Contacts of the helix formed by residues 212 - 225 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50D VAL* 3.3 4.3 - - - -
53D THR* 4.2 1.3 - - + -
54D THR* 3.3 35.0 - - + +
57D ALA* 3.8 6.1 - - + -
131D ILE* 3.1 44.2 - - + -
135D MET* 3.4 21.3 - - + -
197D ILE 4.4 0.4 - - - +
199D GLU 4.2 9.0 - - - +
203D VAL* 5.0 11.2 - - + +
210D PRO 4.0 0.2 + - - -
211D MET* 1.3 77.8 - - - +
213D ALA* 1.3 55.0 + - - +
214D PRO* 2.9 24.2 - - + -
215D THR* 2.6 39.7 + - - +
216D LEU 3.3 3.8 + - - -
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Residues in contact with ALA 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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98C PRO* 5.4 1.3 - - + -
50D VAL* 3.1 13.8 - - + +
51D VAL* 4.9 6.7 - - + -
54D THR* 2.8 22.2 + - + +
55D TYR* 6.1 1.3 - - + -
212D ILE* 1.3 69.5 - - - +
214D PRO* 1.3 69.8 - - + +
216D LEU* 4.0 5.8 - - + +
217D ILE* 3.0 29.5 + - - +
236D LEU* 3.3 33.9 - - + -
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Residues in contact with PRO 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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98C PRO* 3.4 30.7 - - + -
100C THR* 2.9 30.3 + - - +
197D ILE 3.5 9.9 - - - +
198D SER 4.1 0.7 - - - +
199D GLU 3.3 25.8 - - - +
200D PHE* 3.9 17.7 - - + -
212D ILE* 3.0 18.6 - - + -
213D ALA* 1.3 96.3 - - + +
215D THR* 1.3 60.1 + - - +
217D ILE* 4.7 1.1 - - + -
218D TYR* 3.2 11.3 + - - +
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Residues in contact with THR 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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200D PHE* 3.6 18.6 - - + -
203D VAL* 5.6 3.3 - - - +
204D VAL* 3.6 20.8 + - + +
207D ALA 5.5 1.4 + - - -
208D TYR* 3.5 46.9 + - + +
211D MET* 4.1 13.2 - - - +
212D ILE* 2.6 22.4 + - - +
214D PRO* 1.3 68.7 - - - +
216D LEU* 1.3 59.8 + - - +
217D ILE 2.9 1.6 - - - -
218D TYR* 2.6 24.2 + - + +
219D GLU* 2.7 12.7 + - + +
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Residues in contact with LEU 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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46D ALA* 5.2 6.5 - - + +
47D VAL* 4.0 24.2 - - + -
50D VAL* 4.1 29.8 - - + -
209D TYR* 6.0 0.7 - - - +
211D MET* 3.7 21.9 - - - -
212D ILE 3.3 2.2 + - - -
213D ALA* 4.1 7.0 - - - +
214D PRO 3.6 0.2 - - - -
215D THR* 1.3 76.9 - - - +
217D ILE* 1.3 60.7 + - - +
219D GLU* 3.9 6.8 - - + +
220D ARG* 3.2 47.8 + - + +
232D VAL* 3.7 29.8 - - + -
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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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100C THR* 3.3 13.9 - - + -
101C VAL* 3.2 31.4 - - + +
104C ILE* 3.0 33.7 - - + -
213D ALA 3.0 15.7 + - - +
214D PRO 3.6 1.8 - - - +
215D THR 2.9 1.0 - - - -
216D LEU* 1.3 77.8 - - - +
218D TYR* 1.3 55.3 + - - +
220D ARG* 3.3 5.1 + - - +
221D TYR* 2.8 33.6 + - - +
229D ALA* 4.2 8.9 - - + +
232D VAL* 3.9 13.5 - - + -
233D ALA* 3.7 21.8 - - + +
236D LEU* 3.3 16.8 - - + -
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Residues in contact with TYR 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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100C THR* 3.5 8.3 - - + +
200C PHE* 5.6 1.9 - + - -
204C VAL* 3.8 32.0 - - + +
205C VAL* 4.2 19.1 - - + -
208C TYR* 4.9 11.6 - - - -
218C TYR* 5.1 17.0 - + - -
200D PHE* 3.2 39.3 - + + -
208D TYR* 5.2 9.9 - + - -
214D PRO 3.2 6.9 + - - +
215D THR* 2.6 13.0 + - + +
217D ILE* 1.3 75.1 - - - +
219D GLU* 1.3 63.1 + - - +
221D TYR* 3.1 13.7 + + - +
222D LEU* 3.0 65.0 + - + +
