Contacts of the helix formed by residues 227 - 240 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209D ASN* 4.2 3.9 - - - +
225D ASP 3.8 3.2 + - - -
226D SER* 1.3 70.7 - - - +
228D VAL* 1.3 65.3 + - - +
230D GLU* 3.3 24.0 - - - -
231D ASN* 2.8 31.8 + - - -
269D LEU* 4.7 9.8 + - - +
272D ASP* 2.5 30.8 + - - +
275D LYS* 4.6 11.4 - - - -
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Residues in contact with VAL 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D ASN* 3.5 14.5 + - + +
212D LEU* 4.2 12.3 - - + -
213D ILE* 4.9 4.0 - - + -
219D LEU* 3.3 41.7 - - + +
220D ALA* 3.6 16.6 - - + +
223D TYR* 3.8 12.7 - - + -
225D ASP* 3.4 39.9 - - - +
226D SER 3.7 2.7 - - - +
227D SER* 1.3 77.3 - - - +
229D LEU* 1.3 64.2 + - - +
231D ASN* 3.4 2.9 + - - +
232D HIS* 3.1 20.4 + - - +
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Residues in contact with LEU 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D HIS* 3.5 23.6 - - + +
205D PRO* 3.5 23.8 - - + -
207D VAL 3.3 26.5 - - - +
208D SER* 4.9 0.7 - - - -
209D ASN* 2.8 29.5 + - - +
212D LEU* 3.5 24.5 - - + -
219D LEU* 4.1 12.8 - - + -
228D VAL* 1.3 72.2 - - - +
230D GLU* 1.3 62.8 + - - +
232D HIS* 3.1 7.3 + - + +
233D HIS* 2.8 48.8 + - + +
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Residues in contact with GLU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D ASN* 3.2 27.4 + - - -
227D SER* 3.3 21.6 - - - +
229D LEU* 1.3 79.6 - - - +
231D ASN* 1.3 61.4 + - - +
233D HIS* 3.4 15.8 + - + +
234D LEU* 3.3 26.9 + - - +
268D VAL* 3.9 13.4 - - + +
269D LEU* 4.5 9.2 - - - +
271D THR* 3.7 23.4 - - - +
272D ASP* 3.6 29.0 - - - +
273D MET 4.8 0.5 + - - -
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Residues in contact with ASN 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C TYR 4.7 3.5 - - - +
224C ASN* 3.1 39.0 + - - +
226C SER* 6.1 0.3 - - - -
223D TYR* 3.6 33.2 + - + +
226D SER* 3.1 16.4 + - - -
227D SER* 2.8 35.2 + - - +
228D VAL 3.7 2.9 - - - +
230D GLU* 1.3 77.2 - - - +
232D HIS* 1.3 63.5 + - - +
234D LEU 3.4 0.7 + - - -
235D ALA* 3.1 14.9 + - - +
269D LEU* 3.9 14.5 - - - +
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Residues in contact with HIS 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D VAL 4.6 1.6 - - - -
203D ASP* 2.6 45.5 + - + -
219D LEU* 3.7 44.8 - - + +
222D MET* 5.9 1.2 - - + +
223D TYR* 4.0 10.4 + - + -
228D VAL 3.1 14.1 + - - +
229D LEU* 3.4 12.3 - - + +
231D ASN* 1.3 74.5 - - - +
233D HIS* 1.3 67.0 + - - +
235D ALA* 3.2 5.0 + - - +
236D VAL* 3.0 44.0 + - + +
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Residues in contact with HIS 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D ILE* 3.6 13.3 - - - +
200D HIS* 2.9 29.2 - - - +
201D ASP* 3.2 30.9 + - - -
202D VAL* 2.7 34.8 + - - +
203D ASP 4.4 0.9 + - - -
204D HIS* 3.5 29.2 - + + -
229D LEU* 2.8 45.3 + - + +
230D GLU* 3.6 12.1 - - + +
232D HIS* 1.3 72.7 - + - +
234D LEU* 1.3 57.9 + - - +
237D GLY* 3.0 25.1 + - - -
268D VAL* 4.5 2.0 - - + -
513D ZN 4.3 5.4 - - - -
