Contacts of the helix formed by residues 214 - 225 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132C ASP* 3.5 23.5 - - - +
133C GLU* 4.4 4.7 - - - +
212C ASP 4.3 0.4 - - - -
213C THR* 1.3 76.4 - - - +
215C GLN* 1.3 68.6 + - - +
216C GLU* 3.6 12.1 - - + +
217C GLU* 2.8 26.3 + - + +
218C VAL 3.0 5.5 + - - -
255C GLU* 4.0 0.9 - - - +
455C MG 2.8 27.6 - - - -
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Residues in contact with GLN 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C GLU 2.7 26.6 + - - +
132C ASP* 2.7 43.5 + - - +
137C LEU* 3.8 22.6 - - + +
213C THR 4.0 1.8 - - - -
214C ASP* 1.3 71.7 - - - +
216C GLU* 1.3 53.8 + - - +
218C VAL* 3.0 9.0 + - - +
219C ALA* 2.6 34.8 + - - +
248C VAL* 4.9 0.7 - - - +
251C VAL* 3.1 36.6 - - + +
254C ALA* 5.6 3.5 - - - +
255C GLU* 4.8 13.8 + - - +
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Residues in contact with GLU 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C ASP* 3.2 9.8 - - + +
215C GLN* 1.3 77.1 - - - +
217C GLU* 1.3 58.9 + - - +
219C ALA* 3.0 10.0 - - - +
220C ARG* 2.8 48.1 + - - +
251C VAL* 4.1 1.8 - - - +
255C GLU* 2.7 51.9 + - + +
259C ASP* 4.6 1.2 - - - +
418C ASP* 4.8 3.0 - - - +
452C MG 2.6 27.9 - - - -
455C MG 3.4 7.1 - - - -
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Residues in contact with GLU 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C THR* 3.5 18.6 - - + -
214C ASP* 2.8 25.7 + - + +
216C GLU* 1.3 76.4 - - - +
218C VAL* 1.3 65.2 + - - +
220C ARG* 3.2 40.6 + - - +
221C LEU* 3.4 11.4 + - + +
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Residues in contact with VAL 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C ALA* 4.8 10.5 - - + +
137C LEU* 5.5 6.3 - - + -
209C VAL* 3.6 18.4 - - + -
213C THR* 2.8 46.9 - - + +
214C ASP 3.1 3.8 - - - +
215C GLN* 3.0 7.6 + - - +
217C GLU* 1.3 75.7 - - - +
219C ALA* 1.3 66.5 + - - +
221C LEU* 3.3 21.1 + - - +
222C MET* 3.7 7.6 + - + +
230C LEU* 3.5 27.0 - - + +
243C VAL* 5.3 10.3 - - + -
248C VAL* 5.0 1.8 - - + -
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Residues in contact with ALA 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C GLN 2.6 17.0 + - - +
216C GLU* 3.0 15.9 - - - +
218C VAL* 1.3 71.1 - - - +
220C ARG* 1.3 67.3 + - + +
222C MET* 2.9 19.8 + - - +
223C ALA* 3.6 7.4 + - - +
248C VAL* 3.6 29.5 - - + +
251C VAL* 4.3 6.1 - - + -
252C LEU* 4.4 20.6 - - + -
249D LEU* 5.5 1.8 - - - +
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Residues in contact with ARG 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C GLU* 2.8 35.0 + - - +
217C GLU* 3.3 33.1 + - - +
219C ALA* 1.3 71.7 - - + +
221C LEU* 1.3 64.8 + - + +
223C ALA* 2.8 21.8 + - - +
224C ASP* 3.1 22.9 + - - +
252C LEU* 5.8 0.6 - - - +
342C LEU 5.5 0.6 + - - -
343C ALA* 3.5 28.5 + - - +
344C THR 5.7 0.6 - - - -
345C ARG* 5.2 16.4 - - - +
413C ARG* 5.5 4.9 - - - +
253D GLU* 5.7 5.6 + - - -
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Residues in contact with LEU 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C VAL* 5.0 10.8 - - + -
208C TYR 4.2 17.5 - - - +
209C VAL* 4.7 6.7 - - + -
213C THR* 5.9 1.3 - - + -
217C GLU* 3.4 11.0 + - + +
218C VAL* 3.3 14.5 + - - +
219C ALA 3.0 0.4 + - - -
220C ARG* 1.3 79.3 - - + +
222C MET* 1.3 56.8 + - - +
223C ALA 2.9 6.1 + - - -
224C ASP* 4.6 3.8 - - - +
225C TYR* 3.0 58.4 + - + +
227C PHE* 5.7 2.2 - - + -
230C LEU* 4.2 21.8 - - + -
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Residues in contact with MET 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C VAL* 3.7 5.1 + - + +
219C ALA 2.9 12.4 + - - +
221C LEU* 1.3 73.6 - - - +
223C ALA* 1.3 56.4 + - - +
226C ASP* 4.0 2.8 - - - -
227C PHE* 3.7 43.0 + - + +
228C THR* 3.9 10.3 - - - +
229C VAL 3.9 20.6 - - - -
230C LEU* 3.7 36.6 - - + -
243C VAL* 3.9 24.5 - - + +
244C THR 4.1 0.4 - - - +
245C VAL* 4.1 18.4 - - + -
248C VAL* 3.8 22.2 - - + -
246D ASP* 4.4 0.5 - - - +
249D LEU* 3.0 18.0 - - + +
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Residues in contact with ALA 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C ALA 3.6 4.0 + - - +
220C ARG* 2.8 17.2 + - - +
222C MET* 1.3 77.8 - - - +
224C ASP* 1.3 63.8 + - - +
226C ASP* 3.0 5.5 - - - +
252C LEU* 6.4 0.4 - - + -
454C MG 2.1 31.5 - - - -
249D LEU* 3.7 26.2 - - + -
250D ASP* 4.1 5.7 - - - +
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Residues in contact with ASP 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C ARG* 3.1 25.5 + - - +
221C LEU* 4.0 2.9 + - - +
223C ALA* 1.3 75.5 - - - +
225C TYR* 1.3 65.7 + - + +
226C ASP* 2.5 29.1 + - - +
345C ARG* 4.1 25.0 + - - -
31D GLN* 2.9 28.9 + - + +
63D HIS* 3.4 9.5 - - - -
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Residues in contact with TYR 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207C VAL* 3.3 45.3 - - + +
221C LEU* 3.0 37.2 + - + +
224C ASP* 1.3 82.8 - - + +
226C ASP* 1.3 66.7 + - - +
227C PHE* 2.8 33.0 + + + -
29D HIS* 4.5 25.4 - + + +
31D GLN* 3.4 40.4 - - + +
32D ASP* 4.3 14.7 + - - -
63D HIS* 5.4 1.3 - - - -
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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