Contacts of the helix formed by residues 218 - 229 (chain F) in PDB entry 1I43
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 ASP 218 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217F VAL* 1.3 70.6 - - - +
219F ILE* 1.3 63.8 + - - +
220F GLU* 3.3 10.9 + - - +
221F LEU* 2.9 42.3 + - + +
222F VAL* 2.9 24.4 + - + +
350F ILE* 3.6 36.0 - - + +
353F LYS* 3.0 30.6 + - - +
354F GLN* 3.7 2.1 - - - +
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Residues in contact with ILE 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208F SER* 4.8 3.6 - - - +
217F VAL* 2.6 17.0 + - + +
218F ASP* 1.3 70.9 - - - +
220F GLU* 1.3 60.9 + - - +
222F VAL* 3.9 5.1 - - - +
223F SER* 2.7 43.8 + - - +
235F ILE* 4.3 22.9 - - + -
245F GLN* 4.1 15.9 - - - +
247F ALA* 3.9 28.9 - - + +
250F LEU* 3.4 39.3 - - + -
252F ALA* 4.1 9.4 - - + +
354F GLN* 3.1 20.9 + - - +
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Residues in contact with GLU 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218F ASP* 3.3 8.0 + - - +
219F ILE* 1.3 79.3 - - - +
221F LEU* 1.3 65.7 + - - +
223F SER* 3.7 2.4 - - - -
224F LYS* 3.3 46.5 + - - +
250F LEU* 3.2 34.1 + - + +
353F LYS* 3.9 21.9 + - - -
354F GLN* 4.5 1.6 + - - +
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Residues in contact with LEU 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F VAL* 4.1 28.7 - - + -
218F ASP* 2.9 34.5 + - + +
220F GLU* 1.3 72.8 - - - +
222F VAL* 1.3 69.5 + - + +
224F LYS* 2.9 23.1 + - + +
225F LEU* 3.1 38.0 + - + +
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Residues in contact with VAL 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F VAL* 5.4 11.2 - - + -
192F LEU* 3.6 23.1 - - + -
204F PHE* 3.3 35.9 - - + -
217F VAL* 3.5 26.7 - - + -
218F ASP* 2.9 18.1 + - + +
219F ILE* 3.9 4.0 - - - +
221F LEU* 1.3 75.8 - - + +
223F SER* 1.3 64.3 + - - +
225F LEU* 3.6 4.0 + - - +
226F CYS* 2.9 33.6 + - - -
233F VAL* 4.4 9.0 - - + -
235F ILE* 5.6 1.6 - - + -
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Residues in contact with SER 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F ILE* 2.7 29.9 + - - +
220F GLU 3.7 4.3 - - - -
222F VAL* 1.3 75.2 - - - +
224F LYS* 1.3 61.1 + - - +
226F CYS* 3.2 2.6 + - - +
227F HIS* 2.8 41.9 + - - -
233F VAL* 3.9 16.2 - - - +
250F LEU 4.4 0.2 - - - -
251F GLY* 3.5 22.3 - - - -
252F ALA* 3.5 21.1 + - - -
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Residues in contact with LYS 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220F GLU* 3.3 37.8 + - - +
221F LEU* 2.9 15.3 + - + +
223F SER* 1.3 79.2 - - - +
225F LEU* 1.3 68.9 + - + +
227F HIS* 3.2 6.6 + - - +
228F GLU* 3.0 31.3 + - - +
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Residues in contact with LEU 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F VAL* 3.4 36.3 - - + +
192F LEU* 4.2 17.5 - - + -
193F GLU* 4.7 24.0 - - + +
196F LEU* 4.1 8.8 - - + +
221F LEU* 3.1 31.4 + - + +
222F VAL* 3.8 6.1 - - - +
224F LYS* 1.3 80.5 - - + +
226F CYS* 1.3 62.5 + - - +
228F GLU* 3.3 25.9 - - - +
229F LYS* 3.5 13.0 + - - +
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Residues in contact with CYS 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192F LEU* 4.3 3.6 - - - -
196F LEU* 4.2 20.4 - - - -
204F PHE* 3.9 22.2 - - - -
222F VAL* 2.9 31.9 + - - +
223F SER 3.6 0.4 - - - +
225F LEU* 1.3 75.7 - - - +
227F HIS* 1.3 65.2 + - - +
228F GLU 3.1 2.2 - - - -
229F LYS* 3.1 4.2 + - - -
230F GLY 3.0 4.2 + - - -
231F ALA* 2.8 40.9 + - + +
233F VAL* 3.5 27.6 - - + -
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Residues in contact with HIS 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223F SER* 2.8 29.0 + - - +
224F LYS* 3.8 5.9 + - - +
226F CYS* 1.3 74.0 - - - +
228F GLU* 1.3 62.7 + - - +
230F GLY* 3.3 9.7 + - - +
231F ALA 3.6 17.9 - - - +
232F LEU* 5.4 1.6 - - + -
233F VAL* 4.4 5.6 - - + +
251F GLY* 3.2 27.3 + - - -
253F ASP* 3.0 32.5 + - - -
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Residues in contact with GLU 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224F LYS* 3.0 18.4 + - - +
225F LEU* 3.3 22.3 - - - +
226F CYS 3.1 0.2 - - - -
227F HIS* 1.3 80.0 - - - +
229F LYS* 1.3 79.6 + - + +
230F GLY 3.3 0.6 + - - -
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Residues in contact with LYS 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196F LEU* 3.6 57.0 - - + +
197F ASN* 3.3 30.7 + - - +
200F LYS* 5.6 6.9 - - - +
201F VAL 4.9 4.3 - - - +
225F LEU 3.5 5.1 + - - +
226F CYS 3.1 2.8 + - - +
228F GLU* 1.3 95.1 + - + +
230F GLY* 1.3 60.4 + - - +
231F ALA 3.3 1.9 + - - -
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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