Contacts of the helix formed by residues 214 - 225 (chain D) in PDB entry 2YVX
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 214 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132D ASP* 3.5 23.7 - - + +
133D GLU* 4.4 1.8 - - - +
212D ASP 4.3 0.4 - - - -
213D THR* 1.3 76.8 - - - +
215D GLN* 1.3 72.3 + - - +
216D GLU* 3.3 28.4 + - - +
217D GLU* 2.8 22.3 + - + +
218D VAL 3.1 5.2 + - - -
255D GLU* 4.2 13.3 - - - +
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Residues in contact with GLN 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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131D GLU* 2.8 24.6 + - - +
132D ASP* 2.7 24.4 + - - +
133D GLU 5.1 1.1 - - - +
137D LEU* 3.7 24.3 - - + +
213D THR 4.0 1.6 - - - -
214D ASP* 1.3 74.3 - - - +
216D GLU* 1.3 53.0 + - - +
218D VAL* 3.0 9.1 + - - +
219D ALA* 2.6 35.0 + - - +
248D VAL* 5.0 0.5 - - - +
251D VAL* 2.8 50.6 - - + +
254D ALA* 5.1 3.6 - - - +
255D GLU* 4.8 10.7 - - + +
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Residues in contact with GLU 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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253C GLU* 4.4 12.8 - - - +
214D ASP* 3.2 14.7 + - - +
215D GLN* 1.3 77.4 - - - +
217D GLU* 1.3 64.6 + - - +
219D ALA* 3.0 9.7 + - + +
220D ARG* 2.8 56.0 + - - +
251D VAL* 4.6 2.0 - - + +
252D LEU* 4.8 8.5 - - + +
255D GLU* 3.6 37.9 - - + +
259D ASP* 4.8 12.4 - - - +
343D ALA* 5.5 5.9 - - - +
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Residues in contact with GLU 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 THR* 3.4 20.9 - - + -
214D ASP* 2.8 24.9 + - + +
216D GLU* 1.3 75.7 - - - +
218D VAL* 1.3 55.4 + - - +
220D ARG* 3.2 37.2 + - - +
221D LEU* 2.7 37.4 - - + +
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Residues in contact with VAL 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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134D ALA* 4.7 9.6 - - + -
137D LEU* 6.4 2.0 - - + -
209D VAL* 3.3 30.7 - - + -
213D THR* 3.1 29.2 - - + +
214D ASP 3.7 0.7 - - - +
215D GLN* 3.0 8.4 + - - +
217D GLU* 1.3 76.6 - - - +
219D ALA* 1.3 67.7 + - - +
221D LEU* 3.3 21.3 + - - +
222D MET* 3.7 12.6 + - + +
230D LEU* 3.4 26.5 - - + +
243D VAL* 5.0 12.1 - - + -
248D VAL* 5.5 2.5 - - + -
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Residues in contact with ALA 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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249C LEU* 5.4 2.4 - - - +
215D GLN 2.6 17.0 + - - +
216D GLU* 3.0 15.0 - - - +
218D VAL* 1.3 72.3 - - - +
220D ARG* 1.3 67.9 + - + +
222D MET* 2.9 21.6 + - - +
223D ALA* 3.6 4.9 + - - +
248D VAL* 3.6 29.8 - - + +
251D VAL* 4.2 6.7 - - + -
252D LEU* 4.8 18.2 - - + -
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Residues in contact with ARG 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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216D GLU* 2.8 52.4 + - + +
217D GLU* 3.5 35.0 + - - +
219D ALA* 1.3 71.9 - - + +
221D LEU* 1.3 66.4 + - + +
223D ALA* 2.8 21.8 + - - +
224D ASP* 3.1 21.5 + - - +
343D ALA* 3.4 25.1 + - - +
345D ARG* 3.7 45.8 - - - +
413D ARG* 5.3 7.3 - - - +
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Residues in contact with LEU 221 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207D VAL* 5.4 11.4 - - + -
208D TYR 4.3 18.6 - - - +
209D VAL* 5.6 2.7 - - + -
213D THR* 5.8 0.9 - - + -
217D GLU* 2.7 49.8 - - + +
218D VAL* 3.6 11.0 - - - +
219D ALA 3.0 0.6 + - - -
220D ARG* 1.3 74.7 - - + +
222D MET* 1.3 57.7 + - - +
223D ALA 2.9 6.2 + - - -
224D ASP* 3.3 7.6 + - - +
225D TYR* 3.0 48.0 + - + +
227D PHE* 4.9 4.7 - - + -
230D LEU* 4.5 14.4 - - + -
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Residues in contact with MET 222 (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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246C ASP* 4.2 3.8 - - - +
249C LEU* 3.2 21.1 - - + +
218D VAL* 3.7 5.7 + - + +
219D ALA 2.9 14.3 + - - +
221D LEU* 1.3 72.4 - - - +
223D ALA* 1.3 56.4 + - - +
226D ASP* 4.1 2.8 - - - -
227D PHE* 3.7 42.1 + - + +
228D THR* 4.1 13.5 - - - +
229D VAL 4.1 0.7 - - - -
230D LEU* 3.8 26.7 - - + -
243D VAL* 3.6 42.6 - - + +
244D THR 4.0 0.2 - - - +
245D VAL* 3.9 26.2 - - + -
248D VAL* 3.9 20.6 - - + -
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Residues in contact with ALA 223 (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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246C ASP 4.8 1.1 - - - +
249C LEU* 3.7 28.9 - - + -
250C ASP* 4.7 6.5 - - - +
253C GLU* 5.9 1.8 - - - +
219D ALA 3.6 2.4 + - - +
220D ARG* 2.8 15.8 + - - +
222D MET* 1.3 78.2 - - - +
224D ASP* 1.3 71.2 + - - +
226D ASP* 3.2 6.6 - - - +
453D MG 2.3 32.9 - - - -
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Residues in contact with ASP 224 (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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31C GLN* 3.4 37.6 - - - +
63C HIS* 4.1 8.7 - - - -
220D ARG* 3.1 25.1 + - - +
221D LEU* 3.7 6.9 + - - +
223D ALA* 1.3 79.1 - - - +
225D TYR* 1.3 66.0 + - + +
226D ASP* 2.6 27.6 + - - +
345D ARG* 3.2 33.7 + - - -
453D MG 4.7 0.4 - - - -
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Residues in contact with TYR 225 (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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29C HIS* 3.8 37.1 - + + +
31C GLN* 4.4 21.2 - - + +
32C ASP* 4.8 9.4 + - - -
207D VAL* 3.7 23.1 - - + -
221D LEU* 3.0 29.2 + - + +
224D ASP* 1.3 93.4 - - + +
226D ASP* 1.3 68.8 + - - +
227D PHE* 2.9 49.5 + + + -
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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