Contacts of the helix formed by residues 212 - 225 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50H VAL* 2.9 6.5 - - - +
53H THR* 5.5 0.2 - - + -
54H THR* 3.2 26.7 - - + +
131H ILE* 3.1 39.0 - - + -
135H MET* 4.3 8.1 - - + -
199H GLU 4.9 1.6 - - - +
203H VAL* 3.0 42.0 - - + -
207H ALA 5.5 0.4 - - - +
208H TYR 5.7 0.7 - - - +
210H PRO 3.9 1.1 - - - +
211H MET* 1.3 78.6 - - - +
213H ALA* 1.3 69.5 + - - +
214H PRO* 2.9 32.1 - - + -
215H THR* 2.7 24.2 + - - +
216H LEU 3.0 9.2 + - - -
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Residues in contact with ALA 213 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H VAL* 2.7 17.1 - - + +
51H VAL* 4.8 5.8 - - + +
54H THR* 2.9 21.9 + - + +
55H TYR* 6.1 1.6 - - + -
197H ILE 5.7 0.2 - - - +
212H ILE* 1.3 69.7 - - - +
214H PRO* 1.4 69.3 - - + +
216H LEU* 3.4 5.2 + - - +
217H ILE* 3.1 26.9 + - - +
236H LEU* 3.3 35.4 - - + +
98I PRO* 5.7 1.3 - - + -
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Residues in contact with PRO 214 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197H ILE 3.6 16.6 - - - +
198H SER 5.0 0.2 - - - +
199H GLU 3.2 28.3 - - - +
200H PHE* 3.9 18.4 - - + -
212H ILE* 2.9 31.0 - - + -
213H ALA* 1.4 83.1 - - + +
215H THR* 1.3 59.9 + - - +
217H ILE* 3.5 2.1 + - + -
218H TYR* 3.2 13.5 + - - +
236H LEU* 5.3 0.7 - - + -
98I PRO* 3.9 16.4 - - + -
100I THR* 3.1 30.2 + - - +
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Residues in contact with THR 215 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200H PHE* 3.9 10.4 - - + -
203H VAL* 5.5 2.1 - - - +
204H VAL* 3.7 20.8 + - + +
208H TYR* 3.5 48.1 + - + +
211H MET* 3.6 19.1 - - + -
212H ILE* 2.7 24.5 + - - +
214H PRO* 1.3 69.3 - - - +
216H LEU* 1.3 59.2 + - - +
217H ILE 2.9 1.3 - - - -
218H TYR* 2.7 25.3 + - + +
219H GLU* 2.7 12.9 + - - +
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Residues in contact with LEU 216 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46H ALA* 5.1 7.0 - - + +
47H VAL* 3.9 24.2 - - + -
50H VAL* 4.2 21.3 - - + -
211H MET* 2.9 38.6 - - + +
212H ILE 3.0 7.0 + - - +
213H ALA* 3.8 8.5 - - - +
215H THR* 1.3 77.6 - - - +
217H ILE* 1.3 60.4 + - - +
219H GLU* 3.9 2.4 - - + +
220H ARG* 3.2 34.9 + - - +
232H VAL* 3.7 29.8 - - + -
203J GLU* 4.3 22.4 - - + +
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Residues in contact with ILE 217 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213H ALA 3.1 15.9 + - - +
214H PRO* 3.6 1.6 - - + +
215H THR 2.9 0.8 - - - -
216H LEU* 1.3 76.7 - - - +
218H TYR* 1.3 60.0 + - - +
220H ARG* 3.3 5.6 + - - +
221H TYR* 2.8 27.9 + - - +
229H ALA* 4.2 8.4 - - + +
232H VAL* 3.9 13.5 - - + -
233H ALA* 3.7 21.1 - - - +
236H LEU* 3.4 26.5 - - + -
100I THR* 3.3 15.5 - - + -
101I VAL* 3.5 20.9 - - + -
104I ILE* 3.1 35.0 - - + -
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Residues in contact with TYR 218 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200H PHE* 3.4 37.2 - + + -
208H TYR* 5.7 8.5 - + - -
214H PRO 3.2 6.7 + - - +
215H THR* 2.7 13.2 + - + +
217H ILE* 1.3 75.1 - - - +
219H GLU* 1.3 62.8 + - - +
221H TYR* 3.1 19.9 + + + +
