Contacts of the helix formed by residues 227 - 240 (chain B) in PDB entry 4OGB
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 227 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209B ASN* 4.2 4.1 - - - +
225B ASP 4.2 1.4 + - - -
226B SER* 1.3 71.6 - - - +
228B VAL* 1.3 65.7 + - - +
229B LEU 3.4 2.0 - - - -
230B GLU* 3.1 19.8 + - - -
231B ASN* 2.9 27.9 + - - +
269B LEU* 4.3 9.0 - - - +
272B ASP* 2.6 31.2 + - - +
275B LYS* 3.5 20.3 + - - -
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Residues in contact with VAL 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ASN* 3.5 14.5 + - + +
212B LEU* 4.2 13.9 - - + -
213B ILE* 4.3 10.1 - - + -
219B LEU* 3.6 42.0 - - + +
220B ALA* 3.7 15.9 - - + +
223B TYR* 3.8 9.6 - - + -
225B ASP* 3.7 34.5 - - - +
226B SER 3.8 3.6 - - - +
227B SER* 1.3 77.6 - - - +
229B LEU* 1.3 64.5 + - - +
231B ASN* 3.6 2.9 + - - +
232B HIS* 3.1 19.2 + - - +
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Residues in contact with LEU 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B HIS* 3.5 21.1 - - + +
205B PRO* 3.5 24.0 - - + -
207B VAL 3.3 27.1 - - - +
208B SER* 4.6 0.7 - - - -
209B ASN* 2.8 32.4 + - - +
212B LEU* 3.6 18.8 - - + -
219B LEU* 4.6 11.2 - - + -
228B VAL* 1.3 72.4 - - - +
230B GLU* 1.3 66.4 + - - +
232B HIS* 3.0 8.2 + - + +
233B HIS* 2.8 51.9 + - + +
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Residues in contact with GLU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ASN* 3.1 26.2 + - - -
227B SER* 3.1 16.5 + - - +
229B LEU* 1.3 80.0 - - - +
231B ASN* 1.3 64.5 + - - +
233B HIS* 3.2 14.2 + - + +
234B LEU* 3.1 25.5 + - - +
268B VAL* 3.9 7.7 - - - +
269B LEU* 3.8 20.6 - - + -
271B THR* 3.9 13.3 - - - +
272B ASP* 3.6 40.9 + - + +
273B MET 4.9 0.2 + - - -
503B ZN 4.1 13.3 - - - -
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Residues in contact with ASN 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A TYR* 4.8 5.5 + - - +
224A ASN* 2.5 34.8 + - - +
223B TYR* 3.5 39.4 + - + +
226B SER 3.1 24.1 - - - +
227B SER* 2.9 15.7 + - - +
228B VAL 3.7 0.2 - - - +
230B GLU* 1.3 74.5 - - - +
232B HIS* 1.3 57.6 + - - +
234B LEU* 3.2 6.4 + - - +
235B ALA* 3.0 26.0 + - - +
269B LEU* 3.9 14.8 - - - +
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Residues in contact with HIS 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B VAL 4.4 1.8 - - - -
203B ASP* 2.6 46.0 + - + -
219B LEU* 3.5 45.2 - - + +
223B TYR* 4.0 8.9 + - + -
228B VAL 3.1 13.1 + - - +
229B LEU* 3.0 16.8 + - + +
231B ASN* 1.3 72.9 - - - +
233B HIS* 1.3 68.4 + - - +
235B ALA* 3.2 6.9 + - + +
236B VAL* 2.9 42.0 + - + +
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Residues in contact with HIS 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199B ILE* 3.6 15.2 - - - +
200B HIS* 3.0 29.8 - - - +
201B ASP* 3.1 29.1 + - - -
202B VAL* 2.8 33.5 + - - +
203B ASP 4.6 0.4 - - - -
204B HIS* 3.8 25.0 - + + -
229B LEU* 2.8 49.4 + - + +
230B GLU* 3.2 12.8 + - + +
232B HIS* 1.3 72.4 - + - +
234B LEU* 1.3 63.3 + - - +
237B GLY* 3.0 21.7 + - - -
268B VAL* 4.4 2.5 - - + -
503B ZN 4.2 6.2 - - - -
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ASN* 3.7 31.0 - - - +
199B ILE* 4.3 4.6 - - + +
