Contacts of the helix formed by residues 218 - 229 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217E VAL* 1.3 71.8 - - - +
219E ILE* 1.3 64.2 + - - +
220E GLU* 3.4 10.2 + - - +
221E LEU* 2.9 41.7 + - + +
222E VAL* 2.8 23.3 + - + +
350E ILE* 3.7 35.1 - - + +
353E LYS* 3.1 28.5 + - - +
354E GLN* 3.7 2.7 - - - +
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Residues in contact with ILE 219 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208E SER* 4.6 4.9 - - - +
217E VAL* 2.6 15.9 + - + +
218E ASP* 1.3 69.6 - - - +
220E GLU* 1.3 53.7 + - - +
222E VAL* 4.5 5.8 - - - -
223E SER* 2.6 51.2 + - - +
233E VAL* 5.8 0.4 - - + -
235E ILE* 4.0 25.4 - - + -
245E GLN* 4.1 23.3 - - - +
247E ALA* 3.9 20.9 - - + +
250E LEU* 3.4 34.5 - - + +
252E ALA* 4.2 8.3 - - + +
354E GLN* 3.2 30.1 + - - +
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Residues in contact with GLU 220 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218E ASP* 3.3 7.9 + - - +
219E ILE* 1.3 80.9 - - - +
221E LEU* 1.3 66.1 + - - +
223E SER* 3.6 2.4 - - - -
224E LYS* 3.3 41.5 + - - +
250E LEU* 3.2 33.9 - - + +
353E LYS* 3.8 23.0 + - - +
354E GLN* 4.6 1.8 + - - +
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Residues in contact with LEU 221 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E VAL* 3.9 36.1 - - + -
218E ASP* 2.9 33.6 + - + +
220E GLU* 1.3 74.2 - - - +
222E VAL* 1.3 71.5 + - + +
224E LYS* 2.8 23.4 + - + +
225E LEU* 3.2 32.2 + - + +
353E LYS* 5.8 0.2 - - - +
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Residues in contact with VAL 222 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186E PRO 5.9 0.9 - - - +
189E VAL* 5.6 8.7 - - + -
192E LEU* 3.8 21.5 - - + -
204E PHE* 3.3 37.0 - - + -
217E VAL* 3.4 27.4 - - + -
218E ASP* 2.8 18.7 + - + +
219E ILE* 3.8 4.0 - - - +
221E LEU* 1.3 77.0 - - + +
223E SER* 1.3 66.2 + - - +
225E LEU* 3.3 4.4 + - - +
226E CYS* 3.1 27.0 + - - -
233E VAL* 4.3 8.5 - - + -
235E ILE* 5.5 1.1 - - + -
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Residues in contact with SER 223 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219E ILE* 2.6 32.4 + - - +
220E GLU 3.6 4.9 - - - -
222E VAL* 1.3 73.4 - - - +
224E LYS* 1.3 58.0 + - - +
226E CYS* 3.3 1.9 + - - +
227E HIS* 2.9 41.2 + - - -
233E VAL* 4.0 17.3 - - - +
251E GLY* 3.4 38.4 - - - -
252E ALA* 3.5 6.4 + - - -
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Residues in contact with LYS 224 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E GLU* 3.3 32.4 + - - +
221E LEU* 2.8 20.9 + - + +
223E SER* 1.3 75.8 - - - +
225E LEU* 1.3 67.6 + - + +
227E HIS* 3.9 5.3 - - - +
228E GLU* 3.0 30.1 + - - +
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Residues in contact with LEU 225 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E VAL* 3.6 34.8 - - + +
192E LEU* 4.2 17.5 - - + -
193E GLU* 4.6 25.1 - - + +
196E LEU* 4.1 8.2 - - + +
221E LEU* 3.2 31.1 + - + +
222E VAL 3.7 5.2 - - - +
224E LYS* 1.3 78.4 - - + +
226E CYS* 1.3 64.5 + - - +
228E GLU* 3.3 28.6 - - - +
229E LYS* 3.5 11.8 + - - +
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Residues in contact with CYS 226 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192E LEU* 4.6 3.6 - - - -
196E LEU* 4.3 20.2 - - - -
204E PHE* 3.7 27.1 - - - -
222E VAL* 3.1 20.8 + - - -
223E SER 3.6 2.2 - - - +
225E LEU* 1.3 76.1 - - - +
227E HIS* 1.3 58.5 + - - +
229E LYS* 2.8 21.3 + - - +
230E GLY 3.0 8.5 + - - -
231E ALA* 3.1 26.1 + - + +
233E VAL* 3.5 31.4 - - + -
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Residues in contact with HIS 227 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223E SER* 2.9 29.5 + - - +
224E LYS* 4.0 5.5 - - - +
226E CYS* 1.3 73.1 - - - +
228E GLU* 1.3 62.1 + - - +
230E GLY* 3.2 12.5 + - - +
231E ALA 3.6 18.2 - - - -
232E LEU* 5.3 0.9 - - + -
233E VAL* 4.4 5.4 - - + +
251E GLY* 3.2 27.8 + - - -
253E ASP* 3.0 33.1 + - - -
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Residues in contact with GLU 228 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224E LYS* 3.0 18.4 + - - +
225E LEU* 3.3 23.6 - - - +
226E CYS 3.0 0.4 - - - -
227E HIS* 1.3 76.9 - - - +
229E LYS* 1.3 81.4 + - + +
230E GLY 3.7 0.3 + - - -
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Residues in contact with LYS 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E LEU* 3.6 46.6 - - + +
197E ASN* 3.2 36.3 + - - +
200E LYS* 5.6 7.4 - - - +
201E VAL 4.7 5.2 + - - +
225E LEU 3.9 10.5 - - - +
226E CYS 2.8 3.2 + - - +
228E GLU* 1.3 99.3 + - + +
230E GLY* 1.3 60.7 + - - +
231E ALA 3.3 2.4 + - - -
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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