Contacts of the helix formed by residues 186 - 205 (chain B) in PDB entry 2OX4
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 PRO 186 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B PHE 5.7 3.1 - - - +
184B PRO 4.3 2.7 - - - +
185B LEU* 1.3 94.3 - - + +
187B SER* 1.3 64.9 + - - +
188B GLU* 4.2 9.4 - - + +
189B THR* 3.1 28.9 + - - +
190B ILE* 3.3 10.4 + - - +
125H ARG* 5.6 7.6 - - - +
209H ASP* 4.5 12.6 - - - +
236H PHE* 5.2 0.6 - - + -
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Residues in contact with SER 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B LEU 3.8 1.4 + - - -
186B PRO* 1.3 72.0 - - - +
188B GLU* 1.3 57.8 + - - +
190B ILE* 3.3 10.7 + - - +
191B LYS* 2.9 28.6 + - - +
225B GLN* 5.7 0.7 - - - +
206H PRO* 3.4 34.2 + - - +
207H ASP* 3.9 12.4 + - - +
209H ASP* 4.9 6.7 + - - -
234H ASN* 4.6 13.2 + - - -
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Residues in contact with GLU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ARG* 2.9 42.5 + - - +
186B PRO* 3.1 6.5 - - + +
187B SER* 1.3 79.5 + - - +
189B THR* 1.3 57.4 + - - +
191B LYS* 3.3 26.9 + - - +
192B ILE* 2.9 38.3 + - + +
207H ASP* 3.9 24.0 + - - +
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Residues in contact with THR 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 3.9 14.4 - - + +
179B VAL* 6.1 0.4 - - + -
180B PHE 5.6 1.1 + - - +
181B LEU* 3.7 30.7 - - + -
185B LEU* 4.2 15.5 - - + -
186B PRO* 3.1 30.1 + - - +
188B GLU* 1.3 74.4 - - - +
190B ILE* 1.3 65.6 + - - +
192B ILE* 3.4 13.7 + - + +
193B GLY 3.1 17.2 + - - -
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Residues in contact with ILE 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LEU* 5.3 0.2 - - - -
185B LEU* 3.7 26.5 - - + -
186B PRO 3.3 10.7 + - - +
187B SER* 3.5 9.6 - - - +
189B THR* 1.3 75.9 - - - +
191B LYS* 1.3 58.9 + - - +
193B GLY* 3.2 3.1 + - - -
194B VAL* 2.9 31.0 + - + +
225B GLN* 3.7 37.2 - - + +
226B PHE* 3.9 23.5 - - + -
229B ALA* 3.6 28.3 - - + -
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Residues in contact with LYS 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ARG* 3.8 13.3 - - - +
187B SER* 2.9 16.3 + - - +
188B GLU* 3.4 38.0 + - - +
189B THR 3.3 0.2 - - - -
190B ILE* 1.3 77.5 - - - +
192B ILE* 1.3 52.6 + - - +
194B VAL* 3.8 5.6 - - + +
195B GLU* 2.8 45.8 + - + +
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Residues in contact with ILE 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B VAL 4.2 2.7 - - - +
168B LEU* 5.8 1.6 - - + +
170B HIS 4.2 3.8 - - - +
171B ASP* 4.9 6.7 - - + -
172B ARG* 3.4 46.7 - - + +
188B GLU* 2.9 26.1 + - + +
189B THR* 3.6 13.0 - - + +
191B LYS* 1.3 75.5 - - - +
193B GLY* 1.3 62.8 + - - +
195B GLU* 3.2 24.3 - - - +
196B ARG* 3.3 46.7 + - - +
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Residues in contact with GLY 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B VAL* 3.7 18.5 - - - +
168B LEU* 4.1 2.7 - - - +
189B THR 3.1 10.5 + - - -
190B ILE 3.2 2.9 + - - -
192B ILE* 1.3 78.9 - - - +
194B VAL* 1.3 62.3 + - - +
196B ARG* 3.3 4.3 + - - +
197B VAL* 3.1 26.3 + - - +
226B PHE* 3.7 24.2 - - - -
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Residues in contact with VAL 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B ILE* 2.9 22.8 + - + +
191B LYS* 3.8 7.4 - - + +
193B GLY* 1.3 75.7 - - - +
195B GLU* 1.3 59.4 + - - +
197B VAL* 3.2 2.3 + - - +
198B GLU* 2.8 34.0 + - + +
226B PHE* 4.3 1.1 - - + -
229B ALA* 3.5 39.3 - - + +
230B ILE* 4.1 12.1 - - + -
233B PHE* 3.9 21.3 - - + -
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Residues in contact with GLU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LYS* 3.9 47.0 + - + +
172B ARG* 2.8 49.5 + - - +
191B LYS* 2.8 26.8 + - + +
192B ILE* 3.2 20.5 - - - +
194B VAL* 1.3 75.2 - - - +
196B ARG* 1.3 60.6 + - + +
198B GLU* 3.9 11.8 - - - +
199B ALA* 2.9 30.0 + - - +
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Residues in contact with ARG 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B GLY* 2.9 27.5 + - - -
