Contacts of the helix formed by residues 186 - 205 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ARG* 5.6 8.7 - - - +
209A ASP* 4.6 12.6 - - - +
236A PHE* 5.2 0.2 - - - -
180F PHE 5.6 2.7 - - - +
184F PRO 4.2 3.6 - - - +
185F LEU* 1.3 93.4 - - + +
187F SER* 1.3 65.9 + - - +
188F GLU* 4.1 9.4 - - + +
189F THR* 3.1 29.4 + - - +
190F ILE* 3.2 11.8 + - - +
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Residues in contact with SER 187 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A PRO* 3.3 36.2 + - - +
207A ASP* 3.7 12.3 + - - +
209A ASP* 4.9 5.9 + - - -
234A ASN* 4.7 13.2 + - - -
185F LEU 3.7 1.4 + - - -
186F PRO* 1.3 73.3 - - - +
188F GLU* 1.3 58.0 + - - +
190F ILE* 3.3 10.4 + - - +
191F LYS* 2.8 32.8 + - - +
225F GLN* 5.8 0.7 - - - +
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Residues in contact with GLU 188 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ASP* 3.9 22.9 + - - +
172F ARG* 2.6 41.7 + - - +
186F PRO* 3.1 7.1 - - + +
187F SER* 1.3 79.4 + - - +
189F THR* 1.3 56.8 + - - +
191F LYS* 3.3 12.4 + - - +
192F ILE* 3.0 34.2 + - + +
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Residues in contact with THR 189 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F LEU* 4.0 13.6 - - + +
179F VAL* 6.1 0.4 - - + -
180F PHE 5.5 1.7 + - - +
181F LEU* 3.7 30.1 - - + -
185F LEU* 4.2 15.5 - - + -
186F PRO* 3.1 30.1 + - - +
188F GLU* 1.3 76.7 - - - +
190F ILE* 1.3 64.8 + - - +
192F ILE* 3.3 14.1 + - + +
193F GLY 3.2 17.0 + - - -
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Residues in contact with ILE 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168F LEU* 5.3 0.2 - - - -
185F LEU* 3.8 23.6 - - + -
186F PRO 3.2 14.1 + - - +
187F SER* 3.4 10.3 - - - +
189F THR* 1.3 76.7 - - - +
191F LYS* 1.3 57.3 + - - +
193F GLY* 3.2 2.9 + - - -
194F VAL* 2.9 31.8 + - + +
225F GLN* 3.7 37.5 - - + +
226F PHE* 3.8 22.4 - - + -
229F ALA* 3.6 28.5 - - + -
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Residues in contact with LYS 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172F ARG* 4.4 4.7 - - - +
187F SER* 2.8 21.4 + - - +
188F GLU* 3.4 22.7 - - - +
190F ILE* 1.3 77.4 - - - +
192F ILE* 1.3 56.7 - - - +
194F VAL* 3.7 18.6 - - - +
195F GLU* 2.9 61.4 + - - +
198F GLU* 4.9 4.4 + - - -
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Residues in contact with ILE 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167F VAL 4.2 2.0 - - - +
168F LEU* 5.8 1.8 - - - +
170F HIS 4.2 4.0 - - - +
171F ASP* 4.9 7.6 - - + -
172F ARG* 3.5 46.2 - - + +
188F GLU* 3.0 27.1 + - + +
189F THR* 3.6 13.0 - - + +
191F LYS* 1.3 74.0 - - - +
193F GLY* 1.3 61.9 + - - +
195F GLU* 3.2 24.4 - - - +
196F ARG* 3.3 49.7 + - - +
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Residues in contact with GLY 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167F VAL* 3.7 19.7 + - - +
168F LEU* 4.0 4.0 - - - +
189F THR 3.2 9.1 + - - -
192F ILE* 1.3 78.5 - - - +
194F VAL* 1.3 62.7 + - - +
196F ARG* 3.3 4.7 + - - +
197F VAL* 3.1 26.3 + - - +
226F PHE* 3.6 26.5 - - - -
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Residues in contact with VAL 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190F ILE* 2.9 27.5 + - + +
191F LYS* 3.7 18.4 - - - +
193F GLY* 1.3 71.2 - - - +
195F GLU* 1.3 54.8 + - - +
196F ARG 3.2 0.2 + - - -
197F VAL* 3.3 2.8 + - - +
198F GLU* 2.8 39.4 + - - +
226F PHE* 3.7 1.3 - - + -
229F ALA* 3.6 37.7 - - + +
230F ILE* 4.1 12.1 - - + -
233F PHE* 4.1 20.8 - - + -
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Residues in contact with GLU 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F LYS* 3.9 44.9 + - + +
172F ARG* 2.9 47.3 + - - +
191F LYS* 2.9 29.2 + - - +
192F ILE* 3.2 21.2 - - - +
194F VAL* 1.3 76.9 - - - +
196F ARG* 1.3 60.1 + - + +
198F GLU* 3.8 9.7 - - - +
199F ALA* 2.9 29.5 + - - +
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Residues in contact with ARG 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143F GLY* 2.8 29.7 + - - -