230B GLU 3.1 11.0 + - - +
231B ASN 3.3 7.4 - - - +
233B HIS* 1.3 77.9 - - - +
235B ALA* 1.3 62.0 + - - +
237B GLY* 3.9 0.2 - - - -
238B PHE* 3.1 41.7 + - + -
264B VAL* 3.8 20.2 - - + +
265B ILE* 3.9 15.9 - - - +
268B VAL* 3.6 32.3 - - + -
269B LEU* 3.7 34.5 - - + -
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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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221A LEU 6.0 0.9 - - - +
222A MET* 6.0 2.2 - - - +
224A ASN* 5.2 2.1 - - - +
223B TYR* 3.7 22.4 - - - +
231B ASN 3.0 7.5 + - - +
232B HIS* 3.5 13.2 - - + +
234B LEU* 1.3 75.8 - - - +
236B VAL* 1.3 63.7 + - + +
238B PHE* 5.1 0.4 - - - -
239B LYS* 2.9 48.5 + - + +
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Residues in contact with VAL 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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152B HIS* 4.4 12.6 - - + -
202B VAL* 3.6 25.6 - - + -
203B ASP* 4.0 11.7 - - + +
232B HIS* 2.9 48.1 + - + +
235B ALA* 1.3 72.5 - - + +
237B GLY* 1.3 64.7 + - - +
239B LYS* 3.2 4.2 + - - +
240B LEU* 2.9 54.3 + - + +
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Residues in contact with GLY 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B TYR* 2.8 26.0 + - - -
149B LEU* 4.5 4.5 - - - -
195B PHE* 4.2 2.6 - - - -
199B ILE* 4.0 25.6 - - - -
202B VAL* 3.7 4.7 - - - +
233B HIS 3.0 17.2 + - - -
234B LEU 3.9 0.7 - - - -
236B VAL* 1.3 77.4 - - - +
238B PHE* 1.3 66.7 + - - +
240B LEU* 3.7 4.4 + - - +
241B LEU* 4.0 1.4 - - - +
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Residues in contact with PHE 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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221A LEU 5.9 0.2 - - - -
224A ASN* 4.4 6.1 - - - -
195B PHE* 3.8 19.3 - + - -
199B ILE* 4.7 1.1 - - + -
234B LEU* 3.1 29.0 + - + +
235B ALA 3.9 2.0 - - - +
237B GLY* 1.3 73.5 - - - +
239B LYS* 1.3 76.0 + - + +
241B LEU* 2.8 44.7 + - + +
242B GLN* 4.7 3.9 + - - -
249B PHE* 6.2 0.4 - + - -
260B LEU* 6.5 0.4 - - + -
261B ARG* 3.7 39.9 - - + -
264B VAL* 3.6 37.9 - - + -
265B ILE* 3.9 19.3 - - + -
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Residues in contact with LYS 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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221A LEU* 4.1 36.7 + - - +
222A MET* 5.0 1.6 - - - +
235B ALA* 2.9 43.2 + - + +
236B VAL* 4.0 4.0 - - - +
238B PHE* 1.3 89.9 - - + +
240B LEU* 1.3 60.0 + - + +
242B GLN* 3.0 45.9 + - - +
243B GLU* 4.2 3.6 + - - +
239C LYS* 5.6 7.9 - - - +
218D GLU* 4.8 22.9 - - + +
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Residues in contact with LEU 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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145B TYR* 3.8 13.6 - - + -
148B THR* 4.0 7.1 - - + +
149B LEU* 4.0 25.6 - - + -
152B HIS* 3.5 57.2 - - + +
236B VAL* 2.9 32.1 + - + +
237B GLY 4.0 5.8 - - - +
238B PHE 3.1 0.8 + - - -
239B LYS* 1.3 77.6 - - + +
241B LEU* 1.3 60.8 + - - +
242B GLN 3.1 0.8 + - - -
243B GLU* 3.5 26.0 + - + +
246B CYS* 3.3 20.8 - - - +
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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