Contacts of the helix formed by residues 236 - 249 (chain C) in PDB entry 3OLJ
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 PHE 236 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133C PHE* 4.0 7.2 - + - -
134C PHE* 3.6 25.3 - + + -
137C SER* 3.5 35.9 - - - -
138C ASP* 4.1 16.2 - - - -
141C VAL* 4.5 6.3 - - + -
231C VAL* 3.4 20.7 + - + -
232C GLU* 3.6 30.1 - - + +
234C ILE 3.1 0.8 - - - +
235C PHE* 1.3 82.8 - - - +
237C SER* 1.3 59.6 + - - +
238C GLY 3.4 1.8 - - - -
239C SER* 3.2 4.9 + - - -
240C PHE* 2.9 50.6 + + + -
266C GLU* 3.3 33.7 - - + -
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Residues in contact with SER 237 (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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233C GLY 3.4 21.6 + - - -
234C ILE* 2.7 20.5 + - - -
236C PHE* 1.3 78.5 - - - +
238C GLY* 1.3 59.1 + - - +
240C PHE* 3.5 9.8 + - - +
241C ALA* 3.0 29.8 + - - +
323C TYR* 3.5 11.0 + - - -
324C ILE* 3.5 16.1 - - - +
327C VAL* 4.0 22.9 - - - +
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Residues in contact with GLY 238 (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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237C SER* 1.3 79.0 + - - +
239C SER* 1.3 60.2 - - - +
241C ALA 3.5 0.7 + - - -
242C SER* 2.8 30.2 + - - -
300C GLU* 3.0 16.3 + - - -
304C LEU* 3.5 23.1 - - - -
320C MET* 3.7 12.8 - - - +
324C ILE* 3.8 6.1 - - - -
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Residues in contact with SER 239 (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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130C VAL* 3.7 16.1 - - - +
133C PHE* 3.9 13.5 - - - -
134C PHE* 3.3 32.5 - - - -
206C LYS* 4.7 0.9 + - - -
235C PHE 4.7 0.5 + - - -
236C PHE 3.2 4.0 + - - -
238C GLY* 1.3 73.0 - - - +
240C PHE* 1.3 64.5 + - - +
242C SER* 3.1 23.2 - - - -
243C ILE* 3.2 13.7 + - - +
300C GLU* 4.0 1.4 + - - -
303C PHE* 3.7 24.6 - - - -
304C LEU* 4.7 0.8 - - - +
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Residues in contact with PHE 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C PHE* 3.6 18.6 - + - -
176C TYR* 3.8 13.5 - - - -
232C GLU 4.5 2.7 - - - -
236C PHE* 2.9 45.0 + + + +
237C SER* 3.8 7.6 - - - +
239C SER* 1.3 76.1 - - - +
241C ALA* 1.3 62.4 + - - +
243C ILE 3.2 2.3 + - - -
244C PHE* 3.0 30.6 + - + -
259C ASN* 3.2 25.2 + - - +
262C ILE* 4.0 4.3 - - + -
263C SER* 3.7 45.1 - - - -
266C GLU* 3.8 26.2 - - + -
323C TYR* 6.0 0.2 - - - +
350C MET* 4.9 4.9 - - + -
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Residues in contact with ALA 241 (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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237C SER 3.0 19.6 + - - +
238C GLY 3.7 4.9 - - - +
240C PHE* 1.3 75.6 - - - +
242C SER* 1.3 50.9 + - - +
244C PHE* 3.2 2.8 + - - +
245C TRP* 2.8 34.6 + - - +
315C MET* 4.7 2.5 - - + -
320C MET* 3.9 14.4 - - + -
323C TYR* 3.7 20.6 - - + -
347C PHE* 4.5 4.9 - - + -
349C PHE* 3.6 4.7 - - + -
350C MET* 3.8 23.2 - - + +
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Residues in contact with SER 242 (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* 3.3 38.0 - - - -
130C VAL* 5.2 0.7 - - - -
238C GLY 2.8 18.9 + - - -
239C SER* 3.1 13.6 - - - -
241C ALA* 1.3 77.0 - - - +
243C ILE* 1.3 64.1 + - - +
245C TRP* 3.2 5.0 - - - +
246C LEU* 3.2 19.7 + - - +
304C LEU* 4.7 0.3 - - - +
310C VAL* 3.9 11.8 - - - +
313C ILE* 3.5 11.1 - - - +
315C MET* 3.9 12.4 - - - -
320C MET* 4.4 0.6 - - - +