222H LEU* 3.0 64.6 + - + +
100I THR* 3.9 6.7 - - + +
200I PHE* 5.7 1.6 - + - -
204I VAL* 4.2 26.3 - - + +
205I VAL* 4.8 8.5 - - + -
208I TYR* 4.2 22.5 - - - -
218I TYR* 4.7 21.4 - + - -
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Residues in contact with GLU 219 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208H TYR* 3.2 28.7 + - - +
209H TYR* 5.0 4.2 + - - -
211H MET* 3.6 20.6 - - + +
215H THR 2.7 18.3 + - - +
216H LEU* 3.9 7.6 - - - +
218H TYR* 1.3 73.1 - - - +
220H ARG* 1.3 54.4 + - + +
222H LEU* 3.0 9.0 + - - +
223H SER* 2.6 48.9 + - - +
202J SER* 4.0 18.9 + - - +
203J GLU* 3.5 27.9 - - + +
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Residues in contact with ARG 220 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H ALA* 5.2 7.1 - - - +
44H ASP* 2.8 32.1 + - - -
46H ALA* 4.6 2.0 - - - +
47H VAL* 4.2 8.7 - - - +
216H LEU* 3.2 26.1 + - - +
217H ILE* 3.9 3.1 - - - +
219H GLU* 1.3 79.0 - - + +
221H TYR* 1.3 62.2 + - - +
223H SER* 4.2 7.2 - - - -
224H GLU* 2.8 37.3 + - - +
225H GLY 3.3 8.3 + - - +
228H ALA* 3.9 22.6 + - - +
229H ALA* 4.5 4.5 - - + -
232H VAL* 3.4 31.2 - - - +
203J GLU* 2.6 43.1 + - - +
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Residues in contact with TYR 221 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217H ILE 2.8 14.8 + - - +
218H TYR* 3.1 23.1 + + - +
220H ARG* 1.3 77.2 - - - +
222H LEU* 1.3 77.0 + - + +
225H GLY* 2.9 32.2 + - - -
226H LEU* 4.0 26.0 - - + -
229H ALA* 4.1 7.8 - - + +
100I THR* 6.1 0.2 - - + -
104I ILE* 4.6 15.5 - - + -
107I LEU* 3.5 25.3 - - + +
204I VAL 5.5 0.4 - - - -
205I VAL* 3.4 35.1 + - + -
80J LEU* 3.1 23.2 - - + +
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Residues in contact with LEU 222 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218H TYR* 3.0 57.8 + - + +
219H GLU* 3.6 7.2 - - - +
221H TYR* 1.3 94.2 - - + +
223H SER* 1.3 65.6 + - - +
208I TYR* 6.5 0.9 - - + -
75J ARG* 4.7 8.3 + - - +
76J LYS* 6.1 2.7 - - - -
79J GLU* 4.3 5.7 - - - +
80J LEU* 3.7 35.6 - - + +
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Residues in contact with SER 223 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219H GLU* 2.6 38.1 + - - +
220H ARG* 4.2 2.7 - - - -
222H LEU* 1.3 75.2 - - - +
224H GLU* 1.3 70.4 + - - +
75J ARG* 3.6 19.2 - - - +
79J GLU* 3.5 16.3 - - - +
152J ASP* 5.0 8.4 + - - -
202J SER* 4.2 14.9 + - - -
203J GLU* 6.1 0.2 - - - -
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Residues in contact with GLU 224 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220H ARG* 2.8 33.2 + - - +
223H SER* 1.3 83.8 - - - +
225H GLY* 1.3 61.8 + - - +
228H ALA* 3.3 27.2 + - + +
79J GLU* 3.4 22.2 - - - +
203J GLU* 4.4 4.9 - - - +
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Residues in contact with GLY 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220H ARG 3.5 10.0 - - - +
221H TYR* 2.9 27.2 + - - +
223H SER 3.7 0.6 - - - -
224H GLU* 1.3 79.8 - - - +
226H LEU* 1.3 67.8 + - - +
227H SER 3.6 1.1 - - - -
228H ALA* 3.4 8.0 + - - +
229H ALA 3.6 1.4 + - - -
79J GLU* 3.3 25.1 - - - +
80J LEU* 4.5 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