Contacts of the helix formed by residues 238 - 259 (chain B) in PDB entry 4OL0
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 238 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B GLU* 2.6 40.6 + - - -
236B LYS 3.5 3.5 + - - -
237B THR* 1.3 76.4 - - - +
239B SER* 1.3 65.0 + - - +
240B ASN* 4.0 6.0 + - - +
241B LEU* 3.7 10.2 + - - +
242B HIS* 3.0 24.8 + - - +
291B LYS* 4.7 0.9 - - - -
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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
----------------------------------------------------------
238B SER* 1.3 74.0 - - - +
240B ASN* 1.3 62.3 + - - +
242B HIS* 3.3 6.9 + - - +
243B GLU* 2.8 34.6 + - - +
288B ASP* 4.7 8.8 + - - -
290B ASP* 3.6 32.5 + - - +
291B LYS* 5.0 5.8 - - - +
294B ASN* 4.5 1.1 + - - +
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Residues in contact with ASN 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASN* 5.8 1.4 + - - -
195B GLU* 5.3 2.3 + - - +
199B MET* 3.8 29.1 - - + +
238B SER* 3.4 6.6 + - - +
239B SER* 1.3 80.2 - - - +
241B LEU* 1.3 57.3 + - - +
243B GLU* 3.0 9.8 + - - +
244B ALA* 2.9 27.5 + - - +
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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
----------------------------------------------------------
195B GLU* 4.1 26.0 - - + +
198B LEU* 3.8 25.1 - - + -
199B MET* 3.7 26.1 - - + -
202B PHE* 3.6 28.3 - - + -
231B VAL* 3.6 26.2 - - + -
237B THR* 4.0 9.6 - - + -
238B SER* 3.6 14.1 + - - +
239B SER 3.5 0.2 - - - -
240B ASN* 1.3 78.3 - - - +
242B HIS* 1.3 57.7 + - - +
244B ALA* 3.2 1.2 + - - +
245B ALA* 2.9 30.2 + - - +
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Residues in contact with HIS 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B VAL* 5.3 0.2 - - - -
232B LEU* 3.7 22.2 - - + +
234B GLN 5.3 0.2 - - - -
237B THR* 3.9 15.3 - - + +
238B SER 3.0 18.8 + - - +
239B SER* 3.3 9.2 - - - +
241B LEU* 1.3 77.4 - - - +
243B GLU* 1.3 52.8 + - - +
245B ALA* 4.7 0.4 - - - -
246B SER* 2.5 38.8 + - - -
291B LYS* 3.7 46.3 - - + +
294B ASN* 3.2 29.5 + - + +
295B TYR* 3.1 44.8 + + - -
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Residues in contact with GLU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASN* 5.8 2.3 + - - -
141A LYS* 3.3 29.5 + - - +
142A LYS* 5.1 13.2 + - - +
143A ASN* 5.3 1.6 - - - +
239B SER* 2.8 14.4 + - - +
240B ASN* 3.4 10.9 - - - +
242B HIS* 1.3 77.0 - - - +
244B ALA* 1.3 56.6 + - - +
246B SER* 3.3 3.2 + - - -
247B ASP* 2.8 40.6 + - - +
290B ASP* 6.2 2.0 - - + -
294B ASN* 3.6 25.7 - - - +
297B ARG* 4.8 0.4 - - - +
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Residues in contact with ALA 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B MET* 3.9 37.5 - - + +
202B PHE* 4.3 12.2 - - + +
203B ARG* 5.2 10.5 - - + +
240B ASN 2.9 12.7 + - - +
241B LEU* 3.4 7.6 - - - +
243B GLU* 1.3 77.5 - - - +
245B ALA* 1.3 58.0 + - - +
247B ASP* 3.2 7.9 + - - +
248B CYS* 2.9 28.4 + - - +
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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
----------------------------------------------------------
202B PHE* 4.0 12.9 - - + -
228B LEU* 3.5 27.8 - - + +
231B VAL* 4.4 5.6 - - + -
232B LEU* 3.7 23.6 - - + -
241B LEU 2.9 19.7 + - - +
244B ALA* 1.3 71.9 - - - +
246B SER* 1.3 64.1 + - - +
248B CYS* 3.1 4.0 + - - +
249B VAL* 2.9 28.0 + - - +
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Residues in contact with SER 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B LEU* 3.6 7.5 - - - +
242B HIS* 2.5 26.6 + - - -
243B GLU 3.5 4.3 - - - -
245B ALA* 1.3 76.6 - - - +
247B ASP* 1.3 57.4 + - - +
249B VAL* 3.2 3.8 + - - +
250B CYS* 2.9 34.4 + - - -
294B ASN* 3.4 21.1 - - - +
297B ARG* 3.9 17.7 - - - -
298B ILE* 3.8 23.4 - - - +
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Residues in contact with ASP 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A LYS* 3.2 33.3 + - - +
243B GLU* 2.8 28.5 + - - +
244B ALA* 3.5 6.9 + - - +
246B SER* 1.3 72.3 - - - +
248B CYS* 1.3 58.4 + - - +
250B CYS* 3.4 6.3 + - - +
251B SER* 2.8 36.8 + - - +
297B ARG* 3.2 17.0 + - - -
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Residues in contact with CYS 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B PHE* 3.5 27.1 - - + +
205B LEU* 3.8 17.9 - - - -
206B GLY* 3.8 16.6 - - - -
209B PHE* 4.2 4.7 - - - -
228B LEU* 3.7 28.3 - - + -
244B ALA 2.9 13.8 + - - +
245B ALA* 3.1 8.9 + - - +
247B ASP* 1.3 77.4 - - - +
249B VAL* 1.3 57.8 + - - +
