Contacts of the helix formed by residues 212 - 225 (chain C) in PDB entry 2ONK
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 ILE 212 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C VAL* 2.9 6.1 - - - -
53C THR* 5.5 0.7 - - + -
54C THR* 3.3 27.1 - - + +
131C ILE* 3.3 27.4 - - + -
135C MET* 4.3 8.5 - - + -
199C GLU 4.8 2.0 - - - +
203C VAL* 3.1 42.0 - - + -
207C ALA 5.6 0.7 - - - +
208C TYR 5.7 0.7 - - - +
210C PRO 3.9 9.6 - - - +
211C MET* 1.3 77.8 - - - +
213C ALA* 1.3 67.9 + - - +
214C PRO* 3.0 25.4 - - + -
215C THR* 2.7 25.5 + - - +
216C LEU 3.1 9.4 + - - -
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Residues in contact with ALA 213 (chain C).
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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50C VAL* 2.7 17.4 - - + +
51C VAL* 4.8 6.1 - - + +
54C THR* 2.9 20.5 + - + +
55C TYR* 6.1 1.1 - - + -
197C ILE 5.7 0.2 - - - +
212C ILE* 1.3 70.8 - - - +
214C PRO* 1.3 71.6 - - + +
216C LEU* 3.3 5.7 + - - +
217C ILE* 3.2 25.8 + - - +
236C LEU* 3.4 33.9 - - + -
98D PRO* 5.7 1.3 - - + -
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Residues in contact with PRO 214 (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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197C ILE 3.6 17.3 - - - +
198C SER 4.9 0.4 - - - +
199C GLU 3.4 25.4 - - - +
200C PHE* 4.1 16.2 - - + -
212C ILE* 3.0 19.1 - - + -
213C ALA* 1.3 94.4 - - + +
215C THR* 1.3 59.3 + - - +
217C ILE* 3.5 3.3 + - + -
218C TYR* 3.2 16.1 + - - +
98D PRO* 3.7 20.6 - - + -
100D THR* 3.2 27.4 + - - +
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Residues in contact with THR 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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200C PHE* 4.0 14.1 - - + -
203C VAL* 5.7 1.9 - - - +
204C VAL* 3.9 17.7 - - - +
208C TYR* 3.6 46.2 + - + +
211C MET* 3.7 18.2 - - + -
212C ILE* 2.7 24.9 + - - +
214C PRO* 1.3 69.5 - - - +
216C LEU* 1.3 59.5 + - - +
217C ILE 2.9 2.0 - - - -
218C TYR* 2.7 26.5 + - + +
219C GLU* 2.7 13.1 + - + +
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Residues in contact with LEU 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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46C ALA* 5.2 5.8 - - + +
47C VAL* 3.8 25.4 - - + -
50C VAL* 4.3 17.0 - - + -
211C MET* 3.0 37.3 - - + +
212C ILE 3.1 7.4 + - - +
213C ALA* 3.7 8.7 - - - +
215C THR* 1.3 77.8 - - - +
217C ILE* 1.3 61.2 + - - +
219C GLU* 3.9 2.7 - - - +
220C ARG* 3.2 31.6 + - - +
232C VAL* 3.7 28.9 - - + -
203E GLU* 3.6 29.4 - - + +
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Residues in contact with ILE 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 ALA 3.2 15.2 + - - +
214C PRO 3.7 1.3 - - - +
215C THR 2.9 0.8 - - - -
216C LEU* 1.3 77.1 - - - +
218C TYR* 1.3 60.1 + - - +
220C ARG* 3.3 5.6 + - - +
221C TYR* 2.8 28.3 + - - +
229C ALA* 4.2 9.7 - - + +
232C VAL* 3.9 13.9 - - + +
233C ALA* 3.7 22.7 - - + +
236C LEU* 3.4 26.2 - - + -
100D THR* 3.6 13.7 - - + -
101D VAL* 3.5 20.2 - - + -
104D ILE* 3.0 34.1 - - + -
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Residues in contact with TYR 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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200C PHE* 3.4 33.9 - + + -
208C TYR* 6.0 5.4 - + - -
214C PRO 3.2 11.1 + - - +
215C THR* 2.7 15.2 + - + +
217C ILE* 1.3 73.9 - - - +
219C GLU* 1.3 63.8 + - - +
221C TYR* 3.1 20.5 + + - +
222C LEU* 3.0 64.7 + - + +
100D THR* 3.9 8.5 - - + +
200D PHE* 6.0 1.6 - + - -
204D VAL* 4.3 23.6 - - + +
205D VAL* 4.6 13.0 - - + -
208D TYR* 4.4 21.7 - - - -
218D TYR* 5.1 16.5 - + - -
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Residues in contact with GLU 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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208C TYR* 3.1 29.6 + - - +
209C TYR* 5.3 2.6 - - - -
211C MET* 3.7 19.2 - - - +
215C THR* 2.7 18.0 + - - +
216C LEU* 3.9 7.2 - - - +
218C TYR* 1.3 74.0 - - - +
220C ARG* 1.3 53.0 + - + +
222C LEU* 3.0 8.0 + - - +
223C SER* 2.6 49.7 + - - +
152E ASP* 6.0 1.8 - - - +
202E SER* 3.2 31.8 - - - +
203E GLU* 3.4 23.7 + - - +
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Residues in contact with ARG 220 (chain C).
