Contacts of the helix formed by residues 181 - 195 (chain X) in PDB entry 1O1F
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 ALA 181 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155X SER* 4.5 0.9 - - - +
156X GLY 3.3 16.2 - - - +
157X ASP 3.4 17.9 - - - +
158X GLY 3.7 13.5 - - - -
159X VAL 3.8 9.4 - - - +
160X THR* 4.3 3.8 - - - +
180X LEU* 1.3 77.5 - - - +
182X GLY* 1.3 61.5 + - - +
183X ARG 3.2 2.7 + - - -
184X ASP* 3.2 10.0 + - - +
185X LEU* 3.0 33.2 + - - +
261X LEU* 5.3 0.2 - - - -
303X THR* 4.2 5.8 - - - -
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Residues in contact with GLY 182 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156X GLY 3.0 10.4 + - - -
157X ASP* 4.6 4.9 - - - -
181X ALA* 1.3 76.3 - - - +
183X ARG* 1.3 56.0 + - - +
185X LEU* 3.5 7.3 - - - +
186X THR* 3.0 18.2 + - - -
213X LYS* 2.8 30.4 + - - -
303X THR* 3.1 22.3 + - - -
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Residues in contact with ARG 183 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14X SER* 2.8 36.4 + - - -
69X TYR* 3.5 29.0 + - - +
71X ILE 4.8 6.1 + - - -
72X GLU* 4.6 13.7 + - - +
73X HIS* 5.2 7.7 - - - +
157X ASP* 2.9 47.4 + - - +
158X GLY* 4.4 14.8 - - - -
182X GLY* 1.3 71.6 - - - +
184X ASP* 1.3 71.0 + - - +
186X THR* 3.3 13.7 + - - -
187X ASP* 3.3 25.6 + - - +
206X ARG* 6.1 2.5 - - - +
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Residues in contact with ASP 184 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73X HIS* 5.4 3.5 - - - -
157X ASP 4.5 0.9 - - - +
158X GLY* 4.7 4.9 - - - +
179X ASP 3.9 13.3 - - - +
180X LEU* 3.8 12.2 - - + +
181X ALA* 3.2 28.4 + - - +
183X ARG* 1.3 82.0 - - - +
185X LEU* 1.3 62.9 + - + +
187X ASP* 3.2 9.5 + - - +
188X TYR* 3.1 27.3 + - - +
267X ILE* 5.0 12.7 - - + +
269X MET* 5.6 0.7 - - - +
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Residues in contact with LEU 185 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180X LEU* 3.9 24.2 - - + -
181X ALA 3.0 17.9 + - - +
182X GLY* 3.5 7.2 - - - +
183X ARG 3.2 0.2 - - - -
184X ASP* 1.3 77.6 - - + +
186X THR* 1.3 60.8 + - - +
188X TYR* 3.9 5.2 - - - +
189X LEU* 3.3 8.8 + - - +
213X LYS* 4.1 2.9 - - + -
257X CYS* 3.2 39.5 - - - +
258X PRO* 5.1 0.4 - - + -
260X THR* 4.3 19.5 - - + -
261X LEU* 4.0 11.2 - - + -
267X ILE* 5.7 0.4 - - + -
303X THR* 3.8 16.8 - - + -
306X TYR* 3.0 41.1 - - + +
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Residues in contact with THR 186 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182X GLY 3.0 7.0 + - - -
183X ARG* 3.3 8.2 + - - -
185X LEU* 1.3 75.9 - - - +
187X ASP* 1.3 65.8 + - - +
189X LEU* 3.4 5.1 + - - +
190X MET* 3.1 25.5 + - - +
206X ARG* 4.6 10.5 - - - +
209X VAL* 3.6 26.9 - - + +
210X ARG* 3.7 25.6 - - + +
213X LYS* 2.7 38.6 + - - +
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Residues in contact with ASP 187 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183X ARG* 3.3 17.8 + - - +
184X ASP* 3.2 11.5 + - - +
186X THR* 1.3 79.0 - - - +
188X TYR* 1.3 64.2 + - - +
190X MET* 3.1 20.3 - - - +
191X LYS* 3.3 9.2 + - - +
206X ARG* 3.4 34.8 + - - -
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Residues in contact with TYR 188 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184X ASP 3.1 13.8 + - - +
