Contacts of the helix formed by residues 158 - 177 (chain G) 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 ASP 158 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F PRO* 5.4 12.7 - - + +
33F THR 6.1 0.2 - - - +
185F HIS* 4.3 24.2 - - + +
187F LEU* 6.0 1.0 - - - +
225F PHE* 4.1 24.8 - - + +
228F ALA* 5.0 1.7 - - - +
157G VAL* 1.3 74.9 - - - +
159G LEU* 1.3 80.5 + - - +
160G LYS* 2.9 34.5 + - - +
161G THR* 2.9 20.6 + - - +
162G LYS* 2.9 18.7 + - - +
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Residues in contact with LEU 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185F HIS* 5.2 3.5 + - - +
186F ASP* 3.5 26.9 - - - +
187F LEU* 4.3 19.3 - - + +
188F ILE* 4.4 3.8 - - + -
228F ALA* 3.9 10.3 - - + +
231F LEU* 3.3 12.9 - - + +
232F LEU* 4.2 31.9 - - + -
157G VAL 3.5 3.0 + - - -
158G ASP* 1.3 75.0 + - - +
160G LYS* 1.3 65.9 + - - +
162G LYS* 2.9 40.4 + - + +
163G GLY 3.2 4.7 + - - -
188G ILE* 4.0 26.9 - - + -
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Residues in contact with LYS 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224F GLU* 4.6 21.1 - - + +
225F PHE* 4.4 11.7 - - + +
227F SER* 3.9 21.5 + - - +
228F ALA* 3.7 15.2 - - + +
231F LEU* 3.6 18.9 - - + +
158G ASP* 2.9 21.9 + - - +
159G LEU* 1.3 80.1 - - - +
161G THR* 1.3 65.6 + - - +
163G GLY 3.6 1.9 + - - -
164G VAL* 3.8 27.5 - - - +
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Residues in contact with THR 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G GLN* 5.7 1.1 - - - +
157G VAL* 3.6 17.0 - - + +
158G ASP* 2.9 25.7 + - - +
160G LYS* 1.3 76.7 - - - +
162G LYS* 1.3 65.6 + - - +
164G VAL* 2.6 38.3 - - + +
165G LEU* 3.0 16.5 + - + +
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Residues in contact with LYS 162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G LEU* 4.1 33.7 - - + +
155G SER* 6.0 0.2 - - - +
157G VAL* 3.8 14.2 + - + +
158G ASP 2.9 11.3 + - - +
159G LEU* 2.9 33.6 + - + +
161G THR* 1.3 74.1 - - - +
163G GLY* 1.3 65.7 + - - +
165G LEU* 2.8 9.6 + - - +
166G MET* 2.7 32.8 + - - +
186G ASP* 2.8 33.1 + - - +
188G ILE* 4.7 6.4 - - + +
189G GLU* 3.4 27.5 + - + -
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Residues in contact with GLY 163 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231F LEU* 3.8 26.2 - - - +
159G LEU 3.2 7.7 + - - -
160G LYS 3.6 0.2 + - - -
161G THR 3.3 0.2 - - - -
162G LYS* 1.3 79.5 - - - +
164G VAL* 1.3 62.5 + - - +
166G MET* 3.1 20.4 + - - +
167G GLU* 3.1 23.3 + - - +
170G ARG* 5.5 0.2 + - - -
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Residues in contact with VAL 164 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231F LEU* 5.1 0.8 - - + +
160G LYS* 3.8 34.4 + - - +
161G THR* 2.6 34.1 + - + +
163G GLY* 1.3 74.5 - - - +
165G LEU* 1.3 76.5 + - + +
167G GLU* 3.3 15.7 + - - +
168G GLU* 3.2 30.6 + - + +
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Residues in contact with LEU 165 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G GLY* 5.4 0.2 - - - -
133G GLN* 3.3 43.7 - - + +
134G ARG* 6.2 1.1 - - - +
154G LEU* 3.9 24.9 - - + -
157G VAL* 4.1 20.4 - - + -
161G THR* 3.5 18.2 - - + +
162G LYS* 2.8 13.5 + - - +
164G VAL* 1.3 78.5 - - + +
166G MET* 1.3 65.6 + - - +
168G GLU* 2.9 36.8 + - + +
169G LEU* 3.0 16.4 + - + +
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Residues in contact with MET 166 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G LEU* 3.8 10.3 - - + -
162G LYS* 2.7 42.1 + - - +
163G GLY* 3.5 11.0 - - - +
165G LEU* 1.3 71.3 - - - +
167G GLU* 1.3 63.8 + - - +
169G LEU* 2.8 17.2 + - - +
170G ARG* 3.0 16.0 + - - +
188G ILE* 4.3 5.2 - - - +
189G GLU* 3.0 47.3 - - + -
192G MET* 3.6 28.3 - - + -
193G LEU* 3.2 35.9 - - + +
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Residues in contact with GLU 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231F LEU* 4.9 6.6 - - - +
234F LYS* 4.7 12.2 + - - -
163G GLY* 3.1 24.3 + - - +
164G VAL* 3.4 13.1 + - - +
165G LEU 3.2 0.2 - - - -