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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41C ALA* 5.1 7.1 - - - +
44C ASP* 2.8 29.9 + - - -
46C ALA* 4.7 1.2 - - - +
47C VAL* 4.2 8.9 - - - +
216C LEU* 3.2 22.8 + - - +
217C ILE* 3.8 3.8 - - - +
219C GLU* 1.3 80.1 - - + +
221C TYR* 1.3 63.3 + - - +
223C SER* 4.2 6.5 - - - -
224C GLU* 2.8 39.0 + - - +
225C GLY 3.3 7.8 + - - +
228C ALA* 3.9 23.0 + - - +
229C ALA* 4.5 4.3 - - + -
232C VAL* 3.4 30.3 - - - +
203E GLU* 2.5 44.2 + - - +
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Residues in contact with TYR 221 (chain C).
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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217C ILE 2.8 15.1 + - - +
218C TYR* 3.1 23.1 + + - +
220C ARG* 1.3 76.3 - - - +
222C LEU* 1.3 70.9 + - + +
225C GLY* 2.9 20.3 + - - -
226C LEU* 4.0 27.8 - - + -
229C ALA* 4.1 7.4 - - + +
100D THR* 6.2 0.2 - - + -
104D ILE* 4.4 17.0 - - + -
107D LEU* 3.2 33.9 - - + +
205D VAL* 3.5 27.1 + - + -
80E LEU* 2.6 52.7 + - + +
82E ARG* 5.8 2.4 - - - +
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Residues in contact with LEU 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 TYR* 3.0 55.5 + - + +
219C GLU* 3.6 7.0 - - - +
221C TYR* 1.3 88.8 - - + +
223C SER* 1.3 65.5 + - - +
225C GLY 4.4 0.5 + - - -
72E ALA* 5.8 5.2 - - + -
75E ARG* 3.7 20.1 + - - +
76E LYS* 5.9 4.5 - - + -
79E GLU* 4.7 0.9 - - - +
80E LEU* 3.0 42.1 - - + +
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Residues in contact with SER 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 GLU* 2.6 38.6 + - - +
220C ARG* 4.2 2.5 - - - -
222C LEU* 1.3 73.9 - - - +
224C GLU* 1.3 71.1 + - - +
75E ARG* 3.2 31.3 + - - +
79E GLU* 4.4 4.0 - - - +
152E ASP* 4.5 11.1 + - - -
202E SER* 4.9 6.6 + - - -
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Residues in contact with GLU 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* 2.8 33.5 + - - +
223C SER* 1.3 86.8 - - - +
225C GLY* 1.3 62.7 + - - +
228C ALA* 3.3 26.4 + - + +
79E GLU* 3.5 19.3 - - - +
203E GLU* 5.2 2.1 - - - +
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Residues in contact with GLY 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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220C ARG 3.5 10.0 - - - +
221C TYR* 2.9 26.7 + - - +
223C SER 3.7 0.8 - - - -
224C GLU* 1.3 79.8 - - - +
226C LEU* 1.3 66.9 + - - +
227C SER 3.6 1.3 - - - -
228C ALA* 3.4 7.3 + - - +
229C ALA 3.6 2.3 + - - -
79E GLU* 4.0 14.2 - - - +
80E LEU* 3.9 11.5 - - - +
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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