Contacts of the helix formed by residues 236 - 249 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133B PHE* 3.9 7.6 - + - -
134B PHE* 3.8 23.3 - + + -
137B SER* 3.4 34.8 - - - -
138B ASP* 4.1 17.0 - - - -
141B VAL* 4.5 13.0 - - + -
231B VAL* 3.5 14.6 + - + -
232B GLU* 3.6 28.0 - - + +
234B ILE 3.1 0.8 - - - +
235B PHE* 1.3 84.8 - - + +
237B SER* 1.3 59.5 + - - +
238B GLY 3.4 1.6 - - - -
239B SER* 3.2 6.0 + - - -
240B PHE* 2.9 49.6 + + + -
266B GLU* 3.3 35.2 - - + -
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Residues in contact with SER 237 (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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233B GLY 3.4 20.9 + - - -
234B ILE* 2.8 20.4 + - - -
236B PHE* 1.3 78.1 - - - +
238B GLY* 1.3 62.7 + - - +
240B PHE* 3.4 10.5 + - - +
241B ALA* 3.0 28.4 + - - +
323B TYR* 3.6 10.9 + - - -
324B ILE* 3.4 17.0 - - - +
327B VAL* 3.9 24.8 - - - +
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Residues in contact with GLY 238 (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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237B SER* 1.3 79.7 + - - +
239B SER* 1.3 56.7 - - - +
241B ALA* 3.4 2.8 + - - +
242B SER* 2.9 30.4 + - - -
300B GLU* 2.9 19.5 + - - -
304B LEU* 3.5 22.2 - - - -
320B MET* 3.6 11.4 - - - +
324B ILE* 3.9 6.7 - - - -
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Residues in contact with SER 239 (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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130B VAL* 3.7 14.8 - - - +
133B PHE* 3.8 14.0 - - - -
134B PHE* 3.3 30.7 - - - -
235B PHE 4.8 1.0 + - - -
236B PHE 3.2 4.8 + - - -
238B GLY* 1.3 73.0 - - - +
240B PHE* 1.3 67.2 + - - +
242B SER* 3.2 10.7 - - - -
243B ILE* 3.1 25.8 + - - +
300B GLU* 4.1 2.0 + - - -
303B PHE* 3.8 24.1 - - - -
304B LEU* 4.2 0.6 - - - +
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Residues in contact with PHE 240 (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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134B PHE* 3.7 16.2 - + - -
176B TYR* 3.9 12.1 - - - -
232B GLU 4.4 2.5 - - - -
236B PHE* 2.9 46.5 + + + +
237B SER* 3.7 9.0 - - - +
239B SER* 1.3 78.1 - - - +
241B ALA* 1.3 57.2 + - - +
243B ILE 3.3 1.6 + - - -
244B PHE* 3.0 38.9 + - + -
259B ASN* 3.3 21.9 + - - +
262B ILE* 4.0 2.9 - - + -
263B SER* 3.6 47.1 - - - -
266B GLU* 3.7 28.0 - - + -
350B MET* 4.8 5.6 - - + -
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Residues in contact with ALA 241 (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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237B SER 3.0 17.8 + - - +
238B GLY 3.6 5.4 - - - +
239B SER 3.2 0.2 - - - -
240B PHE* 1.3 76.3 - - - +
242B SER* 1.3 51.4 + - - +
244B PHE* 3.2 2.8 + - - +
245B TRP* 2.8 35.3 + - - +
315B MET* 4.5 3.1 - - + -
320B MET* 4.0 13.9 - - + -
323B TYR* 3.9 20.0 - - + -
347B PHE* 4.6 5.6 - - + -
349B PHE* 3.7 3.5 - - + -
350B MET* 3.9 22.8 - - + +
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Residues in contact with SER 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B PHE* 3.4 37.6 - - - -
130B VAL* 5.1 0.7 - - - -
238B GLY 2.9 17.0 + - - -
239B SER* 3.2 13.7 - - - -
241B ALA* 1.3 75.3 - - - +
243B ILE* 1.3 66.9 + - - +
245B TRP* 3.3 5.2 + - - +
246B LEU* 3.1 24.4 + - - +
304B LEU* 4.7 0.2 - - - +
310B VAL* 3.9 9.7 - - - +
313B ILE* 3.8 5.2 - - - +
315B MET* 3.8 13.6 - - - -
