Contacts of the helix formed by residues 229 - 250 (chain D) in PDB entry 2ONK
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 ALA 229 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104C ILE* 3.5 27.6 - - + -
217D ILE* 4.2 7.8 - - + +
220D ARG* 4.5 4.3 - - + -
221D TYR* 4.1 17.3 - - + +
225D GLY 3.6 8.0 + - - +
226D LEU* 2.6 15.6 + - - +
228D ALA* 1.3 72.9 - - - +
230D MET* 1.3 65.0 + - - +
231D PRO* 3.2 2.9 - - - -
232D VAL* 2.9 11.0 + - - +
233D ALA* 2.9 21.3 + - - +
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Residues in contact with MET 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ILE* 4.7 3.0 - - + +
108C VAL* 3.4 41.1 - - + -
27D THR* 4.4 16.0 + - - +
30D LEU* 4.1 17.9 - - + -
31D GLN* 3.7 17.7 - - - +
226D LEU* 3.1 36.8 + - + +
227D SER* 4.2 12.3 - - - +
229D ALA* 1.3 75.5 - - - +
231D PRO* 1.3 72.6 - - + +
233D ALA* 2.9 9.8 + - - +
234D ALA* 2.9 23.9 + - - +
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Residues in contact with PRO 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D GLN* 3.5 26.4 - - - +
34D ASN* 6.3 0.4 - - + -
37D GLU* 4.4 21.3 - - + +
38D PHE* 4.4 5.9 - - + +
41D ALA* 3.8 21.8 - - + -
227D SER 3.6 17.5 - - - +
228D ALA* 4.1 4.0 - - - +
229D ALA 3.4 5.8 - - - +
230D MET* 1.3 94.5 - - + +
232D VAL* 1.3 59.6 + - + +
234D ALA* 3.2 2.6 + - - +
235D ILE* 2.8 34.9 + - - +
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Residues in contact with VAL 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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41D ALA* 4.8 6.1 - - + -
47D VAL* 4.5 17.9 - - + -
216D LEU* 3.7 24.2 - - + -
217D ILE* 3.9 19.7 - - + -
220D ARG* 3.4 40.6 - - - +
228D ALA 4.6 4.0 - - - +
229D ALA* 2.9 11.6 + - - +
231D PRO* 1.3 72.9 - - + +
233D ALA* 1.3 63.8 + - - +
235D ILE* 3.3 9.4 + - + +
236D LEU* 2.9 29.3 + - + +
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Residues in contact with ALA 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C VAL* 3.7 18.8 - - + +
104C ILE* 3.9 21.5 - - + -
105C ALA* 5.7 0.4 - - + +
27D THR* 4.9 7.2 - - + +
217D ILE* 3.7 15.8 - - + +
229D ALA 2.9 11.7 + - - +
230D MET* 3.1 10.8 - - - +
232D VAL* 1.3 75.5 - - - +
234D ALA* 1.3 52.6 + - - +
236D LEU* 2.6 25.8 + - - +
237D ILE* 2.7 22.0 + - - +
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Residues in contact with ALA 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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27D THR* 4.1 7.9 + - - +
28D VAL* 4.0 18.2 - - + -
31D GLN* 3.3 34.8 - - + -
38D PHE* 4.3 5.4 - - + -
230D MET 2.9 10.4 + - - +
231D PRO 3.6 5.2 - - - +
233D ALA* 1.3 72.8 - - - +
235D ILE* 1.3 62.5 + - - +
237D ILE* 3.5 10.0 - - - +
238D LEU* 2.9 31.6 + - - +
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Residues in contact with ILE 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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38D PHE* 3.7 22.4 - - + +
41D ALA* 3.4 22.0 - - + +
42D ALA* 3.4 35.7 - - + +
47D VAL* 4.9 15.5 - - + -
48D TRP* 4.7 17.3 - - + -
231D PRO 2.8 17.0 + - - +
232D VAL* 3.5 12.6 - - + +
234D ALA* 1.3 75.6 - - - +
236D LEU* 1.3 55.8 + - + +
238D LEU* 3.7 3.7 - - - +
239D LEU* 2.6 51.3 + - + +
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Residues in contact with LEU 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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98C PRO* 4.3 12.8 - - + +
101C VAL* 4.0 13.7 - - + -
47D VAL* 5.6 1.3 - - + -
51D VAL* 3.9 11.2 - - + -
55D TYR* 5.1 5.6 + - + +
213D ALA* 3.3 39.7 - - + +
217D ILE* 3.3 26.9 - - + -
232D VAL* 2.9 19.6 + - + +
233D ALA 2.6 13.9 + - - +
235D ILE* 1.3 71.8 - - + +
237D ILE* 1.3 68.2 + - - +
239D LEU* 3.5 23.6 - - + +