145B LYS* 4.3 9.9 - - - -
148B TYR* 3.3 53.2 + - + +
167B VAL* 2.9 39.1 + - + -
170B HIS 2.8 22.2 + - - +
171B ASP 3.0 26.7 + - - -
172B ARG* 3.9 1.6 - - - +
192B ILE* 3.3 27.2 + - - +
193B GLY 3.6 5.8 - - - +
194B VAL 3.1 0.4 - - - -
195B GLU* 1.3 79.3 + - + +
197B VAL* 1.3 66.1 + - - +
199B ALA* 3.5 5.7 + - - +
200B ILE* 3.0 31.0 + - - +
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Residues in contact with VAL 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B VAL* 5.4 1.8 - - + -
167B VAL* 3.8 24.2 - - + -
193B GLY 3.1 13.7 + - - +
194B VAL 3.8 5.4 - - - +
196B ARG* 1.3 74.7 - - - +
198B GLU* 1.3 57.8 + - - +
200B ILE* 3.3 9.2 + - - +
201B ARG* 2.8 27.5 + - - +
210B ILE* 4.4 10.2 - - + +
212B VAL* 4.2 14.6 - - + -
230B ILE* 4.1 15.7 - - + -
233B PHE* 3.7 32.8 - - + -
235B ILE* 3.8 16.2 - - + -
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Residues in contact with GLU 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B VAL* 2.8 25.1 + - - +
195B GLU* 3.9 10.7 - - - +
197B VAL* 1.3 72.0 - - - +
199B ALA* 1.3 59.7 + - - +
201B ARG* 3.8 0.4 - - - -
202B ASN* 2.9 54.8 + - - +
232B GLU* 5.6 0.2 - - - +
233B PHE* 3.7 37.7 - - + -
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Residues in contact with ALA 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B LYS* 3.6 34.8 - - + +
146B GLU* 5.3 0.7 - - - -
149B ALA* 3.7 10.3 - - + +
195B GLU 2.9 20.1 + - - +
196B ARG 3.7 3.8 - - - +
198B GLU* 1.3 74.4 + - - +
200B ILE* 1.3 62.4 + - - +
202B ASN* 3.9 6.5 - - - +
203B ALA* 3.1 24.9 + - - +
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Residues in contact with ILE 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU* 4.4 5.2 - - + -
148B TYR* 3.7 38.6 - - + +
149B ALA* 4.2 5.4 - - - +
152B ALA* 3.7 18.6 - - + -
163B VAL* 4.3 6.7 - - + -
165B VAL* 3.7 35.4 - - + -
167B VAL* 4.9 0.2 - - + -
196B ARG 3.0 24.5 + - - +
197B VAL* 3.3 5.8 + - - +
199B ALA* 1.3 76.4 - - - +
201B ARG* 1.3 57.6 + - - +
203B ALA* 3.1 2.5 + - - +
204B VAL* 2.9 34.4 + - + +
210B ILE* 3.8 24.0 - - + -
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Residues in contact with ARG 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B VAL 2.8 20.7 + - - +
198B GLU* 3.8 7.6 - - - +
200B ILE* 1.3 71.7 - - - +
202B ASN* 1.3 63.7 + - - +
204B VAL* 4.1 2.3 - - - +
205B GLY* 2.9 51.9 + - - -
206B PRO* 4.1 12.3 + - - -
208B VAL 2.8 26.9 + - - -
209B ASP* 4.8 1.6 + - - +
210B ILE* 3.5 36.2 - - + +
233B PHE* 2.8 37.6 + - + +
234B ASN* 2.9 37.7 + - - +
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Residues in contact with ASN 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B GLU* 2.9 42.2 + - - +
199B ALA* 3.9 5.8 - - - +
201B ARG* 1.3 82.0 - - - +
203B ALA* 1.3 62.5 + - - +
205B GLY* 4.0 4.5 + - - -
233B PHE* 5.9 0.7 - - - -
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Residues in contact with ALA 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ALA* 3.9 20.6 - - + +
153B LEU* 3.6 35.6 - - + +
199B ALA 3.1 18.7 + - - +
200B ILE* 3.5 4.7 - - - +
202B ASN* 1.3 80.2 - - - +
204B VAL* 1.3 63.3 + - + +
205B GLY 3.7 0.2 + - - -
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Residues in contact with VAL 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ALA* 3.8 29.6 - - + -
153B LEU* 4.7 4.5 - - + +
156B VAL* 3.8 21.4 - - + +
163B VAL* 5.6 0.9 - - + -
200B ILE* 2.9 33.2 + - + +
201B ARG* 4.0 11.9 - - - +
203B ALA* 1.3 76.6 - - + +
205B GLY* 1.3 73.2 + - - +
207B ASP 4.7 0.9 + - - -
208B VAL* 3.7 39.9 + - + +
210B ILE* 4.4 2.0 - - + -
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Residues in contact with GLY 205 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ARG* 2.9 40.2 + - - -
202B ASN 4.0 4.4 + - - -
203B ALA 3.4 3.2 + - - -
204B VAL* 1.3 83.8 - - - +
206B PRO* 1.3 71.5 - - - +
207B ASP 3.4 1.2 + - - -
208B VAL 3.9 0.9 + - - -
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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