Contacts of the helix formed by residues 235 - 249 (chain B) in PDB entry 1OI4
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 GLU 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234B PHE* 1.3 76.4 - - - +
236B ASP* 1.3 73.3 + - - +
237B SER* 4.6 5.2 + - - +
238B GLU* 2.8 60.2 + - + +
239B PHE 3.6 0.2 + - - -
267B LYS* 4.1 18.0 + - - +
268B LYS* 2.9 40.4 + - - +
294B GLY 3.2 7.9 + - - +
295B GLY* 3.7 12.9 - - - +
325B CYS* 5.5 3.2 - - - -
377B PRO* 3.9 16.8 - - + +
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Residues in contact with ASP 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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234B PHE* 3.0 15.4 + - - -
235B GLU* 1.3 72.3 + - - +
237B SER* 1.3 63.4 + - - +
239B PHE 3.2 3.8 + - - -
240B THR* 3.1 27.0 + - - +
266B GLY* 3.5 11.0 - - - -
267B LYS* 3.1 4.9 + - - -
268B LYS* 2.7 39.5 + - + +
269B GLY 3.7 0.2 + - - -
270B GLU* 2.9 25.9 + - + +
271B ALA* 2.8 32.9 + - + +
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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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235B GLU* 3.4 5.1 + - - +
236B ASP* 1.3 74.8 - - - +
238B GLU* 1.3 61.7 + - - +
239B PHE 3.0 5.8 - - - -
240B THR* 3.3 11.9 - - - -
241B SER* 2.9 29.3 + - - -
242B PRO* 3.3 5.2 - - - +
377B PRO* 3.6 28.1 - - - +
380B LEU* 3.6 11.6 - - - +
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Residues in contact with GLU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B GLU* 2.8 29.0 + - + +
237B SER* 1.3 80.4 + - - +
239B PHE* 1.3 56.6 + - - +
242B PRO* 3.5 17.7 - - - +
291B LEU* 4.2 5.2 - - - +
293B PRO* 3.6 13.3 - - + +
294B GLY* 2.7 42.6 + - - +
324B ILE* 3.6 31.6 - - + +
325B CYS* 3.1 26.1 - - - +
376B THR 4.2 0.2 - - - -
377B PRO* 3.3 31.9 - - + +
380B LEU* 4.6 3.6 - - + -
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Residues in contact with PHE 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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228B VAL* 4.0 23.1 - - + -
230B ILE* 3.9 11.4 - - + -
234B PHE* 3.7 23.3 - + + -
235B GLU 3.6 1.0 + - - -
236B ASP 3.2 1.6 + - - -
237B SER 3.0 0.2 - - - -
238B GLU* 1.3 81.1 - - - +
240B THR* 1.3 74.3 + - + +
241B SER 3.5 0.7 - - - -
242B PRO* 3.6 2.0 - - - +
243B ALA* 3.0 46.3 + - + +
253B VAL* 4.1 15.9 - - + -
255B THR* 3.8 30.5 - - + -
272B SER 5.4 0.7 - - - -
273B VAL* 3.4 30.3 - - + -
291B LEU* 4.4 7.0 - - + +
293B PRO* 4.4 4.0 - - + -
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Residues in contact with THR 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 ASP 3.1 16.6 + - - +
237B SER* 3.3 10.4 - - - -
239B PHE* 1.3 89.4 - - + +
241B SER* 1.3 60.2 + - - +
243B ALA* 3.7 3.3 - - - +
244B ASP* 2.9 41.5 + - - +
271B ALA* 3.6 24.5 - - + -
272B SER 6.2 0.2 - - - +
273B VAL* 5.7 0.2 - - + -
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Residues in contact with SER 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* 2.9 16.4 + - - -
240B THR* 1.3 78.1 + - - +
242B PRO* 1.3 72.7 - - - +
244B ASP* 3.2 7.1 + - - +
245B GLU* 3.0 26.3 + - - +
380B LEU* 3.6 19.2 - - - +
384B ASN* 3.1 18.8 + - - -
