Contacts of the helix formed by residues 168 - 176 (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 SER 168 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F GLU* 3.2 13.9 - - - +
166H GLY 4.3 0.2 - - - -
167H SER* 1.3 74.4 - - - +
169H PRO* 1.3 77.8 - - - +
170H LEU* 3.7 9.6 + - - +
171H ARG* 2.8 42.6 + - - +
172H VAL* 2.8 11.6 + - - +
2I ARG* 5.2 2.7 - - - -
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Residues in contact with PRO 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68F GLU* 3.4 7.0 - - - +
74H TYR* 5.8 0.2 + - - -
163H ARG* 2.8 32.9 - - + +
168H SER* 1.3 88.7 - - - +
170H LEU* 1.3 62.4 + - + +
172H VAL* 3.4 7.6 + - + +
173H PHE* 3.0 24.3 + - - +
2I ARG* 4.0 27.4 - - + +
5I PHE* 3.9 22.0 - - + -
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Residues in contact with LEU 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H SER* 3.8 9.9 - - - +
169H PRO* 1.3 78.8 - - + +
171H ARG* 1.3 69.0 + - + +
173H PHE* 3.4 4.5 + - - +
174H PHE* 3.1 59.9 - - + -
5I PHE* 3.4 38.2 - - + +
8I LEU* 5.8 2.0 - - + -
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Residues in contact with ARG 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F GLY* 6.0 2.6 - - - -
96F ARG* 3.2 67.7 + - - +
97F ASN* 4.1 23.4 + - - +
165H LEU 5.4 0.2 + - - -
166H GLY 3.2 21.0 + - - -
167H SER* 2.9 31.3 + - - +
168H SER* 2.8 32.5 + - - +
170H LEU* 1.3 79.4 - - + +
172H VAL* 1.3 60.8 + - - +
174H PHE* 3.1 2.9 + - - +
175H THR* 2.3 33.5 + - - +
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Residues in contact with VAL 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F TYR* 4.1 7.0 - - - -
74H TYR* 5.4 2.2 - - - +
159H GLU* 3.5 44.2 - - + +
162H ALA* 4.0 13.5 - - + -
163H ARG* 3.5 29.8 - - + -
167H SER* 3.5 6.9 + - - +
168H SER 2.8 22.4 + - - +
169H PRO* 3.5 8.3 - - + +
171H ARG* 1.3 71.7 - - - +
173H PHE* 1.3 58.3 + - - +
175H THR* 3.1 2.9 + - - -
176H VAL* 2.6 37.1 + - + -
177H SER* 3.2 6.2 + - - +
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Residues in contact with PHE 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70H THR* 4.3 10.3 - - + -
71H PRO* 5.3 2.0 - - + -
74H TYR* 3.8 42.4 + + + +
151H PHE* 3.8 9.6 - + - -
169H PRO 3.0 10.7 + - - +
170H LEU 3.4 9.2 - - - +
171H ARG 3.1 0.2 + - - -
172H VAL* 1.3 80.9 - - - +
174H PHE* 1.3 88.3 + + - +
177H SER* 3.3 15.3 - - - -
178H LEU* 2.7 70.6 + - + +
5I PHE* 3.6 20.0 - + + -
9I LEU* 4.7 13.9 - - + -
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Residues in contact with PHE 174 (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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170H LEU* 3.1 41.7 - - + +
171H ARG* 3.1 5.8 + - - +
173H PHE* 1.3 97.7 - + - +
175H THR* 1.3 60.5 + - - +
178H LEU* 3.9 21.1 - - + +
179H PRO* 3.1 16.4 - - - +
5I PHE* 4.2 3.4 - + - -
8I LEU* 6.2 3.4 - - + -
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Residues in contact with THR 175 (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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84F HIS* 2.8 24.9 + - - -
85F LEU* 5.3 2.1 - - + +
93F TYR* 3.5 32.4 + - + -
171H ARG* 2.3 36.8 + - - +
174H PHE* 1.3 78.5 - - + +
176H VAL* 1.3 59.2 + - - +
179H PRO* 3.0 11.6 - - - +
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Residues in contact with VAL 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82F PHE* 4.0 18.2 - - + -
84F HIS* 4.2 3.4 - - + -
93F TYR* 3.9 11.7 - - + +
154H VAL* 4.7 1.1 - - + -
158H LEU* 3.9 28.7 - - + +
159H GLU* 4.2 6.7 - - + -
162H ALA* 3.5 28.0 - - + -
172H VAL* 2.6 22.3 + - + +
175H THR* 1.3 78.9 - - - +
177H SER* 1.3 70.6 + - - +
178H LEU 3.6 0.2 - - - -
179H PRO* 3.3 1.5 - - - +
180H LEU* 3.1 42.8 + - + +
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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