Contacts of the helix formed by residues 209 - 219 (chain A) in PDB entry 2O8F
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 209 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A MET* 3.4 25.5 - - + +
159A ARG* 2.7 33.2 + - - -
184A PHE* 4.5 9.0 - - - -
205A GLU* 4.8 0.8 - - - +
208A GLY* 1.3 71.4 - - - -
210A MET* 1.3 64.7 + - + +
211A GLY 3.3 0.9 + - - -
212A LYS* 3.5 17.5 + - - +
213A LEU* 4.0 2.4 + - - +
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Residues in contact with MET 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A VAL 5.2 2.2 - - - +
151A LYS* 6.0 0.4 - - - -
152A MET* 3.9 34.1 - - - +
201A LEU* 4.2 34.8 - - + -
202A PRO* 4.6 14.6 - - + -
203A GLY* 5.1 5.4 - - - +
205A GLU* 3.3 35.4 - - + +
208A GLY 3.3 0.8 - - - -
209A ASP* 1.3 76.5 - - + +
211A GLY* 1.3 64.0 + - - +
212A LYS 3.3 0.4 - - - -
213A LEU* 3.1 20.7 + - + +
214A ARG* 3.1 31.0 + - - +
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Residues in contact with GLY 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A GLU* 4.7 3.0 + - - -
208A GLY 3.7 10.5 + - - +
209A ASP 3.2 1.8 - - - -
210A MET* 1.3 77.7 - - - +
212A LYS* 1.3 60.1 + - - +
214A ARG* 3.4 17.6 + - - +
215A GLN* 3.4 29.9 + - - +
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Residues in contact with LYS 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A ASP 4.2 10.5 + - - +
183A GLN* 5.4 3.6 - - - -
184A PHE* 3.9 21.1 - - + -
208A GLY 4.9 0.8 + - - -
209A ASP* 3.5 13.5 + - - +
210A MET 3.3 0.8 - - - -
211A GLY* 1.3 73.0 - - - +
213A LEU* 1.3 64.2 + - - +
215A GLN* 3.5 24.2 + - + +
216A ILE* 3.3 30.2 + - + +
730A LEU* 5.6 9.7 - - - +
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Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A VAL* 3.8 25.4 - - + -
151A LYS* 6.3 0.2 - - - -
152A MET* 4.1 23.8 - - + -
161A VAL* 5.3 2.2 - - + -
184A PHE* 3.8 39.4 - - + -
187A LEU* 4.1 12.3 - - + -
201A LEU* 4.0 17.7 - - + -
209A ASP 4.0 0.2 + - - -
210A MET* 3.1 22.4 + - + +
212A LYS* 1.3 77.2 - - - +
214A ARG* 1.3 63.9 + - - +
216A ILE* 3.4 4.3 + - - +
217A ILE* 3.3 41.2 + - + +
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Residues in contact with ARG 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A LEU* 3.8 23.4 - - + +
203A GLY* 3.5 28.7 - - - -
205A GLU* 3.1 26.9 + - - -
210A MET* 3.1 23.3 + - - +
211A GLY* 3.6 15.0 - - - +
212A LYS 3.3 0.2 - - - -
213A LEU* 1.3 78.1 - - - +
215A GLN* 1.3 58.4 + - + +
217A ILE 3.4 1.2 + - - -
218A GLN* 2.9 42.6 + - - +
224A ILE* 3.6 15.5 - - + +
226A GLU* 3.7 25.3 + - - -
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Residues in contact with GLN 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLY 3.4 16.7 + - - +
212A LYS* 3.7 29.2 - - + +
213A LEU 3.3 0.4 - - - -
214A ARG* 1.3 74.4 - - + +
216A ILE* 1.3 66.8 + - + +
218A GLN* 4.1 8.6 - - - +
219A ARG* 3.2 31.6 + - - +
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Residues in contact with ILE 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A GLN* 3.3 27.4 - - + +
184A PHE* 4.1 20.0 - - + +
187A LEU* 5.0 8.1 - - + -
188A GLU* 3.6 29.4 - - + +
191A LEU* 6.0 1.3 - - + -
212A LYS* 3.3 23.0 + - + +
213A LEU* 3.6 10.1 - - - +
214A ARG 3.3 0.4 - - - -
215A GLN* 1.3 80.8 - - + +
217A ILE* 1.3 66.3 + - + +
219A ARG* 3.5 31.4 + - - +
220A GLY* 3.5 12.8 + - - -
304A ILE* 3.8 11.6 - - - +
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Residues in contact with ILE 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A VAL* 4.2 11.0 - - + -
187A LEU* 4.8 5.4 - - + -
191A LEU* 4.2 20.0 - - + -
199A CYS* 3.8 26.2 - - + -
201A LEU* 4.5 4.5 - - + -
213A LEU* 3.3 36.6 + - + +
214A ARG 4.0 3.1 - - - +
215A GLN 3.4 0.2 - - - -
216A ILE* 1.3 78.2 - - + +
218A GLN* 1.3 58.6 + - - +
220A GLY* 3.0 19.9 + - - -
221A GLY 3.5 4.5 + - - -
222A ILE* 3.6 39.7 + - + +
224A ILE* 3.8 18.8 - - + -
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Residues in contact with GLN 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A ARG* 2.9 28.3 + - - +
215A GLN* 4.1 7.9 - - - +
216A ILE 3.4 0.2 - - - -
217A ILE* 1.3 72.1 - - - +
219A ARG* 1.3 59.7 + - - +
220A GLY 3.1 5.9 + - - -
221A GLY* 3.3 13.0 + - - -
222A ILE 4.2 7.6 - - - +
224A ILE* 3.8 25.0 - - + +
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Residues in contact with ARG 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A GLN* 6.1 1.4 - - - +
188A GLU* 3.5 22.2 + - - -
215A GLN* 3.2 19.7 + - - +
216A ILE* 3.5 28.2 - - - +
218A GLN* 1.3 74.5 - - - +
220A GLY* 1.3 59.1 + - - +
221A GLY 3.3 1.1 - - - -
303A ASP* 5.6 2.0 + - - -
304A ILE* 3.7 28.3 - - + +
305A ALA* 5.5 3.8 - - - +
308A ARG* 3.2 27.4 + - - +
731A GLU* 5.6 14.9 + - - +
734A SER* 6.2 1.8 - - - -
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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