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Residues in contact with PRO 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B SER 3.3 11.0 - - - +
238B GLU 3.5 15.0 - - - +
239B PHE 3.6 7.0 - - - +
241B SER* 1.3 95.4 - - - +
243B ALA* 1.3 51.3 + - - +
245B GLU* 3.3 1.0 + - + -
246B PHE* 2.7 62.0 + - + -
291B LEU* 4.1 13.2 - - + -
380B LEU* 3.8 12.1 - - + -
383B PHE* 4.0 11.4 - - + -
384B ASN* 3.2 24.9 - - - +
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Residues in contact with ALA 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 PHE* 3.0 46.3 + - + +
240B THR* 3.7 5.6 - - - +
242B PRO* 1.3 77.3 - - - +
244B ASP* 1.3 58.5 + - - +
246B PHE* 3.2 3.8 + - - +
247B ARG* 2.8 40.6 + - + +
253B VAL* 4.2 17.9 - - + -
291B LEU* 5.0 1.9 - - + +
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Residues in contact with ASP 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 THR* 2.9 27.5 + - - +
241B SER* 3.5 6.8 - - - +
243B ALA* 1.3 77.4 - - - +
245B GLU* 1.3 67.7 + - - +
247B ARG* 3.2 9.5 + - - +
248B LYS* 2.9 39.6 + - + +
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Residues in contact with GLU 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 SER* 3.0 21.6 + - - +
242B PRO 3.7 4.0 - - - +
244B ASP* 1.3 80.5 - - - +
246B PHE* 1.3 66.8 + - + +
248B LYS* 3.4 15.4 + - - +
249B ALA* 3.2 21.5 + - - +
384B ASN* 3.8 29.3 - - + +
388B LEU* 3.9 26.1 - - + +
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Residues in contact with PHE 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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226B ILE* 4.2 22.9 - - + -
242B PRO* 2.7 48.6 + - + +
243B ALA* 3.6 5.6 - - - +
245B GLU* 1.3 76.5 - - + +
247B ARG* 1.3 61.7 + - - +
249B ALA* 3.1 9.0 + - - +
251B HIS* 3.0 36.8 + - + +
253B VAL* 4.0 16.4 - - + -
291B LEU* 4.5 11.2 - - + -
322B PHE* 3.8 23.6 - + + -
383B PHE* 5.5 0.9 - + - -
384B ASN* 4.9 4.5 - - - -
387B ALA* 3.7 32.3 - - + -
388B LEU* 3.9 15.0 - - + -
391B LEU* 3.9 18.4 - - + -
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Residues in contact with ARG 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 ALA* 2.8 36.6 + - - +
244B ASP* 3.7 9.2 - - - +
246B PHE* 1.3 71.9 - - - +
248B LYS* 1.3 56.8 + - + +
250B GLY* 2.7 25.5 + - - -
251B HIS 3.7 13.0 + - - +
253B VAL* 4.2 20.2 - - + +
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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 ASP* 2.9 35.4 + - - +
245B GLU* 3.7 17.8 + - - +
246B PHE 3.3 0.2 - - - -
247B ARG* 1.3 76.8 - - + +
249B ALA* 1.3 58.4 + - - +
250B GLY* 3.1 3.2 + - - -
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Residues in contact with ALA 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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220B ALA* 5.0 8.1 - - - +
221B GLY 4.8 15.1 + - - +
223B SER* 5.5 0.3 - - - -
245B GLU 3.2 10.0 + - - +
246B PHE 3.1 9.5 + - - +
247B ARG 3.0 1.0 - - - -
248B LYS* 1.3 77.5 - - - +
250B GLY* 1.3 59.9 + - - +
251B HIS* 3.3 28.7 + - + +
388B LEU* 4.0 11.4 - - + -
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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