185X LEU* 4.1 6.3 - - - +
186X THR 3.3 0.2 - - - -
187X ASP* 1.3 75.6 - - - +
189X LEU* 1.3 66.1 + - - +
191X LYS* 3.2 39.4 + - + +
192X ILE* 3.0 46.2 + - + +
256X ARG* 3.3 20.8 + - - +
257X CYS* 3.8 11.4 - - + -
260X THR* 3.2 26.0 - - + +
266X PHE* 3.1 40.9 - + - +
267X ILE* 3.5 25.6 - - + -
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Residues in contact with LEU 189 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185X LEU 3.3 13.4 + - - +
186X THR 3.7 7.2 - - - +
187X ASP 3.4 0.2 - - - -
188X TYR* 1.3 77.6 - - - +
190X MET* 1.3 54.2 - - - +
192X ILE* 3.0 24.7 + - + +
193X LEU* 2.8 53.6 + - + +
209X VAL* 3.5 33.7 - - + +
212X ILE* 3.7 11.9 - - + -
213X LYS* 3.5 27.8 - - + +
217X CYS* 4.6 7.4 - - - -
250X ILE* 5.5 2.5 - - + -
253X GLU* 4.6 16.6 - - + +
257X CYS* 3.8 9.0 - - + -
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Residues in contact with MET 190 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186X THR 3.1 10.9 + - - +
187X ASP* 3.1 17.5 - - - +
189X LEU* 1.3 78.2 - - - +
191X LYS* 1.3 57.8 + - - +
193X LEU* 3.3 2.6 + - - +
194X THR* 2.9 37.7 + - + +
200X PHE* 3.7 30.3 - - + +
206X ARG* 3.7 43.3 - - + +
209X VAL* 3.2 35.4 - - + -
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Residues in contact with LYS 191 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187X ASP 3.3 5.5 + - - +
188X TYR* 3.2 48.9 + - + +
190X MET* 1.3 77.7 - - - +
192X ILE* 1.3 64.3 + - - +
193X LEU 2.8 6.9 + - - -
194X THR* 2.9 10.6 + - - +
195X GLU* 2.8 55.8 + - + +
266X PHE 5.0 3.7 + - - -
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Residues in contact with ILE 192 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188X TYR* 3.0 49.4 + - + +
189X LEU* 3.2 21.8 - - + +
191X LYS* 1.3 91.0 - - - +
193X LEU* 1.3 55.7 + - - +
195X GLU* 3.5 25.8 - - - +
196X ARG* 3.2 21.7 + - - +
253X GLU* 3.6 38.5 - - + +
256X ARG* 3.6 32.1 + - + +
257X CYS* 4.0 3.6 - - + +
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Residues in contact with LEU 193 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189X LEU* 2.8 36.3 + - + +
190X MET 3.6 4.0 - - - +
191X LYS 2.8 0.8 + - - -
192X ILE* 1.3 76.7 - - - +
194X THR* 1.3 62.0 + - - +
195X GLU 3.2 0.9 - - - -
196X ARG* 3.3 7.8 + - + -
198X TYR* 2.8 39.6 - - + -
200X PHE* 3.6 28.5 - - + -
209X VAL* 4.1 10.3 - - + -
212X ILE* 4.2 18.4 - - + -
248X ILE* 5.5 0.2 - - + -
249X THR 4.5 0.9 - - - +
250X ILE* 3.3 33.4 - - + -
253X GLU* 4.1 13.2 - - + -
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Residues in contact with THR 194 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190X MET* 2.9 27.7 + - + +
191X LYS* 3.0 15.0 + - - +
193X LEU* 1.3 74.8 - - - +
195X GLU* 1.3 58.4 + - - +
197X GLY* 2.9 10.0 + - - -
198X TYR* 2.9 38.0 + - - +
199X SER* 4.9 0.2 - - - -
200X PHE* 3.5 25.4 - - + +
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Residues in contact with GLU 195 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112W PRO* 5.3 18.7 - - + +
191X LYS* 2.8 45.3 + - + +
192X ILE* 3.5 22.6 - - - +
194X THR* 1.3 77.0 + - - +
196X ARG* 1.3 55.5 + - - +
197X GLY* 3.0 8.9 + - - -
256X ARG* 3.7 15.2 + - - -
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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