Contacts of the helix formed by residues 212 - 225 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50I VAL* 3.2 4.7 - - - +
53I THR* 4.0 2.5 - - + +
54I THR* 3.3 34.1 - - + +
57I ALA* 3.7 7.9 - - + -
131I ILE* 3.1 44.0 - - + -
135I MET* 3.5 22.7 - - + -
197I ILE 4.6 0.2 - - - +
199I GLU 4.4 5.8 - - - +
203I VAL* 5.1 11.2 - - + -
210I PRO 5.0 0.2 - - - +
211I MET* 1.3 77.2 - - - +
213I ALA* 1.3 55.1 + - - +
214I PRO* 3.0 24.9 - - + -
215I THR* 2.8 34.7 + - - +
216I LEU 3.2 8.1 + - - -
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Residues in contact with ALA 213 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98H PRO* 5.8 0.7 - - + -
50I VAL* 2.9 15.8 - - + +
51I VAL* 4.7 6.7 - - + +
54I THR* 2.8 23.6 + - + +
55I TYR* 6.1 1.1 - - + -
212I ILE* 1.3 70.2 - - - +
214I PRO* 1.4 66.8 - - + +
216I LEU* 3.9 4.0 - - + +
217I ILE* 3.0 30.1 + - - +
236I LEU* 3.3 35.2 - - + -
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Residues in contact with PRO 214 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98H PRO* 3.7 22.0 - - + -
100H THR* 2.9 30.7 + - - +
54I THR* 4.5 0.2 - - + -
197I ILE 3.5 17.3 - - - +
198I SER 4.2 0.7 - - - +
199I GLU 3.3 26.2 - - - +
200I PHE* 4.0 18.4 - - + -
212I ILE* 3.0 18.2 - - + -
213I ALA* 1.4 95.2 - - + +
215I THR* 1.3 60.8 + - - +
217I ILE* 3.5 1.9 + - + -
218I TYR* 3.2 11.1 + - - +
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Residues in contact with THR 215 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200I PHE* 3.7 16.3 - - + -
203I VAL* 5.6 3.6 - - - +
204I VAL* 3.7 20.4 + - + +
208I TYR* 3.6 46.8 + - + +
211I MET* 4.2 13.1 - - - +
212I ILE* 2.8 23.2 + - - +
214I PRO* 1.3 69.4 - - - +
216I LEU* 1.3 67.0 + - - +
217I ILE 2.9 1.6 - - - -
218I TYR* 2.7 15.0 + - + -
219I GLU* 2.7 13.5 + - + +
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Residues in contact with LEU 216 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46I ALA* 5.1 6.3 - - + +
47I VAL* 4.0 24.7 - - + -
50I VAL* 4.0 30.3 - - + -
209I TYR* 6.1 0.2 - - - +
211I MET* 3.8 21.4 - - - -
212I ILE 3.2 3.6 + - - -
213I ALA* 3.9 7.6 - - + +
215I THR* 1.3 79.0 - - - +
217I ILE* 1.3 61.5 + - - +
219I GLU* 3.9 8.2 - - + +
220I ARG* 3.2 47.0 + - + +
232I VAL* 3.7 29.4 - - + -
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Residues in contact with ILE 217 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H THR* 3.2 15.9 - - + -
101H VAL* 3.3 30.7 - - + +
104H ILE* 3.1 33.7 - - + -
213I ALA 3.0 15.4 + - - +
214I PRO* 3.6 1.8 - - + +
215I THR 2.9 1.0 - - - -
216I LEU* 1.3 75.6 - - - +
218I TYR* 1.3 60.7 + - - +
220I ARG* 3.3 5.2 + - - +
221I TYR* 2.8 27.7 + - - +
229I ALA* 4.1 8.6 - - + +
232I VAL* 3.9 13.2 - - + -
233I ALA* 3.7 20.4 - - - +
236I LEU* 3.3 17.0 - - + -
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Residues in contact with TYR 218 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H THR* 3.6 9.3 - - + +
200H PHE* 5.7 0.9 - + - -
204H VAL* 3.8 32.2 - - + +
205H VAL* 4.3 13.7 - - + -
208H TYR* 4.6 13.3 - - - -
218H TYR* 4.7 22.7 - + - -
200I PHE* 3.3 37.5 - + + -
208I TYR* 5.4 7.6 - + - -
214I PRO 3.2 7.1 + - - +
215I THR* 2.7 13.7 + - + +
217I ILE* 1.3 74.5 - - - +
219I GLU* 1.3 63.5 + - - +
221I TYR* 3.1 18.8 + + - +
