Contacts of the helix formed by residues 186 - 200 (chain C) in PDB entry 4OGB
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 THR 186 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185C PHE* 1.3 75.7 - - - +
187C ASP* 1.3 64.9 + - - +
188C LEU* 3.4 9.4 + - - +
189C GLU* 2.9 41.2 + - - +
190C ILE* 3.0 23.0 + - - +
306C ARG* 4.2 13.0 - - - +
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Residues in contact with ASP 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ARG 5.8 0.2 - - - +
131C LEU* 4.5 5.3 - - + +
134C THR* 3.8 21.3 + - + +
135C PHE* 3.5 24.9 - - + -
186C THR* 1.3 73.4 - - - +
188C LEU* 1.3 56.5 + - - +
190C ILE* 3.4 16.3 + - - +
191C LEU* 2.9 28.8 + - - +
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Residues in contact with LEU 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135C PHE* 3.8 14.8 - - + -
186C THR* 3.1 9.0 + - - +
187C ASP* 1.3 75.5 - - - +
189C GLU* 1.3 61.0 + - - +
191C LEU* 3.4 7.8 + - + +
192C ALA* 2.9 27.0 + - - +
252C LEU* 3.9 27.4 - - + -
256C GLN* 3.9 22.0 - - + +
259C SER* 3.6 22.4 - - - +
260C LEU* 4.2 11.8 - - + +
263C MET* 3.9 10.5 - - + +
505C EDO 3.5 31.9 - - - -
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Residues in contact with GLU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C PHE* 3.2 16.6 - - + -
186C THR* 2.9 27.3 + - - +
188C LEU* 1.3 74.5 - - - +
190C ILE* 1.3 63.4 + - - +
192C ALA* 3.4 3.8 + - - +
193C ALA* 3.1 23.6 + - - +
263C MET* 3.6 29.3 - - + +
303C TYR* 5.9 2.6 - - - -
306C ARG* 2.6 58.3 + - - +
310C LEU* 4.1 20.5 - - + +
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Residues in contact with ILE 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C ARG* 3.8 44.2 - - + +
131C LEU* 4.4 10.5 - - + -
176C LEU* 4.1 18.8 - - + -
185C PHE* 4.1 22.0 - - + +
186C THR 3.0 20.2 + - - +
187C ASP* 3.5 17.3 - - - +
189C GLU* 1.3 74.1 - - - +
191C LEU* 1.3 65.7 - - - +
192C ALA 3.3 0.2 + - - -
193C ALA* 3.3 2.8 + - - +
194C ILE* 3.2 30.9 + - + +
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Residues in contact with LEU 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C PHE* 3.8 35.0 - - + -
131C LEU* 4.2 11.6 - - + +
135C PHE* 3.9 39.0 - - + -
137C ILE* 4.9 2.0 - - + -
187C ASP 2.9 17.2 + - - +
188C LEU* 3.6 8.3 - - + +
190C ILE* 1.3 76.4 - - - +
192C ALA* 1.3 53.7 + - - +
194C ILE* 3.3 3.4 + - - +
195C PHE* 2.8 39.2 + - + +
249C PHE* 3.7 33.0 - - + -
252C LEU* 4.7 1.1 - - + -
260C LEU* 4.1 16.4 - - + -
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Residues in contact with ALA 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C LEU 2.9 18.3 + - - +
189C GLU* 3.5 7.6 - - - +
190C ILE 3.2 0.4 - - - -
191C LEU* 1.3 76.3 - - - +
193C ALA* 1.3 58.3 + - - +
196C ALA* 2.8 34.0 + - - +
260C LEU* 3.6 19.7 - - + +
263C MET* 3.9 30.3 - - + -
264C VAL* 3.5 8.6 - - + +
267C ILE* 4.1 5.4 - - + -
310C LEU* 5.5 0.4 - - + -
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Residues in contact with ALA 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C THR* 4.0 17.7 - - + -
176C LEU* 4.3 7.9 - - + -
189C GLU 3.1 13.3 + - - +
190C ILE 3.3 4.0 + - - +
192C ALA* 1.3 79.4 - - - +
194C ILE* 1.3 54.0 + - - +
196C ALA* 3.8 1.6 - - - +
197C SER* 2.7 36.3 + - - -
267C ILE* 3.7 15.4 - - + +
310C LEU* 4.2 20.4 - - + -
313C MET* 5.3 0.7 - - - -
314C VAL* 3.9 8.7 - - + +
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Residues in contact with ILE 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C MET* 3.8 22.9 - - - -