251B SER* 3.1 8.1 + - - -
252B ALA* 2.9 27.5 + - - +
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Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B LEU* 3.7 22.4 - - + -
229B PHE* 4.0 23.6 - - + -
232B LEU* 3.7 23.1 - - + -
245B ALA 2.9 20.8 + - - +
246B SER* 3.6 7.4 - - - +
248B CYS* 1.3 71.1 - - - +
250B CYS* 1.3 59.2 + - - +
252B ALA* 3.2 8.0 + - - +
253B LEU* 2.9 40.3 + - + +
269B LEU* 5.0 3.6 - - + -
273B VAL* 4.2 2.7 - - + -
298B ILE* 3.9 27.4 - - + -
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Residues in contact with CYS 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B SER 2.9 21.5 + - - +
247B ASP* 3.6 6.7 - - - +
249B VAL* 1.3 75.5 - - - +
251B SER* 1.3 57.2 + - - +
253B LEU* 3.3 3.9 + - - +
254B TYR* 2.8 32.4 + - - +
297B ARG* 3.9 29.2 - - - +
298B ILE* 3.9 18.4 - - - -
301B GLU* 3.4 35.5 - - + +
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Residues in contact with SER 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B GLY* 3.9 24.5 + - - -
209B PHE* 4.5 2.0 - - - +
210B ASN* 4.7 2.5 - - - +
247B ASP* 2.8 28.1 + - - +
248B CYS* 3.4 7.8 - - - -
250B CYS* 1.3 74.4 - - - +
252B ALA* 1.3 56.0 + - - +
254B TYR* 3.7 6.0 - - - +
255B ALA* 2.8 30.7 + - - +
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Residues in contact with ALA 252 (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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209B PHE* 3.7 45.0 - - + -
228B LEU* 6.1 1.1 - - + -
248B CYS 2.9 12.6 + - - +
249B VAL* 3.4 9.6 - - - +
251B SER* 1.3 76.5 - - - +
253B LEU* 1.3 63.8 + - - +
255B ALA* 3.0 4.5 + - - +
256B ILE* 2.9 26.0 + - - +
269B LEU* 3.9 22.0 - - + -
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B VAL* 2.9 36.3 + - + +
250B CYS* 3.6 4.3 - - - +
252B ALA* 1.3 75.3 - - - +
254B TYR* 1.3 62.7 + - - +
256B ILE* 3.3 11.2 + - + +
257B GLU 3.3 1.4 + - - -
269B LEU* 3.9 31.0 - - + -
273B VAL* 4.5 4.5 - - + -
298B ILE* 3.8 7.0 - - + +
301B GLU* 3.8 11.2 - - + +
302B LEU* 3.6 46.4 - - + +
305B THR* 3.2 34.3 - - - +
306B PHE* 4.5 13.7 - - + -
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Residues in contact with TYR 254 (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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210B ASN* 5.9 1.6 - - - -
250B CYS 2.8 21.2 + - - +
251B SER* 3.8 6.1 - - - +
253B LEU* 1.3 70.5 - - - +
255B ALA* 1.3 67.9 + - - +
257B GLU* 3.1 49.2 + - + +
258B ASN* 3.9 13.3 + - - -
301B GLU* 3.7 21.0 + - - +
305B THR* 4.7 1.1 - - - -
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Residues in contact with ALA 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B PHE* 3.8 26.7 - - + +
210B ASN* 3.5 27.1 - - - +
251B SER 2.8 18.4 + - - +
252B ALA 3.3 5.4 - - - +
254B TYR* 1.3 79.0 - - - +
256B ILE* 1.3 64.0 + - + +
258B ASN* 4.1 12.6 + - - +
259B VAL* 4.7 8.1 + - - +
261B THR* 4.4 2.5 + - - +
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Residues in contact with ILE 256 (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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209B PHE* 6.3 0.4 - - + -
252B ALA 2.9 13.4 + - - +
253B LEU* 3.4 13.0 - - + +
255B ALA* 1.3 78.1 - - + +
257B GLU* 1.3 60.8 + - - +
258B ASN 2.8 1.7 + - - -
259B VAL 2.7 17.2 + - - +
260B GLU 5.0 1.1 - - - +
261B THR* 2.2 52.6 + - + +
262B ASN 5.6 1.3 - - - +
265B LEU* 4.4 18.2 - - + -
266B ALA* 4.2 23.8 - - + +
269B LEU* 3.3 33.2 - - + -
305B THR* 4.3 9.6 - - + -
306B PHE* 4.6 10.8 - - + -
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Residues in contact with GLU 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LEU 3.3 3.2 + - - +
254B TYR* 3.1 45.2 + - + +
256B ILE* 1.3 78.7 - - - +
258B ASN* 1.3 85.7 + - - +
259B VAL 3.3 4.6 - - - +
304B GLU 5.5 0.9 - - - +
305B THR* 3.9 35.6 - - + +
308B GLU* 4.6 10.2 - - - +
348B ARG* 5.6 3.5 + - - -
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Residues in contact with ASN 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B TYR* 3.9 22.3 + - - -
255B ALA* 4.1 8.7 + - - +
256B ILE 2.8 4.6 + - - -
257B GLU* 1.3 99.7 + - - +
259B VAL* 1.3 72.0 + - + +
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Residues in contact with VAL 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ALA 4.7 6.5 - - - +
256B ILE 2.7 8.2 + - - +
257B GLU 3.3 6.2 - - - +
258B ASN* 1.3 85.1 - - + +
260B GLU* 1.3 76.2 + - + +
261B THR* 2.7 44.0 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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