222I LEU* 3.0 64.4 + - + +
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Residues in contact with GLU 219 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208I TYR* 3.5 25.1 + - - +
209I TYR* 4.2 7.0 + - - -
211I MET* 3.2 27.9 - - - +
215I THR 2.7 18.5 + - - +
216I LEU* 3.9 9.9 - - - +
218I TYR* 1.3 72.3 - - - +
220I ARG* 1.3 54.7 + - + +
222I LEU* 3.0 8.6 + - - +
223I SER* 2.7 49.8 + - - +
65J THR* 4.2 22.1 + - - +
66J GLU* 4.9 6.5 - - - +
67J ALA* 5.3 4.8 + - + +
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Residues in contact with ARG 220 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41I ALA* 5.4 5.3 - - - +
44I ASP* 2.9 32.3 + - - +
46I ALA* 4.4 9.5 - - - +
47I VAL* 4.1 9.3 - - - +
216I LEU* 3.2 35.4 + - + +
217I ILE* 3.8 3.6 - - - +
219I GLU* 1.3 82.8 - - + +
221I TYR* 1.3 63.6 + - - +
223I SER* 4.2 6.5 - - - -
224I GLU* 2.8 40.5 + - - +
225I GLY 3.3 7.7 + - - +
228I ALA 3.9 22.7 + - - +
229I ALA* 4.5 4.9 - - + -
232I VAL* 3.4 29.7 - - - +
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Residues in contact with TYR 221 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H THR* 5.9 0.2 - - + -
104H ILE* 4.5 16.6 - - + -
107H LEU* 3.3 21.4 - - + +
205H VAL* 3.1 46.4 + - + -
217I ILE 2.8 14.0 + - - +
218I TYR* 3.1 18.1 + + - +
220I ARG* 1.3 77.4 - - - +
222I LEU* 1.3 71.3 + - + +
225I GLY* 2.9 32.1 + - - -
226I LEU* 4.0 16.6 - - + -
229I ALA* 4.1 7.8 - - + +
219J MET 5.0 0.3 - - - +
223J HIS* 2.8 64.2 + + + -
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Residues in contact with LEU 222 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208I TYR* 6.0 1.3 - - - +
218I TYR* 3.0 57.2 + - + +
219I GLU* 3.6 6.7 - - - +
221I TYR* 1.3 95.1 - - + +
223I SER* 1.3 64.5 + - - +
67J ALA* 6.3 0.2 - - + -
217J MET* 3.9 7.0 - - + +
219J MET* 3.3 30.7 - - - +
220J GLU* 3.5 39.9 + - + +
223J HIS* 4.5 3.4 - - + -
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Residues in contact with SER 223 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219I GLU* 2.7 36.4 + - - +
220I ARG* 4.2 2.5 - - - -
222I LEU* 1.3 74.8 - - - +
224I GLU* 1.3 68.4 + - - +
44J THR* 4.2 15.1 - - - +
67J ALA* 3.4 21.1 - - - +
217J MET* 4.1 9.0 - - - -
219J MET* 3.5 31.9 - - - +
222J ILE* 4.3 0.9 - - - +
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Residues in contact with GLU 224 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220I ARG* 2.8 33.9 + - - +
223I SER* 1.3 85.8 - - - +
225I GLY* 1.3 62.2 + - - +
228I ALA* 3.3 26.9 + - + +
44J THR* 4.4 3.6 - - + -
45J GLU* 3.4 16.2 - - - +
48J LYS* 2.6 36.6 + - - +
222J ILE* 3.7 9.6 - - - +
226J GLU* 4.5 3.6 - - - +
243J HIS* 3.7 25.7 + - - +
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Residues in contact with GLY 225 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220I ARG 3.4 9.9 - - - +
221I TYR* 2.9 25.6 + - - +
222I LEU 4.4 1.2 + - - -
223I SER 3.7 1.2 - - - -
224I GLU* 1.3 78.5 - - - +
226I LEU* 1.3 67.6 + - - +
228I ALA 3.4 6.6 + - - -
229I ALA 3.6 2.9 + - - -
219J MET 4.8 0.4 - - - -
222J ILE* 3.9 12.5 - - - +
223J HIS 4.0 7.9 - - - -
226J GLU* 3.4 7.0 - - - -
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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