Contacts of the helix formed by residues 189 - 205 (chain A) in PDB entry 2OG9
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 189 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLN* 2.8 14.6 + - + +
188A PRO* 1.3 74.5 - - + +
190A GLY* 1.3 50.6 + - - +
191A ALA* 3.2 19.6 + - - +
192A LEU* 2.7 61.1 + - + +
193A ASP 3.7 1.7 + - - -
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Residues in contact with GLY 190 (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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187A GLN 3.5 3.3 + - - -
188A PRO 3.4 7.9 + - - -
189A ASP* 1.3 71.7 - - - +
191A ALA* 1.3 62.5 + - - +
193A ASP* 3.2 8.2 + - - -
194A ILE* 3.1 29.5 + - - +
218A TRP* 6.2 0.9 - - - -
226A MSE 3.6 27.2 - - - +
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Residues in contact with ALA 191 (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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189A ASP* 2.9 13.3 + - - +
190A GLY* 1.3 76.2 - - - +
192A LEU* 1.3 58.4 - - + +
194A ILE* 3.5 12.0 + - - +
195A ALA* 3.0 28.6 + - - +
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Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ILE* 5.8 4.0 - - + -
187A GLN* 3.0 25.6 - - - +
189A ASP* 2.7 44.1 + - + +
191A ALA* 1.3 79.1 - - + +
193A ASP* 1.3 57.8 + - - +
195A ALA* 3.0 9.6 + - + +
196A ARG* 2.8 42.1 + - + +
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Residues in contact with ASP 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU* 3.7 3.6 - - - +
184A LYS 4.4 1.0 - - - +
185A VAL* 3.6 35.2 - - + +
186A GLY* 3.1 17.5 + - - -
187A GLN* 2.9 40.2 + - - +
189A ASP 3.7 0.4 + - - -
190A GLY* 3.2 8.0 + - - +
192A LEU* 1.3 75.0 - - - +
194A ILE* 1.3 60.3 + - - +
196A ARG* 3.0 8.6 + - - +
197A VAL* 2.8 34.9 + - - +
218A TRP* 5.0 0.5 + - - -
226A MSE 4.1 16.7 - - + +
230A PHE* 4.7 1.3 - - + -
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Residues in contact with ILE 194 (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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190A GLY 3.1 17.2 + - - +
191A ALA* 3.7 11.7 - - - +
193A ASP* 1.3 75.7 - - - +
195A ALA* 1.3 53.0 + - - +
197A VAL* 4.0 0.9 - - - +
198A THR* 2.5 45.6 + - - +
226A MSE 4.0 15.0 - - + -
229A ILE* 3.4 53.4 - - + -
230A PHE* 4.6 14.1 - - + -
233A PHE* 4.2 8.9 - - + -
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Residues in contact with ALA 195 (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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163A ILE* 5.1 6.3 - - + -
191A ALA 3.0 14.8 + - - +
192A LEU* 3.3 15.3 - - + +
194A ILE* 1.3 76.2 - - - +
196A ARG* 1.3 61.7 + - + +
198A THR* 3.2 7.2 + - - -
199A ALA* 2.8 30.9 + - - +
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Residues in contact with ARG 196 (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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158A PHE 3.1 21.8 + - - -
159A LEU* 3.5 17.6 + - - +
161A THR 2.9 30.1 + - - -
162A PRO* 4.6 1.0 - - - +
163A ILE* 3.2 38.0 - - + +
166A LEU* 3.8 18.2 - - - +
183A LEU* 4.9 1.6 - - + -
184A LYS 4.9 8.9 + - - -
187A GLN* 3.8 18.5 + - - -
192A LEU* 2.8 33.0 + - + +
193A ASP* 3.6 8.0 + - - +
195A ALA* 1.3 73.0 - - + +
197A VAL* 1.3 57.8 + - + +
199A ALA* 3.2 7.8 + - - +
200A VAL* 2.9 36.7 + - + +
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Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU* 3.9 26.9 - - + -
185A VAL* 4.2 10.1 - - + -
193A ASP 2.8 25.7 + - - +
194A ILE 4.1 2.9 - - - +
196A ARG* 1.3 70.1 - - + +
198A THR* 1.3 61.6 + - - +
200A VAL* 3.3 1.7 + - - +
201A ARG* 2.9 28.1 + - - +
210A LEU* 4.7 4.7 - - + +
