Contacts of the helix formed by residues 223 - 240 (chain D) in PDB entry 1OIK
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 223 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D TYR* 1.3 77.4 - - - +
224D LEU* 1.3 58.6 + - - +
225D ALA* 3.7 6.7 + - - +
226D ASP* 3.2 32.1 + - - +
227D SER* 2.9 27.6 + - - -
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Residues in contact with LEU 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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218D ARG* 6.3 1.1 - - - -
223D SER* 1.3 71.9 - - - +
225D ALA* 1.3 61.0 + - - +
227D SER* 3.5 6.5 + - - -
228D GLN* 3.0 40.9 + - - +
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Residues in contact with ALA 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223D SER* 3.4 5.3 + - - +
224D LEU* 1.3 77.6 - - - +
226D ASP* 1.3 65.0 + - - +
228D GLN* 3.3 15.9 + - - +
229D HIS* 3.2 36.3 + - + +
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Residues in contact with ASP 226 (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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222D TYR* 4.1 23.1 - - + -
223D SER* 3.2 23.1 + - - +
225D ALA* 1.3 76.2 - - - +
227D SER* 1.3 67.7 + - - +
229D HIS* 3.2 9.2 + - - +
230D LEU* 2.9 31.8 + - + +
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Residues in contact with SER 227 (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 LYS 4.9 0.2 + - - -
218D ARG* 3.5 13.2 - - - +
219D ILE* 2.9 48.6 + - - +
222D TYR* 4.1 4.2 - - - +
223D SER 2.9 19.8 + - - -
224D LEU* 3.6 7.6 - - - -
226D ASP* 1.3 75.6 - - - +
228D GLN* 1.3 57.7 + - - +
230D LEU* 3.8 2.0 - - - +
231D PHE* 2.9 34.2 + - - +
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Residues in contact with GLN 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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224D LEU* 3.0 23.4 + - - +
225D ALA* 3.4 16.2 - - - +
226D ASP 3.2 0.2 - - - -
227D SER* 1.3 78.2 + - - +
229D HIS* 1.3 62.1 + - + +
231D PHE* 3.9 6.5 - - - +
232D ALA* 3.0 30.3 + - - +
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Residues in contact with HIS 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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225D ALA* 3.2 26.1 + - + -
226D ASP* 3.2 10.0 + - - +
228D GLN* 1.3 83.3 - - + +
230D LEU* 1.3 66.8 + - + +
232D ALA* 3.5 5.9 + - + +
233D VAL* 3.2 28.6 + - + +
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Residues in contact with LEU 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D LEU* 5.9 2.7 - - + -
154D LEU* 4.0 24.9 - - + -
158D LEU* 4.7 17.9 - - + -
219D ILE* 4.7 11.2 - - + -
222D TYR* 3.9 41.7 - - + -
226D ASP* 2.9 22.6 + - + +
227D SER* 3.9 3.1 - - - +
229D HIS* 1.3 76.4 - - + +
231D PHE* 1.3 63.9 - - - +
233D VAL* 3.3 7.9 + - + +
234D LEU* 3.1 32.1 + - + +
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Residues in contact with PHE 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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212D LEU* 3.9 18.8 - - + -
213D GLY 3.3 38.6 - - - -
214D HIS* 5.4 0.4 - - - -
216D VAL* 3.7 31.6 - - + -
219D ILE* 4.7 9.8 - - + +
227D SER* 2.9 18.9 + - - +
228D GLN* 3.9 5.8 - - - +
230D LEU* 1.3 74.6 - - - +
232D ALA* 1.3 60.8 + - + +
234D LEU* 3.2 3.9 + - - +
235D GLN* 2.7 64.5 + - + +
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Residues in contact with ALA 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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228D GLN 3.0 19.7 + - - +
229D HIS* 3.7 9.9 - - + +
231D PHE* 1.3 82.9 - - + +
233D VAL* 1.3 57.6 + - + +
235D GLN* 4.7 2.0 - - - -
236D GLY* 3.0 24.9 + - - -
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Residues in contact with VAL 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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151D LEU* 3.8 32.8 - - + -
