Contacts of the helix formed by residues 233 - 249 (chain B) in PDB entry 4OSI
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 SER 233 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232B TRP* 1.3 86.7 + - - +
234B GLY* 1.3 66.8 + - - -
236B ARG* 2.7 31.8 + - - +
237B ALA* 2.8 14.3 + - - +
269B VAL* 4.2 6.9 - - - +
1G T 4.3 7.3 + - - -
2G G 3.7 22.5 + - - -
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Residues in contact with GLY 234 (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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232B TRP* 3.2 31.5 - - - -
233B SER* 1.3 79.1 - - - +
235B ALA* 1.3 64.9 + - - +
237B ALA* 3.2 11.5 + - - +
238B LEU* 3.1 18.7 + - - +
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Residues in contact with ALA 235 (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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232B TRP* 2.9 44.6 + - + +
233B SER 2.9 0.2 + - - -
234B GLY* 1.3 76.3 - - - +
236B ARG* 1.3 64.3 + - + +
238B LEU* 3.1 16.1 + - - +
239B GLU* 3.1 28.5 + - - +
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Residues in contact with ARG 236 (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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232B TRP* 2.8 20.7 + - - +
233B SER* 2.7 36.8 + - - +
235B ALA* 1.3 67.4 - - + +
237B ALA* 1.3 57.5 + - - +
238B LEU 2.8 4.3 - - - -
239B GLU* 2.5 43.4 + - + +
240B ALA* 2.6 16.1 + - + -
269B VAL* 4.2 21.1 - - + +
1G T 3.6 31.7 + - - -
2G G 3.1 21.1 + - - -
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Residues in contact with ALA 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 SER 2.8 14.8 + - - +
234B GLY* 3.3 16.4 - - - +
236B ARG* 1.3 70.7 - - - +
238B LEU* 1.3 52.5 + - - +
240B ALA* 3.7 2.1 - - - +
241B LEU* 2.7 36.9 + - - +
264B ALA* 4.4 18.8 - - + +
268B GLY* 4.8 1.6 - - - -
269B VAL* 3.8 30.3 - - + +
272B VAL* 5.4 3.5 - - + +
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Residues in contact with LEU 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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234B GLY 3.1 8.7 + - - +
235B ALA* 3.1 13.3 + - - +
236B ARG 2.5 4.2 + - - -
237B ALA* 1.3 71.0 - - - +
239B GLU* 1.3 62.6 + - + +
240B ALA 3.0 1.8 - - - -
241B LEU* 3.0 12.3 + - + +
242B LEU* 2.9 56.0 + - + +
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Residues in contact with GLU 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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235B ALA* 3.1 28.0 + - - +
236B ARG* 2.5 23.7 + - - +
238B LEU* 1.3 76.8 - - + +
240B ALA* 1.3 53.0 + - - +
242B LEU* 4.0 12.4 + - + +
243B THR* 2.7 30.7 + - - -
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Residues in contact with ALA 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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236B ARG* 2.6 23.0 + - + +
237B ALA* 4.1 3.4 - - - +
239B GLU* 1.3 71.7 - - - +
241B LEU* 1.3 58.5 + - - +
243B THR* 4.2 3.8 - - - -
244B VAL* 3.2 33.9 + - + +
269B VAL* 4.3 20.6 - - + +
272B VAL* 4.3 6.9 - - + +
273B GLU* 4.6 14.8 - - + -
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Residues in contact with LEU 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 ALA 2.7 18.4 + - - +
238B LEU* 3.0 15.0 + - + +
240B ALA* 1.3 75.0 - - - +
242B LEU* 1.3 54.6 + - + +
244B VAL* 5.1 0.7 - - + -
245B ALA* 2.5 57.8 + - + +
248B LEU* 6.4 0.2 - - + -
260B LEU* 4.2 28.7 - - + +