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Residues in contact with ILE 243 (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* 6.1 0.9 - - + -
127C ILE* 6.2 2.2 - - + -
130C VAL* 4.2 11.7 - - + -
131C LEU* 5.0 3.4 - - + -
134C PHE* 4.0 19.1 - - + -
176C TYR* 5.4 2.7 - - + -
239C SER 3.2 11.6 + - - +
240C PHE 3.2 2.2 + - - +
242C SER* 1.3 77.6 - - - +
244C PHE* 1.3 61.9 + - - +
246C LEU* 3.1 15.8 + - + +
247C LYS* 3.0 22.6 + - - -
255C LEU* 3.8 42.6 - - + +
256C THR* 3.7 11.4 - - + +
259C ASN* 3.5 44.2 - - + +
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Residues in contact with PHE 244 (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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240C PHE* 3.0 15.6 + - + -
241C ALA 3.2 7.4 + - - +
243C ILE* 1.3 77.6 - - - +
245C TRP* 1.3 55.7 + - - +
247C LYS* 3.2 27.4 + - + +
248C LYS* 3.0 27.2 + - - +
256C THR* 5.4 0.7 - - - -
259C ASN* 3.3 25.8 - - - -
260C GLU* 3.8 31.9 - - + -
263C SER* 3.7 23.8 - - - -
349C PHE* 4.0 20.5 - - + +
350C MET* 3.6 34.5 - - + -
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Residues in contact with TRP 245 (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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241C ALA 2.8 16.3 + - - +
242C SER 3.2 9.4 - - - +
244C PHE* 1.3 73.2 - - - +
246C LEU* 1.3 62.4 + - - +
248C LYS* 3.1 32.7 + - + +
249C ARG* 3.1 43.6 + - + +
313C ILE* 3.1 35.1 + - + -
314C GLY* 3.7 18.0 - - - -
315C MET* 3.5 36.1 - - + +
347C PHE* 5.9 1.6 - + - -
349C PHE* 3.5 32.6 - + + -
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Residues in contact with LEU 246 (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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119C LEU* 5.4 2.0 - - + -
123C GLU* 5.6 0.4 - - - +
126C PHE* 6.0 0.9 - - + -
127C ILE* 3.7 36.8 - - + -
242C SER 3.2 13.0 + - - +
243C ILE* 3.1 16.9 + - + +
245C TRP* 1.3 75.5 - - + +
247C LYS* 1.3 64.9 + - - +
249C ARG* 3.0 37.1 + - - +
250C GLY 3.1 0.2 + - - -
251C LEU* 3.1 45.9 + - + +
252C MET* 5.1 2.7 - - + -
255C LEU* 3.7 22.7 - - + -
256C THR* 4.5 1.8 - - + -
313C ILE* 4.5 15.7 - - + -
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Residues in contact with LYS 247 (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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117A GLU* 3.8 21.4 + - - +
243C ILE 3.0 9.1 + - - +
244C PHE* 3.3 32.8 - - + +
246C LEU* 1.3 74.5 - - - +
248C LYS* 1.3 57.5 + - - +
250C GLY* 2.8 21.9 + - - +
251C LEU 4.6 2.0 - - - +
256C THR* 3.7 28.0 - - + +
260C GLU* 2.7 32.1 + - - +
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Residues in contact with LYS 248 (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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244C PHE 3.0 12.4 + - - +
245C TRP* 3.2 42.4 - - + +
247C LYS* 1.3 75.6 - - - +
249C ARG* 1.3 58.7 + - + +
250C GLY 3.6 0.3 + - - -
348C ASP* 4.0 20.8 + - - -
349C PHE* 3.8 31.0 - - + -
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Residues in contact with ARG 249 (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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119C LEU* 4.9 0.6 - - - +
123C GLU* 2.7 34.6 + - - -
245C TRP* 3.1 37.4 + - + +
246C LEU* 3.0 25.4 + - - +
248C LYS* 1.3 78.3 - - + +
250C GLY* 1.3 61.1 + - - +
251C LEU* 3.4 34.2 + - + +
313C ILE* 3.0 21.2 + - - +
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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