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Residues in contact with GLU 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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208D TYR* 3.5 24.6 + - + +
209D TYR* 4.0 3.8 + - - -
211D MET* 3.2 29.2 - - - +
215D THR 2.7 18.1 + - - +
216D LEU* 3.9 10.8 - - + +
218D TYR* 1.3 72.6 - - - +
220D ARG* 1.3 55.5 + - + +
222D LEU* 3.0 8.0 + - - +
223D SER* 2.6 50.6 + - - +
65E THR* 3.9 26.6 + - - +
66E GLU* 4.4 7.4 - - - +
67E ALA* 4.8 7.0 + - + +
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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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41D ALA* 5.3 6.5 - - - +
44D ASP* 3.0 31.5 + - - -
46D ALA* 4.6 6.1 - - - +
47D VAL* 4.1 9.7 - - - +
216D LEU* 3.2 36.5 + - + +
217D ILE* 3.8 3.6 - - - +
219D GLU* 1.3 82.6 - - + +
221D TYR* 1.3 63.2 + - - +
223D SER* 4.2 7.0 - - - -
224D GLU* 2.8 39.4 + - - +
225D GLY 3.2 8.6 + - - +
228D ALA 3.9 22.0 + - - +
229D ALA* 4.5 4.7 - - + -
232D VAL* 3.4 30.3 - - + +
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Residues in contact with TYR 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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100C THR* 5.9 0.2 - - + -
104C ILE* 4.2 22.9 - - + -
107C LEU* 3.2 23.4 - - + +
205C VAL* 3.0 43.5 + - + -
217D ILE 2.8 14.5 + - - +
218D TYR* 3.3 17.3 - + - +
220D ARG* 1.3 77.8 - - - +
222D LEU* 1.3 72.0 + - + +
225D GLY* 2.9 32.0 + - - -
226D LEU* 4.0 16.8 - - - -
229D ALA* 4.1 2.9 - - - +
219E MET 4.9 0.3 - - - +
223E HIS* 2.8 63.2 + + + -
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Residues in contact with LEU 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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208D TYR* 5.9 1.8 - - - +
218D TYR* 3.0 58.1 + - + +
219D GLU* 3.6 6.7 - - - +
221D TYR* 1.3 94.8 - - + +
223D SER* 1.3 63.1 + - - +
67E ALA* 6.0 0.4 - - + -
215E ARG* 6.2 0.2 - - - +
217E MET* 3.9 9.5 - - + +
219E MET* 3.2 31.4 - - - +
220E GLU* 3.3 43.1 + - + +
223E HIS* 4.6 2.5 - - + -
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Residues in contact with SER 223 (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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219D GLU* 2.6 34.2 + - - +
220D ARG* 4.2 2.5 - - - -
222D LEU* 1.3 73.4 - - - +
224D GLU* 1.3 64.9 + - - +
44E THR* 3.9 21.6 - - - +
67E ALA* 3.1 23.5 - - - +
217E MET* 4.1 8.3 - - - -
219E MET* 3.4 31.4 - - - +
222E ILE* 4.2 1.9 - - - +
243E HIS* 4.7 0.2 + - - -
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Residues in contact with GLU 224 (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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220D ARG* 2.8 34.3 + - - +
223D SER* 1.3 86.1 - - - +
225D GLY* 1.3 61.6 + - - +
228D ALA* 3.3 26.6 + - + +
44E THR* 4.3 3.8 - - + -
45E GLU* 3.4 14.7 - - - +
48E LYS* 2.4 40.0 + - - +
222E ILE* 3.8 11.3 - - - +
226E GLU* 4.5 4.0 - - - +
243E HIS* 3.8 21.7 + - - +
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Residues in contact with GLY 225 (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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220D ARG 3.4 10.2 - - - +
221D TYR* 2.9 26.7 + - - +
222D LEU 4.4 1.2 + - - -
223D SER 3.7 0.8 - - - -
224D GLU* 1.3 80.0 - - - +
226D LEU* 1.3 67.5 + - - +
227D SER 3.6 0.2 - - - -
228D ALA* 3.4 8.4 + - - +
229D ALA 3.6 1.4 + - - -
219E MET 4.9 0.2 - - - -
222E ILE* 3.9 12.2 - - - +
223E HIS 4.1 8.1 - - - -
226E GLU* 3.5 7.9 - - - -
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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