145F LYS* 4.4 6.7 - - - -
148F TYR* 3.4 51.8 + - + +
167F VAL* 2.8 50.1 + - + -
170F HIS 2.8 22.2 + - - +
171F ASP 3.0 26.3 + - - -
172F ARG* 3.9 1.4 - - - +
192F ILE* 3.3 27.7 + - - +
193F GLY 3.3 3.5 + - - +
194F VAL 3.1 0.8 - - - -
195F GLU* 1.3 84.4 + - + +
197F VAL* 1.3 65.9 + - - +
199F ALA* 3.4 4.9 + - - +
200F ILE* 3.0 31.9 + - - +
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Residues in contact with VAL 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165F VAL* 5.6 1.3 - - + -
167F VAL* 3.9 22.0 - - + +
193F GLY 3.1 14.1 + - - +
194F VAL 3.7 5.4 - - - +
196F ARG* 1.3 73.7 - - - +
198F GLU* 1.3 58.6 + - - +
200F ILE* 3.3 9.3 + - - +
201F ARG* 2.8 29.3 + - - +
210F ILE* 4.3 8.8 - - + +
212F VAL* 4.2 15.0 - - + -
226F PHE* 4.6 0.2 - - + -
230F ILE* 4.1 17.7 - - + -
233F PHE* 3.7 33.2 - - + -
235F ILE* 3.8 16.4 - - + -
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Residues in contact with GLU 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191F LYS* 4.9 4.0 + - - -
194F VAL* 2.8 25.7 + - - +
195F GLU* 3.8 11.6 - - - +
197F VAL* 1.3 73.7 - - - +
199F ALA* 1.3 58.5 + - - +
201F ARG* 3.3 1.5 + - + +
202F ASN* 2.9 53.3 + - - +
232F GLU* 5.6 0.2 - - - +
233F PHE* 3.7 37.6 - - + -
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Residues in contact with ALA 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F LYS* 3.6 34.1 - - + +
146F GLU* 5.4 0.7 - - - -
149F ALA* 3.7 10.7 - - + +
195F GLU 2.9 20.7 + - - +
196F ARG 3.7 3.6 - - - +
198F GLU* 1.3 75.9 - - - +
200F ILE* 1.3 61.9 + - - +
202F ASN* 3.6 7.1 + - - +
203F ALA* 3.1 24.8 + - - +
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Residues in contact with ILE 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F LEU* 4.5 5.4 - - + -
148F TYR* 3.7 37.9 - - + +
149F ALA* 4.6 1.8 - - - +
152F ALA* 3.8 18.8 - - + -
163F VAL* 4.2 8.7 - - + -
165F VAL* 3.7 35.2 - - + -
167F VAL* 4.8 0.4 - - + -
196F ARG 3.0 23.7 + - - +
197F VAL* 3.7 5.6 - - - +
199F ALA* 1.3 73.3 - - - +
201F ARG* 1.3 60.3 + - - +
203F ALA* 3.1 5.9 + - - +
204F VAL* 2.9 36.3 + - + +
210F ILE* 3.7 23.8 - - + -
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Residues in contact with ARG 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197F VAL 2.8 20.1 + - - +
198F GLU 3.8 3.6 - - - +
200F ILE* 1.3 72.9 - - - +
202F ASN* 1.3 62.6 + - - +
204F VAL* 4.1 1.9 - - - +
205F GLY* 2.9 51.2 + - - -
206F PRO* 4.1 12.3 + - - -
208F VAL 2.7 27.5 + - - -
209F ASP* 4.7 2.2 + - - +
210F ILE* 3.5 37.0 - - + +
233F PHE* 2.9 40.1 + - + +
234F ASN* 2.9 37.6 + - - +
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Residues in contact with ASN 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198F GLU* 2.9 42.7 + - - +
199F ALA* 3.8 6.7 - - - +
201F ARG* 1.3 82.6 - - - +
203F ALA* 1.3 60.8 + - - +
205F GLY* 4.1 3.8 + - - -
233F PHE* 5.9 1.0 - - - -
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Residues in contact with ALA 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F ALA* 3.9 20.9 - - + +
153F LEU* 3.7 36.5 - - + +
199F ALA 3.1 18.8 + - - +
200F ILE* 3.6 3.6 - - - +
202F ASN* 1.3 78.6 - - - +
204F VAL* 1.3 62.3 + - + +
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Residues in contact with VAL 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152F ALA* 3.8 29.4 - - + -
153F LEU* 4.7 3.8 - - + +
156F VAL* 3.8 22.2 - - + +
163F VAL* 5.5 0.9 - - + -
200F ILE* 2.9 31.5 + - + +
201F ARG* 3.9 10.8 - - - +
203F ALA* 1.3 79.6 - - + +
205F GLY* 1.3 73.6 + - - +
207F ASP 4.7 0.7 + - - -
208F VAL* 3.6 40.5 + - + +
210F ILE* 4.3 2.7 - - + -
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Residues in contact with GLY 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201F ARG* 2.9 40.1 + - - -
202F ASN 4.1 3.1 + - - -
203F ALA 3.5 2.4 - - - -
204F VAL* 1.3 84.3 - - - +
206F PRO* 1.3 71.4 - - - +
207F ASP 3.4 1.0 + - - -
208F VAL 3.9 1.0 + - - +
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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