Contacts of the helix formed by residues 209 - 218 (chain P) in PDB entry 2IMW
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 GLU 209 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207P SER 3.7 2.2 + - - -
208P ILE* 1.3 81.8 - - - +
210P PHE* 1.3 68.4 + - - +
211P ASP* 4.3 23.0 - - + +
212P LYS* 3.4 19.2 + - + +
213P LEU* 3.2 17.0 + - - +
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Residues in contact with PHE 210 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208P ILE 3.4 4.3 + - - -
209P GLU* 1.3 74.2 - - - +
211P ASP* 1.3 65.3 + - - +
213P LEU* 3.0 6.5 + - + +
214P LYS* 2.7 57.1 + - + +
219P GLU* 4.4 8.3 - - + -
222P ALA* 3.7 27.1 - - + -
223P LYS* 4.0 33.7 - - + -
226P ILE* 3.5 30.1 - - + -
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Residues in contact with ASP 211 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209P GLU* 3.4 19.5 - - - +
210P PHE* 1.3 88.8 - - - +
212P LYS* 1.3 56.7 + - - +
214P LYS* 4.3 12.7 + - - +
215P GLY* 2.9 26.7 + - - -
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Residues in contact with LYS 212 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196P LYS 5.6 1.6 + - - -
197P LEU* 3.7 33.4 + - + +
208P ILE* 4.2 13.2 - - + -
209P GLU* 3.4 27.0 + - + +
210P PHE 3.2 0.8 - - - -
211P ASP* 1.3 79.4 - - - +
213P LEU* 1.3 64.1 + - - +
215P GLY* 4.0 0.7 - - - -
216P MET* 3.3 26.7 + - + +
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Residues in contact with LEU 213 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194P LEU* 3.7 18.6 - - + -
197P LEU* 4.0 8.5 - - + -
199P ILE* 3.4 28.3 - - + -
205P THR* 4.0 28.0 - - + -
208P ILE* 4.0 12.0 - - + +
209P GLU 3.2 9.4 + - - +
210P PHE* 3.0 8.8 + - - +
212P LYS* 1.3 78.2 - - - +
214P LYS* 1.3 62.6 + - - +
216P MET* 3.2 5.0 + - - +
217P ILE* 3.1 33.5 + - + +
222P ALA* 3.9 26.5 - - + +
225P LEU* 5.4 0.2 - - + -
226P ILE* 4.1 16.2 - - + -
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Residues in contact with LYS 214 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210P PHE* 2.7 49.0 + - + +
211P ASP* 4.0 12.0 + - - +
213P LEU* 1.3 72.3 - - - +
215P GLY* 1.3 59.6 + - - +
218P GLY* 2.7 39.8 + - - -
219P GLU* 3.7 46.7 + - + +
222P ALA* 4.1 2.6 - - - +
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Residues in contact with GLY 215 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211P ASP 2.9 22.6 + - - -
212P LYS 4.0 1.6 - - - -
214P LYS* 1.3 75.8 - - - +
216P MET* 1.3 66.6 + - - +
218P GLY 4.9 0.5 + - - -
1808S G 4.9 8.5 + - - -
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Residues in contact with MET 216 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193P LYS* 3.1 53.0 + - + +
196P LYS* 6.1 2.7 - - + -
197P LEU* 3.6 41.3 - - + -
212P LYS* 3.3 12.9 + - + +
213P LEU 3.2 3.3 + - - +
214P LYS 3.0 0.6 - - - -
215P GLY* 1.3 84.4 - - - +
217P ILE* 1.3 62.6 + - + +
218P GLY 3.7 0.7 - - - -
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Residues in contact with ILE 217 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190P THR* 4.0 24.5 - - + -
193P LYS* 4.1 20.0 + - + +
194P LEU* 4.1 15.0 - - + +
197P LEU* 4.9 0.4 - - + -
213P LEU* 3.1 30.9 + - + +
216P MET* 1.3 89.5 - - + +
218P GLY* 1.3 68.5 + - - +
221P LYS* 3.8 21.9 + - + +
222P ALA* 3.6 20.0 - - - +
225P LEU* 3.7 26.9 - - + -
1807S A 4.6 7.2 - - - +
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Residues in contact with GLY 218 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214P LYS* 2.7 23.4 + - - +
215P GLY 4.7 0.2 - - - -
216P MET 3.7 1.0 - - - -
217P ILE* 1.3 74.8 - - - +
219P GLU* 1.3 65.5 + - - -
220P ALA 3.3 0.7 - - - -
221P LYS 3.6 0.2 + - - -
222P ALA* 3.2 24.1 + - - +
1807S A 3.2 26.2 - - - -
1808S G 5.1 4.7 - - - -
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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