166G MET* 1.3 76.6 - - - +
168G GLU* 1.3 57.5 + - + +
170G ARG* 3.2 39.3 + - - +
171G PHE* 3.0 27.9 + - - +
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Residues in contact with GLU 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114G LEU* 6.1 0.5 - - - +
134G ARG* 3.6 35.1 + - - +
164G VAL* 3.2 21.0 + - - +
165G LEU* 2.9 34.2 + - + +
167G GLU* 1.3 76.0 - - + +
169G LEU* 1.3 58.6 + - + +
171G PHE* 3.4 9.3 + - + +
172G VAL* 2.8 38.9 + - + +
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Residues in contact with LEU 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G TYR* 3.2 34.3 - - + +
137G LEU* 4.5 23.1 - - + -
150G LEU* 4.4 16.8 - - + -
153G PRO* 5.2 2.2 - - + -
154G LEU* 4.2 20.0 - - + -
165G LEU 3.0 14.2 + - - +
166G MET* 2.8 8.3 + - - +
168G GLU* 1.3 73.9 - - + +
170G ARG* 1.3 66.1 + - - +
172G VAL* 3.1 6.1 + - + +
173G GLN* 2.8 24.4 + - - +
180G ILE* 4.7 5.4 - - + +
182G HIS* 3.8 18.8 - - + -
193G LEU* 3.9 11.2 - - + -
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Residues in contact with ARG 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238F ILE* 5.9 0.8 - - - +
26G TYR* 4.7 5.6 - - + -
163G GLY 5.5 0.2 + - - -
166G MET* 3.0 18.5 + - - +
167G GLU* 3.2 42.2 + - - +
169G LEU* 1.3 76.4 - - - +
171G PHE* 1.3 65.0 + - - +
173G GLN* 3.0 8.3 + - - +
174G ARG* 2.9 47.9 + - - +
192G MET* 3.2 51.3 + - - +
193G LEU* 3.7 15.8 - - + +
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Residues in contact with PHE 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G LYS 5.6 5.8 - - - -
167G GLU 3.0 13.7 + - - +
168G GLU* 3.5 9.9 - - + +
170G ARG* 1.3 79.0 - - - +
172G VAL* 1.3 60.5 + - + +
174G ARG* 3.0 11.3 + - + +
175G GLU* 2.6 72.4 + - + +
176G PHE* 6.0 1.6 - + - -
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Residues in contact with VAL 172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G LEU* 4.6 14.1 - - + -
137G LEU* 4.1 27.1 - - + -
141G LEU* 3.9 21.3 - - + -
148G LEU* 5.7 0.4 - - + -
168G GLU* 2.8 36.0 + - + +
169G LEU* 3.5 7.0 - - + +
171G PHE* 1.3 78.2 - - + +
173G GLN* 1.3 56.9 + - - +
175G GLU* 4.2 2.2 - - - -
176G PHE* 2.9 59.1 + - + +
178G VAL* 5.5 0.8 - - + +
180G ILE* 5.5 6.3 - - + -
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Residues in contact with GLN 173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G ARG 5.4 0.9 - - - -
25G ASP* 2.7 13.4 - - - +
26G TYR* 2.6 50.6 + - + +
169G LEU 2.8 12.6 + - - +
170G ARG* 3.4 9.2 + - - +
172G VAL* 1.3 75.8 - - - +
174G ARG* 1.3 71.7 + - - +
177G ASP* 2.8 30.1 + - - +
178G VAL* 3.2 26.7 - - - +
180G ILE* 3.9 16.6 - - + +
195G ASP* 4.5 5.3 + - - -
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Residues in contact with ARG 174 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170G ARG* 2.9 37.1 + - - +
171G PHE* 3.6 11.9 - - + +
173G GLN* 1.3 86.9 - - - +
175G GLU* 1.3 58.6 + - - +
177G ASP* 3.2 21.3 - - - +
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Residues in contact with GLU 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113G LYS* 5.4 7.1 + - + +
171G PHE* 2.6 55.5 + - + +
172G VAL* 3.8 3.6 - - - +
174G ARG* 1.3 76.8 - - - +
176G PHE* 1.3 83.1 + - + +
177G ASP* 5.2 1.2 - - - +
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Residues in contact with PHE 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G MET* 3.9 31.4 - - + -
113G LYS* 4.0 38.6 - - + -
114G LEU* 5.2 4.0 - - + -
141G LEU* 4.1 14.6 - - + -
171G PHE* 6.0 1.3 - + - -
172G VAL* 2.9 52.7 + - + +
175G GLU* 1.3 96.7 - - + +
177G ASP* 1.3 73.5 + - - +
178G VAL* 3.0 24.1 + - + +
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Residues in contact with ASP 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G ARG* 5.5 2.9 - - - +
173G GLN* 2.8 13.6 + - - +
174G ARG* 3.2 20.9 - - - +
175G GLU 5.2 1.5 - - - +
176G PHE* 1.3 78.8 - - - +
178G VAL* 1.3 59.0 + - - +
179G PRO* 3.7 8.7 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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