Contacts of the helix formed by residues 210 - 221 (chain D) in PDB entry 1EJI
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 210 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183D TYR* 3.0 33.0 + - + +
208D ASN 4.0 0.6 + - - -
209D LEU* 1.3 69.3 - - - +
211D TYR* 1.3 63.5 + - - +
212D ALA* 3.5 11.4 - - - +
213D ARG* 3.0 38.0 + - - +
214D LEU* 2.9 24.8 + - - +
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Residues in contact with TYR 211 (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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200D ALA* 3.9 28.2 + - + -
208D ASN* 6.3 0.7 - - + -
209D LEU* 2.9 53.0 + - + +
210D ASP* 1.3 70.7 - - - +
212D ALA* 1.3 58.5 + - - +
214D LEU* 3.7 5.9 - - + +
215D ARG* 2.8 33.3 + - - +
225D LEU* 4.0 1.8 - - + +
227D ALA* 4.5 1.8 - - + +
229D MSE 5.5 1.7 - - - +
232D ILE* 4.0 19.6 - - - +
242D PRO* 4.3 16.4 - - + -
243D SER 4.2 4.7 - - - -
244D PRO* 3.4 43.3 - - + +
247D HIS* 3.6 25.9 - + + +
248D CYS* 4.1 14.4 - - - -
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Residues in contact with ALA 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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210D ASP* 3.0 10.7 - - - +
211D TYR* 1.3 80.2 - - - +
213D ARG* 1.3 62.7 + - - +
215D ARG* 3.4 4.3 - - - +
216D LYS* 3.2 17.0 + - - +
247D HIS* 3.2 33.2 + - + +
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Residues in contact with ARG 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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183D TYR* 3.7 25.6 + - + +
184D ASP* 2.7 43.2 + - - +
187D GLU* 2.7 32.5 + - - -
210D ASP* 3.0 30.3 + - + +
212D ALA* 1.3 76.6 - - - +
214D LEU* 1.3 66.0 + - - +
216D LYS* 3.0 19.2 + - + +
217D ILE* 3.0 31.5 + - + +
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Residues in contact with LEU 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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172D TYR* 4.7 8.3 - - + +
181D ILE* 5.9 0.9 - - + -
183D TYR* 3.8 22.2 - - + +
186D LEU* 3.5 32.1 - - + -
198D ILE* 4.7 11.9 - - + +
200D ALA* 3.5 30.7 - - + -
209D LEU* 4.5 9.9 - - + -
210D ASP 2.9 24.8 + - - +
211D TYR* 3.7 8.7 - - + +
213D ARG* 1.3 76.3 - - - +
215D ARG* 1.3 57.4 + - - +
217D ILE* 3.2 8.2 + - + +
218D ALA* 2.8 29.1 + - - +
225D LEU* 3.9 16.4 - - + +
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Residues in contact with ARG 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211D TYR 2.8 16.0 + - - +
212D ALA 3.4 6.7 - - - +
214D LEU* 1.3 77.5 - - - +
216D LYS* 1.3 63.0 + - - +
218D ALA* 3.2 3.6 + - - +
219D ASP* 2.5 80.5 + - - +
225D LEU* 3.7 9.3 - - + +
247D HIS* 2.8 47.9 + - + +
248D CYS 5.5 1.0 + - - -
249D HIS* 3.3 33.7 + - - -
270D ARG* 5.3 7.3 - - - +
274D ARG* 5.4 0.4 - - - +
286D TYR* 4.2 7.1 + - - -
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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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187D GLU* 2.9 31.5 + - - +
212D ALA 3.2 9.4 + - - +
213D ARG* 3.0 23.6 + - + +
215D ARG* 1.3 80.5 - - - +
217D ILE* 1.3 59.0 + - + +
219D ASP* 3.2 5.3 + - - +
220D ASP* 2.9 57.6 + - - +
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Residues in contact with ILE 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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183D TYR* 3.7 12.3 - - + +
186D LEU* 4.0 17.7 - - + -
187D GLU* 3.5 58.6 - - + +
190D ALA* 4.0 18.6 - - + -
198D ILE* 4.3 9.6 - - + -
213D ARG* 3.0 26.1 + - + +
214D LEU* 3.5 10.8 - - + +
216D LYS* 1.3 77.6 - - + +
218D ALA* 1.3 63.7 + - - +
220D ASP* 3.2 11.6 + - - +
221D ASN* 3.0 27.0 + - - +
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Residues in contact with ALA 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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198D ILE* 4.0 19.0 - - + +
214D LEU 2.8 13.5 + - - +
215D ARG* 3.2 8.3 + - - +
217D ILE* 1.3 77.8 - - - +
219D ASP* 1.3 56.9 + - - +
221D ASN* 3.2 3.5 + - - -
222D GLY 2.9 8.3 + - - -
223D ALA* 2.7 47.4 + - - +
224D TYR 4.5 0.7 - - - +
225D LEU* 4.1 22.4 - - + +
249D HIS* 5.3 1.3 - - + -
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Residues in contact with ASP 219 (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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215D ARG* 2.5 60.1 + - - +
216D LYS* 3.9 4.9 - - - +
218D ALA* 1.3 74.1 - - - +
220D ASP* 1.3 66.6 + - - +
222D GLY* 3.0 15.2 + - - +
223D ALA 4.4 1.8 - - - +
249D HIS* 4.0 11.1 + - - -
274D ARG* 5.3 4.2 + - - -
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Residues in contact with ASP 220 (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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156B ASP* 4.1 7.6 - - - +
187D GLU* 3.6 10.6 - - + +
216D LYS* 2.9 54.9 + - - +
217D ILE* 3.4 13.9 - - - +
218D ALA 3.2 0.2 - - - -
219D ASP* 1.3 79.1 - - - +
221D ASN* 1.3 64.1 + - - +
222D GLY 3.6 0.3 + - - -
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Residues in contact with ASN 221 (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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156B ASP* 4.1 27.2 - - - +
187D GLU* 4.9 2.4 + - - +
190D ALA* 3.1 46.1 - - - +
191D SER* 3.3 16.5 - - - +
194D HIS* 5.0 7.3 - - + +
195D PRO* 4.2 22.1 - - + +
217D ILE* 3.0 26.0 + - - +
218D ALA* 3.2 3.6 + - - +
219D ASP 3.2 0.2 - - - -
220D ASP* 1.3 83.5 - - - +
222D GLY* 1.3 65.4 + - - +
223D ALA* 3.3 4.0 + - + +
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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