Contacts of the helix formed by residues 207 - 225 (chain D) in PDB entry 1OGU
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 THR 207 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200D MET* 3.4 17.0 - - - +
205D ASP 4.9 2.2 - - - +
206D ILE* 1.3 85.1 - - - +
208D ASN* 1.3 65.0 + - - +
209D SER* 3.1 16.3 + - - -
210D MET* 3.1 26.0 + - - +
211D ARG 3.2 16.3 + - - -
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Residues in contact with ASN 208 (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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200D MET* 3.3 36.2 - - - +
207D THR* 1.3 72.5 - - - +
209D SER* 1.3 61.5 + - - +
211D ARG* 3.3 4.7 + - - +
212D ALA* 3.0 23.4 + - - +
342D ILE 4.8 1.7 - - - +
344D ALA* 3.4 24.3 + - + +
345D ASP* 3.6 29.8 + - - +
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Residues in contact with SER 209 (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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207D THR* 3.1 10.9 + - - -
208D ASN* 1.3 75.8 - - - +
210D MET* 1.3 66.0 + - - +
212D ALA* 3.0 18.4 + - - +
213D ILE* 3.2 23.1 + - - +
406D GLN* 5.0 0.5 - - - +
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Residues in contact with MET 210 (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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205D ASP 3.9 5.8 - - - +
206D ILE* 3.7 29.2 - - + -
207D THR* 3.1 23.8 + - - +
209D SER* 1.3 73.1 - - - +
211D ARG* 1.3 66.9 + - - +
213D ILE* 3.2 17.4 + - + +
214D LEU* 2.9 21.3 + - - +
250D ARG* 3.4 44.2 - - + +
253D LEU* 3.8 18.8 - - + +
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Residues in contact with ARG 211 (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 TYR* 3.4 16.5 + - - +
200D MET* 3.7 22.9 - - + -
207D THR 3.2 5.5 + - - -
208D ASN 3.6 7.4 - - - +
209D SER 3.3 0.2 - - - -
210D MET* 1.3 76.6 - - - +
212D ALA* 1.3 56.3 + - - +
214D LEU* 3.2 12.5 + - + +
215D VAL* 2.8 40.9 + - + +
236D VAL* 3.4 13.7 - - - +
239D ILE* 5.7 3.5 - - + +
240D ASP* 2.6 41.2 + - - -
243D LEU* 5.7 5.6 - - + -
253D LEU* 4.3 6.4 - - + +
341D LEU* 2.7 29.7 + - - +
342D ILE 3.6 16.0 + - - -
344D ALA* 3.9 26.6 - - - +
348D LEU* 4.5 5.1 - - - +
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Residues in contact with ALA 212 (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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208D ASN 3.0 10.2 + - - +
209D SER* 3.0 13.8 + - - +
211D ARG* 1.3 74.7 - - - +
213D ILE* 1.3 60.6 + - - +
215D VAL* 4.8 0.9 - - - -
216D ASP* 2.9 31.0 + - - +
342D ILE* 3.4 38.4 - - + +
343D ASP* 4.7 3.8 - - - +
404D HIS* 4.8 3.1 - - + -
406D GLN* 3.4 16.5 - - - +
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Residues in contact with ILE 213 (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 SER* 3.2 22.2 + - - +
210D MET* 3.3 15.7 - - + +
212D ALA* 1.3 73.6 - - - +
214D LEU* 1.3 58.6 + - - +
216D ASP* 3.2 2.9 + - - +
217D TRP* 2.9 30.7 + - + +
406D GLN* 4.0 21.1 - - - +
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Residues in contact with LEU 214 (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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210D MET 2.9 12.7 + - - +
211D ARG* 3.2 13.4 + - + +
213D ILE* 1.3 74.2 - - - +
215D VAL* 1.3 66.8 - - + +
217D TRP* 3.3 24.5 + - + +
218D LEU* 3.0 26.5 + - + +
239D ILE* 4.2 30.3 - - + -
253D LEU* 4.1 32.8 - - + +
254D GLN* 3.9 30.3 - - + +
257D GLY* 4.3 9.9 - - - +
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Residues in contact with VAL 215 (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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211D ARG* 2.8 44.6 + - + +
212D ALA 4.3 0.4 - - - +
214D LEU* 1.3 73.1 - - + +
216D ASP* 1.3 66.7 + - - +
218D LEU* 3.1 20.8 + - + +
219D VAL* 3.1 18.1 + - + +
232D LEU* 5.1 2.0 - - + -
236D VAL* 3.9 25.6 - - + -
239D ILE* 5.3 4.5 - - + -
341D LEU* 4.0 28.0 - - + +
342D ILE* 3.7 20.6 - - + -
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Residues in contact with ASP 216 (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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212D ALA 2.9 22.0 + - - +
213D ILE 3.4 4.7 - - - +
214D LEU 3.1 0.2 - - - -
215D VAL* 1.3 76.1 - - - +
217D TRP* 1.3 64.2 + - - +
219D VAL* 3.1 21.5 + - - +
220D GLU* 3.4 6.2 + - - +
342D ILE* 3.7 10.7 - - + +