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Residues in contact with ILE 243 (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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126B PHE* 5.5 1.1 - - + -
127B ILE* 5.1 8.1 - - + -
130B VAL* 4.3 21.8 - - + -
131B LEU* 6.0 1.3 - - + -
134B PHE* 4.8 4.0 - - + -
239B SER 3.1 16.2 + - - +
240B PHE 3.3 0.9 + - - +
241B ALA 3.3 0.2 - - - -
242B SER* 1.3 78.6 - - - +
244B PHE* 1.3 65.6 + - - +
246B LEU* 3.2 20.4 + - + +
247B LYS 3.1 17.3 + - - -
255B LEU* 3.8 36.3 - - + -
256B THR* 3.6 12.6 - - + +
259B ASN* 3.5 41.5 - - + +
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Residues in contact with PHE 244 (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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240B PHE 3.0 25.6 + - - -
241B ALA 3.6 6.7 - - - +
243B ILE* 1.3 77.7 - - - +
245B TRP* 1.3 60.4 + - - +
247B LYS* 3.2 25.0 + - + +
248B LYS* 3.1 20.6 + - - +
256B THR* 5.4 0.9 - - - -
259B ASN* 3.4 18.6 - - - -
260B GLU* 3.9 30.7 - - + -
263B SER* 3.6 25.6 - - - -
349B PHE* 3.9 19.6 - - + +
350B MET* 3.6 35.2 - - + -
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Residues in contact with TRP 245 (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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241B ALA 2.8 16.3 + - - +
242B SER 3.3 8.5 - - - +
243B ILE 3.2 0.2 - - - -
244B PHE* 1.3 70.7 - - - +
246B LEU* 1.3 67.0 + - + +
248B LYS* 3.1 28.5 + - + +
249B ARG* 3.0 46.2 + - + +
313B ILE* 3.0 35.4 + - + -
314B GLY* 3.8 18.3 - - - -
315B MET* 3.4 32.7 - - + +
349B PHE* 3.8 30.4 - + + -
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Residues in contact with LEU 246 (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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119B LEU* 5.5 2.9 - - + -
123B GLU* 6.3 0.4 - - + -
127B ILE* 3.6 37.7 - - + -
242B SER 3.1 14.9 + - - +
243B ILE* 3.2 21.9 + - + +
245B TRP* 1.3 75.2 - - - +
247B LYS* 1.3 61.1 + - - +
249B ARG* 3.1 33.8 + - - +
251B LEU* 3.0 43.9 + - + +
252B MET* 5.3 3.1 - - - -
255B LEU* 3.8 21.1 - - + -
256B THR* 4.3 6.3 - - + -
313B ILE* 4.5 16.6 - - + -
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Residues in contact with LYS 247 (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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243B ILE 3.1 8.2 + - - +
244B PHE* 3.4 28.1 - - + +
245B TRP 3.2 0.2 - - - -
246B LEU* 1.3 77.0 - - - +
248B LYS* 1.3 54.2 + - - +
250B GLY* 2.7 24.4 + - - +
251B LEU 4.5 2.5 - - - +
256B THR* 3.7 30.7 - - + +
260B GLU* 3.0 29.7 + - - +
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Residues in contact with LYS 248 (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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244B PHE 3.1 11.7 + - - +
245B TRP* 3.1 31.2 + - + +
247B LYS* 1.3 77.7 - - - +
249B ARG* 1.3 59.8 + - + +
250B GLY 3.1 0.9 + - - -
348B ASP* 3.3 32.1 + - - -
349B PHE* 4.0 28.7 - - + +
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Residues in contact with ARG 249 (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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119B LEU* 4.6 2.4 - - - +
123B GLU* 2.9 33.1 + - - -
245B TRP* 3.0 44.1 + - + +
246B LEU* 3.5 24.5 - - - +
247B LYS 3.1 0.2 - - - -
248B LYS* 1.3 78.9 - - + +
250B GLY* 1.3 61.2 + - - +
251B LEU* 3.4 33.7 + - + +
313B ILE* 3.0 22.2 + - - +
314B GLY* 5.2 0.2 - - - -
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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