212A VAL* 4.1 12.1 - - + -
230A PHE* 3.9 25.6 - - + -
233A PHE* 3.6 25.4 - - + -
235A LEU* 4.5 13.7 - - + -
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Residues in contact with THR 198 (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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194A ILE* 2.5 28.4 + - - +
195A ALA* 3.5 7.6 - - - -
197A VAL* 1.3 77.1 - - - +
199A ALA* 1.3 59.5 + - - +
201A ARG* 3.4 3.0 + - + +
202A LYS* 3.0 31.8 + - + +
233A PHE* 3.3 24.8 - - + -
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Residues in contact with ALA 199 (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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163A ILE* 3.5 27.8 - - + -
167A MSE 3.3 20.5 - - + +
195A ALA 2.8 16.4 + - - +
196A ARG* 3.4 6.1 - - - +
198A THR* 1.3 75.5 - - - +
200A VAL* 1.3 64.6 + - - +
202A LYS* 3.5 5.8 + - - +
203A HIS 3.1 16.6 + - - -
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Residues in contact with VAL 200 (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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163A ILE* 5.2 3.4 - - + -
166A LEU* 3.9 24.7 - - + -
167A MSE 4.5 11.9 - - + -
170A ALA* 5.1 2.0 - - + -
181A ILE* 4.9 1.6 - - + -
183A LEU* 3.6 33.0 - - + -
196A ARG* 2.9 24.3 + - + +
197A VAL 3.7 4.3 - - - +
199A ALA* 1.3 73.6 - - + +
201A ARG* 1.3 66.2 + - - +
203A HIS* 3.2 6.2 + - + +
204A LEU* 3.0 47.0 + - + +
210A LEU* 4.2 11.0 - - + -
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Residues in contact with ARG 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A VAL 2.9 17.7 + - - +
198A THR* 3.7 6.7 - - - +
200A VAL* 1.3 78.0 - - - +
202A LYS* 1.3 57.6 + - - +
204A LEU* 5.3 0.7 - - - -
205A GLY* 2.9 47.9 + - - +
206A ASP* 3.9 29.1 + - - +
208A VAL 4.7 4.0 + - - -
210A LEU* 3.4 42.5 - - + +
232A PRO 5.2 0.8 + - - -
233A PHE* 2.8 48.4 + - + +
234A ASN* 4.2 9.7 + - - +
235A LEU* 4.7 3.0 - - - +
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Residues in contact with LYS 202 (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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167A MSE 6.0 0.4 - - + -
198A THR* 3.0 20.3 + - + +
199A ALA* 3.9 6.1 - - - +
200A VAL 3.3 0.2 - - - -
201A ARG* 1.3 80.2 - - - +
203A HIS* 1.3 62.4 - - - +
205A GLY* 4.1 4.7 + - - -
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Residues in contact with HIS 203 (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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167A MSE 3.0 74.1 + - + +
168A VAL* 4.3 7.1 + - + +
171A SER* 3.8 13.1 + - - -
199A ALA 3.1 8.4 + - - +
200A VAL 3.2 4.9 + - - +
202A LYS* 1.3 80.0 - - - +
204A LEU* 1.3 73.0 + - + +
205A GLY 3.7 0.2 + - - -
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Residues in contact with LEU 204 (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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167A MSE 6.2 0.2 - - - -
170A ALA* 3.9 6.3 - - + -
171A SER* 3.6 39.3 - - - +
174A ILE* 4.4 7.0 - - + -
181A ILE* 3.7 30.3 - - + -
200A VAL* 3.0 36.1 + - + +
201A ARG* 5.3 0.7 - - - -
203A HIS* 1.3 84.3 - - + +
205A GLY* 1.3 61.3 + - - +
207A ALA* 5.3 0.9 + - - +
208A VAL* 3.5 35.7 - - + +
210A LEU* 4.1 5.2 - - + -
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Residues in contact with GLY 205 (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 ARG* 2.9 28.9 + - - +
202A LYS 4.1 4.2 + - - -
203A HIS 3.4 1.8 - - - -
204A LEU* 1.3 80.6 - - - +
206A ASP* 1.3 63.5 + - - -
207A ALA* 3.1 8.6 + - - -
208A VAL* 3.4 13.3 + - - +
210A LEU* 5.5 0.3 - - - +
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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