +
244A ASN* 4.4 0.7 + - - -
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Residues in contact with ALA 241 (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 ALA 3.6 17.6 + - - +
225A VAL* 4.2 4.0 - - + -
237A ILE 2.9 18.1 + - - +
238A MET 3.3 2.7 + - - +
240A THR* 1.3 77.3 - - - +
242A ALA* 1.3 60.8 - - - +
244A ASN* 3.1 7.2 + - - +
246A THR* 2.9 42.8 + - - +
248A VAL* 3.4 29.4 - - + -
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Residues in contact with ALA 242 (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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238A MET* 3.0 12.8 + - + +
239A ALA* 3.1 20.2 - - - +
241A ALA* 1.3 77.1 - - - +
243A LYS* 1.3 61.3 + - + +
245A ILE* 3.0 26.8 + - - +
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Residues in contact with LYS 243 (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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218A GLY* 5.9 1.8 - - - +
239A ALA* 3.9 16.1 + - - +
240A THR* 3.2 30.3 + - + +
242A ALA* 1.3 79.4 - - + +
244A ASN* 1.3 70.5 + - - +
245A ILE* 3.9 2.8 + - - +
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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