406D GLN* 3.4 30.2 + - + +
407D GLN 3.3 8.6 + - - -
408D SER* 2.5 49.6 + - - -
409D ILE* 4.4 1.7 + - - +
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Residues in contact with TRP 217 (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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213D ILE* 2.9 18.5 + - + +
214D LEU* 3.6 21.1 - - + +
216D ASP* 1.3 76.1 + - - +
218D LEU* 1.3 85.6 + - + +
219D VAL 3.2 0.2 + - - -
220D GLU* 3.2 25.8 + - + +
221D VAL* 2.9 48.1 + - + +
254D GLN* 3.3 32.8 + - + -
258D THR* 3.6 28.9 - - - -
281D ILE* 3.8 33.9 + - + +
282D THR* 3.8 8.7 - - + -
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Residues in contact with LEU 218 (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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214D LEU* 3.0 25.4 + - + +
215D VAL* 3.1 17.4 + - + +
217D TRP* 1.3 102.5 - - + +
219D VAL* 1.3 52.1 + - - +
221D VAL* 3.3 4.8 + - + -
222D GLY* 2.8 29.3 + - - -
232D LEU* 3.9 14.7 - - + +
235D ALA* 4.7 9.2 - - + -
236D VAL* 4.8 4.7 - - + -
239D ILE* 3.7 30.5 - - + -
257D GLY 3.8 16.6 - - - +
261D MET* 3.4 32.4 - - + +
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Residues in contact with VAL 219 (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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215D VAL* 3.1 20.6 - - + +
216D ASP* 3.1 11.0 + - - +
218D LEU* 1.3 74.3 - - - +
220D GLU* 1.3 66.2 + - - +
222D GLY* 3.2 3.9 + - - -
223D GLU* 3.1 23.1 + - + +
232D LEU* 4.1 24.0 - - + -
338D GLU* 4.0 11.7 - - - +
408D SER* 3.9 19.5 - - - +
409D ILE* 3.8 37.0 - - + -
412D LYS* 4.0 13.4 - - + +
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Residues in contact with GLU 220 (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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216D ASP* 3.7 9.4 - - - +
217D TRP* 3.2 25.5 + - + +
219D VAL* 1.3 73.7 - - - +
221D VAL* 1.3 66.2 - - - +
223D GLU* 2.7 19.3 + - - +
224D GLU* 2.9 15.2 + - - +
408D SER* 3.1 28.6 + - - +
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Residues in contact with VAL 221 (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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217D TRP* 2.9 59.0 + - + +
218D LEU* 3.4 12.1 - - + +
220D GLU* 1.3 75.8 - - - +
222D GLY* 1.3 62.9 + - - +
224D GLU* 3.4 5.9 + - - -
225D TYR* 3.2 33.9 + - + +
227D LEU* 4.4 4.2 - - + +
261D MET* 4.2 20.9 - - + -
278D PHE* 4.9 2.7 - - + -
281D ILE* 3.5 28.9 - - + -
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Residues in contact with GLY 222 (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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218D LEU 2.8 18.1 + - - -
219D VAL* 3.6 4.7 - - - -
220D GLU 3.1 0.6 - - - -
221D VAL* 1.3 73.1 - - - +
223D GLU* 1.3 64.3 + - - +
226D LYS* 3.1 5.2 + - - -
227D LEU* 2.8 50.6 + - - +
232D LEU* 5.9 3.4 - - - -
261D MET* 4.1 4.0 - - - +
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Residues in contact with GLU 223 (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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219D VAL* 3.1 12.8 + - + +
220D GLU* 2.7 12.2 + - - +
222D GLY* 1.3 81.3 - - - +
224D GLU* 1.3 65.9 + - - +
225D TYR 3.1 2.4 + - - -
226D LYS* 3.2 19.5 + - - +
227D LEU 4.9 3.8 - - - +
408D SER 5.8 0.2 - - - +
412D LYS* 3.1 52.0 - - + +
415D ASN* 4.8 8.1 + - - +
417D LYS* 4.5 8.5 + - - -
418D TYR* 3.9 15.5 + - - -
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Residues in contact with GLU 224 (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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220D GLU 2.9 13.0 + - - +
221D VAL* 3.9 7.6 - - - +
223D GLU* 1.3 76.9 - - - +
225D TYR* 1.3 85.1 + - + +
226D LYS* 3.8 6.9 + - - +
280D TYR* 5.7 6.0 - - + -
281D ILE* 5.0 5.6 - - + -
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Residues in contact with TYR 225 (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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221D VAL* 3.2 27.0 + - + +
223D GLU 3.1 0.6 - - - -
224D GLU* 1.3 94.4 + - + +
226D LYS* 1.3 71.1 + - - +
227D LEU* 3.2 22.4 + - + +
273D PRO* 4.1 19.7 - - + +
277D GLU* 3.4 53.5 + - + +
278D PHE* 6.4 0.9 - + - -
280D TYR* 3.7 19.8 - - - -
281D ILE* 3.4 26.5 - - + -
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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