Contacts of the helix formed by residues 211 - 218 (chain D) in PDB entry 5E9W
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 211 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180D LYS* 3.0 34.7 + - - +
184D ILE* 4.2 6.6 - - + +
203D ASP* 3.8 23.2 - - - +
206D CYS 5.4 1.2 + - - +
209D GLY 3.1 1.0 - - - -
210D GLY* 1.3 75.5 - - - +
212D LEU* 1.3 65.2 + - - +
213D LEU 3.3 2.5 - - - -
214D LYS* 2.9 46.7 + - + +
215D TRP* 3.0 24.9 + - - +
282D SER* 4.8 1.0 + - - -
284D GLN* 3.7 14.6 - - - +
501D SAH 4.0 8.0 + - - +
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Residues in contact with LEU 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203D ASP* 5.4 0.4 + - - -
209D GLY* 3.0 27.7 + - - +
211D ASP* 1.3 76.2 - - - +
213D LEU* 1.3 63.6 + - + +
215D TRP* 3.1 9.4 + - - +
216D LYS* 3.0 21.1 + - - +
223D LEU* 3.7 25.6 - - + -
225D CYS* 4.0 15.0 - - - -
236D CYS* 3.5 26.2 - - - +
239D ARG* 3.7 14.6 - - + +
240D TYR* 3.7 26.9 - - + +
243D MET* 3.8 14.6 - - + -
253D PHE* 3.8 14.8 - - + -
257D PHE* 5.1 0.9 - - + -
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Residues in contact with LEU 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D GLY 4.8 0.2 + - - -
210D GLY 4.9 3.9 + - - +
211D ASP 3.3 1.0 - - - -
212D LEU* 1.3 79.5 - - + +
214D LYS* 1.3 58.5 + - + +
216D LYS* 3.3 13.7 + - + +
217D LYS* 2.9 41.5 + - + +
239D ARG* 6.0 6.0 - - - +
243D MET* 3.8 30.1 - - + -
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Residues in contact with LYS 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177D ASN* 2.8 40.5 + - - -
180D LYS* 4.0 3.6 - - - -
181D SER* 3.2 42.2 - - - +
184D ILE* 4.0 25.3 - - + +
188D LEU* 4.4 6.6 - - - +
210D GLY 2.9 15.3 + - - +
211D ASP* 2.9 34.0 + - - +
213D LEU* 1.3 79.5 - - + +
215D TRP* 1.3 61.6 + - - +
217D LYS* 3.5 6.6 + - - +
218D GLY* 3.2 17.5 + - - -
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Residues in contact with TRP 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D ILE* 3.5 41.5 - - + -
188D LEU* 3.8 23.8 - - + -
201D VAL* 3.6 38.6 - - + -
203D ASP* 3.5 19.6 + - + -
211D ASP* 3.0 29.9 + - - +
212D LEU* 3.1 5.8 + - - +
214D LYS* 1.3 74.6 - - - +
216D LYS* 1.3 64.5 + - - +
218D GLY* 3.3 2.1 + - - +
219D ARG 3.2 15.4 + - - -
220D ILE* 3.5 25.9 + - + +
223D LEU* 3.8 25.5 - - + +
253D PHE* 3.7 15.0 - - + -
280D ILE* 4.3 10.5 - - + -
282D SER* 3.5 29.2 - - - -
315D ILE* 5.1 0.4 - - + -
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Residues in contact with LYS 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212D LEU 3.0 12.7 + - - +
213D LEU* 3.3 16.5 + - + +
215D TRP* 1.3 76.3 - - - +
217D LYS* 1.3 74.7 + - + +
219D ARG* 2.8 25.9 + - - +
243D MET* 3.6 31.6 - - + -
249D SER* 4.7 16.6 - - - +
250D GLU* 5.1 11.3 - - - +
251D TYR 4.9 14.5 - - - +
252D ILE* 4.5 13.2 - - + -
253D PHE* 3.4 13.1 - - + -
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Residues in contact with LYS 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D LEU* 2.9 26.3 + - + +
214D LYS* 4.0 5.8 - - - +
215D TRP 3.3 0.2 - - - -
216D LYS* 1.3 92.4 - - + +
218D GLY* 1.3 61.0 + - - +
219D ARG* 3.4 18.9 + - - +
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Residues in contact with GLY 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188D LEU* 3.7 24.9 - - - -
192D ARG* 2.1 44.5 + - - -
214D LYS 3.2 9.7 + - - -
215D TRP 3.3 4.4 + - - -
216D LYS 3.1 0.6 - - - -
217D LYS* 1.3 76.9 - - - +
219D ARG* 1.3 55.1 + - - +
220D ILE* 3.2 4.8 + - - +
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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