261B LEU* 5.0 12.8 - - + -
264B ALA* 3.7 26.9 - - + -
272B VAL* 4.4 15.5 - - + -
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Residues in contact with LEU 242 (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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238B LEU* 2.9 46.4 + - + +
239B GLU* 4.0 10.5 - - + +
241B LEU* 1.3 78.7 - - + +
243B THR* 1.3 66.9 + - - +
245B ALA* 3.8 4.9 - - - +
246B GLY* 3.4 14.4 + - - -
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Residues in contact with THR 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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239B GLU 2.7 23.9 + - - -
240B ALA* 4.2 5.2 - - - -
241B LEU 3.3 0.2 - - - -
242B LEU* 1.3 81.0 - - - +
244B VAL* 1.3 65.9 + - + +
246B GLY* 3.7 1.2 + - - -
247B GLU* 3.2 40.2 + - - +
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Residues in contact with VAL 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 ALA 3.2 18.4 + - - +
241B LEU* 5.1 1.3 - - + -
243B THR* 1.3 79.3 - - + +
245B ALA* 1.3 73.0 + - - +
246B GLY 3.1 2.0 - - - -
247B GLU* 2.7 20.6 + - - +
248B LEU* 3.1 40.5 + - + +
272B VAL* 3.9 22.4 - - + +
273B GLU* 5.1 7.2 - - + -
276B HIS* 3.4 37.5 - - + +
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Residues in contact with ALA 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 LEU* 2.5 41.1 + - + +
242B LEU* 3.8 5.2 - - - +
244B VAL* 1.3 76.9 - - - +
246B GLY* 1.3 66.9 + - - +
248B LEU* 3.2 8.6 + - - -
249B ARG* 3.3 26.3 + - - +
260B LEU* 4.5 20.1 - - + +
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Residues in contact with GLY 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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242B LEU 3.4 9.2 + - - -
243B THR 4.2 2.9 - - - -
244B VAL 2.8 3.8 + - - -
245B ALA* 1.3 78.8 - - - +
247B GLU* 1.3 56.8 - - - +
248B LEU 2.8 7.4 + - - -
249B ARG* 3.7 8.1 + - - +
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Residues in contact with GLU 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 THR* 3.2 37.1 - - - +
244B VAL* 2.7 11.7 + - - +
246B GLY* 1.3 68.5 - - - -
248B LEU* 1.3 55.5 + - - +
249B ARG 3.9 0.4 - - - -
250B GLY* 4.9 2.9 + - - -
251B PRO 5.1 5.0 - - - +
276B HIS* 2.7 44.9 + - - +
279B ARG* 5.2 10.0 + - - +
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Residues in contact with LEU 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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241B LEU* 6.4 0.2 - - + -
244B VAL* 3.4 30.7 - - + +
245B ALA* 4.8 1.6 - - - -
246B GLY 2.8 5.3 + - - -
247B GLU* 1.3 75.4 - - - +
249B ARG* 1.3 58.5 + - - +
250B GLY* 3.0 7.9 - - - +
251B PRO 5.5 2.9 - - - +
253B LEU* 3.1 25.1 - - + +
255B LEU* 3.7 25.3 + - + +
260B LEU* 4.0 19.5 - - + -
263B ILE* 5.9 1.6 - - + -
272B VAL* 5.3 1.3 - - + +
275B VAL* 4.4 13.5 - - + +
276B HIS* 3.7 38.6 - - + +
279B ARG* 4.9 10.5 - - - +
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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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245B ALA* 3.3 19.3 + - - +
246B GLY* 3.7 5.3 + - - +
248B LEU* 1.3 77.0 - - - +
250B GLY* 1.3 62.5 + - - +
253B LEU 4.1 1.1 - - - -
254B GLN* 4.2 6.1 - - - +
255B LEU 3.1 26.8 - - - +
256B ASP* 3.8 8.1 - - - +
257B THR* 2.3 60.2 + - - +
260B LEU* 3.8 20.3 - - + +
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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