125C ILE* 3.9 14.1 - - + -
126C PHE* 3.8 16.6 - - + -
129C ARG* 3.6 34.1 - - - +
131C LEU* 4.4 6.3 - - + -
169C VAL* 3.9 11.0 - - + +
172C THR* 4.5 6.3 - - + -
173C HIS* 4.8 6.5 - - + +
176C LEU* 3.9 14.4 - - + -
190C ILE* 3.2 22.9 + - + +
191C LEU* 3.8 3.4 - - - +
193C ALA* 1.3 76.9 - - - +
195C PHE* 1.3 67.6 + - - +
197C SER* 3.2 7.7 + - - -
198C ALA* 3.0 21.8 + - - +
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Residues in contact with PHE 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C MET* 4.7 9.4 - - + -
126C PHE* 5.6 2.2 - + + -
145C TYR* 3.2 42.4 - + - -
191C LEU* 2.8 26.6 + - + +
192C ALA 4.0 2.0 - - - +
194C ILE* 1.3 74.1 - - - +
196C ALA* 1.3 63.8 + - - +
198C ALA* 3.1 15.8 + - + +
199C ILE* 3.1 38.3 + - + +
237C GLY 4.1 7.4 - - - -
238C PHE* 3.9 18.4 - + - -
241C LEU* 4.4 6.1 - - + -
248C ILE* 4.0 9.2 - - + -
249C PHE* 3.7 40.4 - + + -
260C LEU* 5.1 1.1 - - + -
264C VAL* 3.9 18.6 - - + -
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Residues in contact with ALA 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C ALA 2.8 20.0 + - - +
193C ALA 3.8 1.8 - - - +
195C PHE* 1.3 78.3 - - - +
197C SER* 1.3 56.4 + - - +
199C ILE* 3.2 3.4 + - - +
200C HIS* 2.9 34.2 + - - +
264C VAL* 3.9 18.4 - - + -
267C ILE* 3.7 32.8 - - + -
268C VAL* 3.7 13.1 - - + +
314C VAL* 5.4 0.2 - - - -
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Residues in contact with SER 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C TYR* 4.4 0.3 + - - -
165C ALA* 4.2 4.5 - - - +
168C VAL* 3.9 6.2 - - - +
169C VAL* 3.7 29.1 - - - +
172C THR* 2.9 22.1 + - - -
193C ALA 2.7 23.2 + - - -
194C ILE* 3.4 7.0 - - - -
196C ALA* 1.3 75.8 - - - +
198C ALA* 1.3 62.0 + - - +
200C HIS* 2.7 32.8 + - - -
314C VAL* 3.8 11.2 - - - +
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Residues in contact with ALA 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LEU* 4.1 7.2 - - + +
122C MET* 3.5 31.6 - - + -
149C LEU* 3.7 18.5 - - + +
153C TYR* 2.6 30.8 + - - -
165C ALA* 3.9 4.3 - - - +
169C VAL* 3.3 13.9 - - + +
194C ILE 3.0 7.6 + - - +
195C PHE* 3.1 11.4 + - + +
197C SER* 1.3 77.9 - - - +
199C ILE* 1.3 53.3 + - + +
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Residues in contact with ILE 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C TYR* 3.5 24.0 - - - +
149C LEU* 3.9 16.4 - - + -
153C TYR* 3.4 3.6 - - - -
195C PHE* 3.1 30.0 + - + +
196C ALA* 3.5 9.9 - - - +
198C ALA* 1.3 77.4 - - - +
200C HIS* 1.3 60.4 + - - +
201C ASP 2.9 11.7 + - - -
202C VAL* 3.1 17.4 + - + +
233C HIS* 3.5 10.1 - - - +
234C LEU* 4.3 16.6 - - + +
237C GLY* 3.9 23.3 - - - -
238C PHE* 4.8 1.8 - - + -
264C VAL* 3.8 25.8 - - + -
268C VAL* 4.2 4.3 - - + -
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Residues in contact with HIS 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C TYR* 4.5 0.6 + - - -
164C HIS* 3.6 8.7 - + - -
165C ALA* 4.6 5.8 - - - -
168C VAL* 3.5 30.4 - - + +
196C ALA 2.9 17.2 + - - +
197C SER* 2.7 23.8 + - - -
198C ALA 3.5 0.4 - - - -
199C ILE* 1.3 76.4 - - - +
201C ASP* 1.3 69.3 + - + +
233C HIS* 2.9 21.4 - - - +
268C VAL* 4.2 22.7 - - + +
271C THR* 4.3 20.4 + - + -
314C VAL* 5.5 2.0 - - + -
318C ASP* 3.1 11.6 + - - -
510C ZN 2.2 36.5 - - - -
511C ZN 4.0 5.3 - - - -
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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