229D HIS* 3.2 16.2 + - + +
230D LEU* 3.7 11.2 - - + +
231D PHE 3.2 0.2 - - - -
232D ALA* 1.3 76.5 - - + +
234D LEU* 1.3 72.9 + - + +
236D GLY* 3.4 1.0 + - - -
237D HIS* 3.1 35.7 + - + +
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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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147D LEU* 3.9 34.1 - - + -
151D LEU* 4.3 19.1 - - + -
154D LEU* 6.2 1.1 - - + -
155D ALA* 4.4 8.3 - - + -
158D LEU* 4.0 26.9 - - + -
198D VAL* 4.0 19.7 - - + -
210D LEU* 3.8 8.1 - - + +
212D LEU* 3.4 20.2 - - + -
219D ILE* 6.0 1.8 - - + -
230D LEU* 3.1 18.6 + - + +
231D PHE* 4.1 2.0 - - - +
233D VAL* 1.3 83.2 - - + +
235D GLN* 1.3 62.0 + - - +
237D HIS* 3.2 16.4 + - - +
238D VAL* 3.4 13.9 + - - +
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Residues in contact with GLN 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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107D TRP* 3.6 11.7 - - - +
212D LEU* 3.3 8.7 - - + +
213D GLY* 3.2 17.8 + - - -
231D PHE* 2.7 50.4 + - + +
232D ALA* 4.5 1.8 - - - +
234D LEU* 1.3 73.7 - - - +
236D GLY* 1.3 61.6 + - - +
238D VAL* 3.0 16.7 + - - +
239D THR* 3.1 35.0 + - + +
263D GLN* 2.8 42.1 + - - -
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Residues in contact with GLY 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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232D ALA 3.0 21.5 + - - -
233D VAL 3.8 2.0 - - - -
234D LEU 3.2 0.2 - - - -
235D GLN* 1.3 77.8 - - - +
237D HIS* 1.3 55.5 + - - +
239D THR* 3.6 7.9 + - - -
240D ARG* 3.1 27.0 + - - +
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Residues in contact with HIS 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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143D ALA* 3.7 15.4 - - + +
146D GLU* 2.6 36.6 + - + +
147D LEU* 3.5 27.9 - - + +
148D PRO* 5.2 5.1 - - + +
151D LEU* 4.9 4.6 - - - +
210D LEU* 5.0 0.4 - - + -
233D VAL* 3.1 34.3 + - + +
234D LEU 3.2 7.9 + - - +
235D GLN 3.2 1.0 - - - -
236D GLY* 1.3 75.3 - - - +
238D VAL* 1.3 59.8 + - - +
239D THR 3.5 0.3 + - - -
240D ARG* 3.6 11.6 + - - +
243D ASN* 2.7 31.2 + - - -
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Residues in contact with VAL 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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138D ALA* 3.3 32.9 - - + +
139D ASN 4.9 0.6 + - - -
140D THR* 3.8 18.4 - - + -
143D ALA* 3.6 18.6 - - + +
210D LEU* 4.0 13.7 - - + -
212D LEU* 4.9 1.1 - - + -
234D LEU 3.4 13.4 + - - +
235D GLN* 3.0 13.9 + - - +
237D HIS* 1.3 80.5 - - - +
239D THR* 1.3 64.5 + - + +
240D ARG 3.5 1.0 + - - +
243D ASN* 3.6 12.5 - - - +
263D GLN* 3.7 37.9 - - - +
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Residues in contact with THR 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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107D TRP* 3.6 42.3 - - + +
138D ALA* 4.8 0.2 - - - -
235D GLN* 3.1 38.9 + - + +
236D GLY* 3.8 7.4 + - - -
237D HIS 3.3 0.2 - - - -
238D VAL* 1.3 79.1 - - + +
240D ARG* 1.3 67.7 + - - +
241D LEU* 3.3 5.4 + - - +
244D THR* 3.9 12.3 - - - +
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Residues in contact with ARG 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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105A ASN* 4.4 9.5 - - - +
265A TYR* 4.5 5.1 + - - +
23D ARG* 3.9 11.1 - - - +
146D GLU* 2.8 43.2 + - - +
236D GLY 3.1 14.0 + - - +
237D HIS* 3.7 18.8 - - - +
238D VAL 3.3 1.2 - - - -
239D THR* 1.3 77.9 - - - +
241D LEU* 1.3 69.2 + - - +
242D GLU* 3.5 46.2 + - - +
243D ASN* 2.8 17.9 + - - +
244D THR* 3.5 5.5 - - - +
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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