Contacts of the helix formed by residues 218 - 229 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217B VAL* 1.3 69.7 - - - +
219B ILE* 1.3 62.8 + - - +
220B GLU* 3.4 11.6 + - - +
221B LEU* 3.2 39.1 + - + +
222B VAL* 2.9 23.8 + - + +
350B ILE* 3.7 29.5 - - + +
353B LYS* 3.1 29.4 + - - +
354B GLN* 3.6 8.7 - - - +
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Residues in contact with ILE 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208B SER* 5.0 3.8 - - - +
217B VAL* 2.6 16.9 + - + +
218B ASP* 1.3 69.4 - - - +
220B GLU* 1.3 55.7 + - - +
222B VAL* 3.9 5.8 - - - +
223B SER* 2.7 49.0 + - - +
233B VAL* 5.7 0.2 - - + -
235B ILE* 4.0 28.5 - - + -
245B GLN* 4.3 13.0 - - - +
247B ALA* 3.9 29.8 - - + +
250B LEU* 3.4 42.0 - - + -
252B ALA* 4.1 9.2 - - + +
354B GLN* 3.1 17.2 + - - +
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Residues in contact with GLU 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B ASP* 3.3 8.0 + - - +
219B ILE* 1.3 78.3 - - - +
221B LEU* 1.3 64.8 + - - +
223B SER* 3.6 2.3 + - - -
224B LYS* 3.2 46.4 + - - +
250B LEU* 3.2 34.8 + - + +
353B LYS* 3.9 21.9 + - - +
354B GLN* 4.5 1.4 + - - +
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Residues in contact with LEU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B VAL* 4.0 31.6 - - + -
218B ASP* 3.2 32.0 + - + +
220B GLU* 1.3 77.2 - - - +
222B VAL* 1.3 60.0 + - + +
224B LYS* 2.7 33.0 + - + +
225B LEU* 3.0 35.2 + - + +
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Residues in contact with VAL 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B PRO 5.9 0.7 - - - +
189B VAL* 5.6 8.7 - - + -
192B LEU* 3.7 23.8 - - + -
204B PHE* 3.3 37.0 - - + -
217B VAL* 3.5 26.9 - - + -
218B ASP* 2.9 17.8 + - + +
219B ILE* 3.9 4.0 - - - +
221B LEU* 1.3 76.2 - - + +
223B SER* 1.3 67.0 + - - +
225B LEU* 3.3 4.5 + - - +
226B CYS* 3.1 26.9 + - - -
233B VAL* 4.2 9.6 - - + -
235B ILE* 5.5 1.6 - - + -
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Residues in contact with SER 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219B ILE* 2.7 31.3 + - - +
220B GLU 3.7 5.2 - - - -
222B VAL* 1.3 72.7 - - - +
224B LYS* 1.3 63.8 + - - +
226B CYS* 3.4 0.7 + - - +
227B HIS* 3.0 35.5 + - - -
233B VAL* 3.9 17.1 - - - +
251B GLY* 3.3 39.5 - - - -
252B ALA* 3.4 7.1 + - - -
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Residues in contact with LYS 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B GLU* 3.2 35.9 + - - +
221B LEU* 2.7 23.2 + - + +
223B SER* 1.3 75.3 - - - +
225B LEU* 1.3 65.0 + - + +
227B HIS* 3.6 5.4 + - - +
228B GLU* 3.2 30.5 + - - +
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Residues in contact with LEU 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B VAL* 3.5 36.1 - - + +
192B LEU* 4.1 17.5 - - + -
193B GLU* 4.5 23.1 - - + +
196B LEU* 4.2 7.8 - - + +
221B LEU* 3.0 35.2 + - + +
222B VAL* 3.8 4.7 - - - +
224B LYS* 1.3 78.7 - - + +
226B CYS* 1.3 64.1 + - - +
228B GLU* 3.2 29.8 - - - +
229B LYS* 3.6 10.7 + - - +
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Residues in contact with CYS 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B LEU* 4.3 4.3 - - - -
196B LEU* 4.0 22.9 - - - -
204B PHE* 3.8 34.3 - - - -
222B VAL* 3.1 20.2 + - - +
225B LEU* 1.3 72.7 - - - +
227B HIS* 1.3 57.7 + - - +
228B GLU 3.0 4.5 - - - -
229B LYS* 2.8 19.2 + - - -
231B ALA* 3.0 34.4 + - + +
233B VAL* 3.5 23.3 - - + -
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Residues in contact with HIS 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B SER* 3.0 26.1 + - - +
224B LYS* 4.1 5.3 - - - +
226B CYS* 1.3 75.1 - - - +
228B GLU* 1.3 61.8 + - - +
229B LYS 3.2 0.2 - - - -
230B GLY* 3.4 11.4 + - - +
231B ALA 3.5 18.4 - - - -
232B LEU* 5.0 1.8 - - + -
233B VAL* 4.4 3.8 - - + +
251B GLY* 3.2 26.0 - - - -
253B ASP* 2.8 35.6 + - - -
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Residues in contact with GLU 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B LYS* 3.2 18.8 + - - +
225B LEU* 3.2 23.7 - - - +
226B CYS 3.0 0.8 - - - -
227B HIS* 1.3 77.9 - - - +
229B LYS* 1.3 79.6 + - + +
230B GLY 3.8 0.2 + - - -
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Residues in contact with LYS 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B LEU* 3.6 54.2 - - + +
197B ASN* 3.2 29.6 + - - +
200B LYS* 5.7 6.2 - - - +
201B VAL 4.7 5.7 + - - +
225B LEU 3.6 5.4 + - - +
226B CYS 2.8 2.6 + - - -
228B GLU* 1.3 101.3 + - + +
230B GLY* 1.3 59.0 + - - +
231B ALA 3.3 2.0 + - - -
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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