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Residues in contact with LEU 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224C ASN* 3.4 22.4 - - - +
199D ILE* 4.2 5.4 - - + -
230D GLU 3.3 13.6 + - - +
231D ASN 3.6 3.6 - - - +
232D HIS 3.2 0.2 - - - -
233D HIS* 1.3 77.3 - - - +
235D ALA* 1.3 66.4 + - - +
237D GLY* 3.2 1.2 + - - -
238D PHE* 2.9 49.6 + - + -
264D VAL* 3.7 16.4 - - + +
265D ILE* 3.6 28.3 - - + +
268D VAL* 3.7 22.9 - - + -
269D LEU* 3.6 32.1 - - + -
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Residues in contact with ALA 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C LEU* 3.7 27.2 - - + +
222C MET* 4.4 9.2 - - - +
224C ASN* 3.8 6.4 + - - +
223D TYR* 3.7 22.4 - - - +
231D ASN 3.1 8.4 + - - +
232D HIS* 3.2 7.2 + - - +
234D LEU* 1.3 78.2 - - - +
236D VAL* 1.3 59.7 + - + +
238D PHE* 3.5 0.6 + - - -
239D LYS* 2.8 32.7 + - - +
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Residues in contact with VAL 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D HIS* 4.6 8.1 - - + -
202D VAL* 3.7 30.5 - - + -
203D ASP* 4.3 11.0 - - + +
232D HIS* 3.0 48.2 + - + +
235D ALA* 1.3 73.2 - - + +
237D GLY* 1.3 66.0 + - - +
239D LYS* 3.1 6.5 + - - +
240D LEU* 3.0 43.5 + - + +
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Residues in contact with GLY 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D TYR* 2.8 32.4 + - - -
149D LEU* 4.7 3.8 - - - -
195D PHE* 4.0 5.4 - - - -
199D ILE* 4.1 18.6 - - - -
202D VAL* 3.8 4.4 - - - +
233D HIS 3.0 15.4 + - - -
234D LEU 3.7 2.7 - - - -
236D VAL* 1.3 77.7 - - - +
238D PHE* 1.3 61.5 + - - +
240D LEU* 3.8 4.7 + - - +
241D LEU* 3.9 2.8 - - - +
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Residues in contact with PHE 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C LEU* 4.7 11.2 - - + -
224C ASN* 4.7 2.0 - - - -
195D PHE* 4.1 13.5 - + - -
199D ILE* 4.6 2.7 - - + -
234D LEU* 2.9 53.0 + - + +
235D ALA* 4.0 2.9 - - - +
237D GLY* 1.3 74.9 - - - +
239D LYS* 1.3 67.5 + - - +
241D LEU* 3.1 39.6 + - + +
242D GLN* 4.3 4.9 + - - +
249D PHE* 5.3 4.3 - + - -
260D LEU* 5.9 2.2 - - + -
261D ARG* 3.3 53.4 - - + +
264D VAL* 3.5 29.2 - - + -
265D ILE* 4.0 7.0 - - + -
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Residues in contact with LYS 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A LYS* 2.9 33.7 - - - +
242A GLN* 3.4 3.6 + - - +
218B GLU* 4.0 50.0 - - + +
221B LEU* 5.4 3.5 - - - +
221C LEU* 4.2 17.2 - - + +
235D ALA 2.8 21.0 + - - +
236D VAL* 3.1 7.2 + - - +
238D PHE* 1.3 77.3 - - - +
240D LEU* 1.3 62.1 + - + +
242D GLN* 2.5 56.9 + - - +
243D GLU* 4.2 2.4 + - - +
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Residues in contact with LEU 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D TYR* 3.8 15.9 - - + -
148D THR* 4.0 9.2 - - + +
149D LEU* 3.8 31.6 - - + +
152D HIS* 3.7 52.0 - - + +
236D VAL* 3.0 30.1 + - + +
237D GLY 4.1 0.4 - - - +
238D PHE 3.2 0.4 - - - -
239D LYS* 1.3 75.7 - - + +
241D LEU* 1.3 61.8 + - - +
242D GLN 2.9 6.6 + - - -
243D GLU* 3.1 33.3 + - + +
246D CYS* 3.2 14.2 - - - +
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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