240D SER* 2.9 23.4 + - - -
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Residues in contact with ILE 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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97C ILE* 4.8 15.7 - - + +
101C VAL* 3.8 22.9 - - + +
105C ALA* 4.9 2.9 - - + -
24D VAL* 3.4 43.5 - - + +
27D THR* 3.3 29.2 - - + +
28D VAL* 3.7 14.4 - - + -
233D ALA 2.7 17.8 + - - +
234D ALA* 3.5 7.6 - - - +
236D LEU* 1.3 71.0 - - - +
238D LEU* 1.3 58.2 + - - +
240D SER* 2.6 28.6 + - - -
241D LEU* 2.9 25.7 + - + +
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Residues in contact with LEU 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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28D VAL* 3.2 37.7 - - + -
38D PHE* 3.8 29.8 - - + -
234D ALA 2.9 17.8 + - - +
235D ILE* 3.8 3.1 - - - +
237D ILE* 1.3 76.6 - - - +
239D LEU* 1.3 65.6 + - - +
240D SER 2.9 1.0 + - - -
241D LEU* 3.1 20.4 + - + +
242D ALA* 3.1 24.6 + - - +
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Residues in contact with LEU 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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48D TRP* 3.9 23.1 - - + -
51D VAL* 3.6 39.0 - - + -
55D TYR* 3.2 30.1 - - + +
235D ILE* 2.6 27.5 + - + +
236D LEU* 3.5 16.6 - - + +
238D LEU* 1.3 73.5 - - - +
240D SER* 1.3 59.4 + - - +
242D ALA* 3.9 4.4 - - + +
243D VAL* 3.1 24.9 + - + +
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Residues in contact with SER 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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96C VAL* 3.0 41.7 + - - +
97C ILE* 5.6 2.7 - - - -
98C PRO* 5.0 3.5 - - - +
55D TYR* 3.9 12.3 + - - -
197D ILE* 5.1 4.2 - - - +
236D LEU 2.9 11.4 + - - -
237D ILE* 2.6 17.5 + - - -
239D LEU* 1.3 70.2 - - - +
241D LEU* 1.3 68.1 + - - -
242D ALA 3.0 1.9 + - - -
243D VAL* 3.0 2.3 + - - +
244D PHE* 2.9 33.2 + - - -
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Residues in contact with LEU 241 (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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93C LEU* 3.6 31.2 - - + -
96C VAL* 5.7 2.7 - - + -
97C ILE* 6.3 0.7 - - + -
24D VAL* 5.8 1.6 - - + -
28D VAL* 6.2 0.4 - - + -
237D ILE* 2.9 30.5 + - + +
238D LEU* 3.7 18.6 - - + +
240D SER* 1.3 74.5 - - - +
242D ALA* 1.3 58.6 + - - +
244D PHE* 5.1 2.0 - - - -
245D VAL* 2.8 44.6 + - + +
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Residues in contact with ALA 242 (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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238D LEU 3.1 14.9 + - - +
239D LEU* 3.9 6.7 - - + +
240D SER 3.0 0.2 - - - -
241D LEU* 1.3 76.3 - - - +
243D VAL* 1.3 60.5 + - + +
244D PHE 3.0 0.2 + - - -
245D VAL* 4.2 2.1 - - - +
246D ALA* 2.8 36.1 + - - +
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Residues in contact with VAL 243 (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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55D TYR* 4.1 12.8 - - + +
193D TRP* 3.7 32.1 - - + -
239D LEU* 3.1 32.5 + - + +
240D SER* 3.0 4.3 + - - +
242D ALA* 1.3 80.9 - - + +
244D PHE* 1.3 64.9 + - + +
246D ALA* 3.7 5.5 - - - +
247D LEU* 3.2 32.1 + - + +
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Residues in contact with PHE 244 (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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96C VAL* 3.1 44.2 - - + -
55D TYR* 5.7 0.4 - - - -
190D ILE* 4.0 26.2 - - + -
193D TRP* 3.7 31.2 - + - -
194D ALA* 3.6 33.2 - - + -
197D ILE* 4.9 6.1 - - + -
240D SER* 2.9 21.6 + - - +
241D LEU* 4.3 2.2 - - - +
243D VAL* 1.3 81.0 - - + +
245D VAL* 1.3 66.6 + - - +
246D ALA 2.9 1.8 - - - -
247D LEU* 2.9 11.0 + - + +
248D ARG* 2.8 26.2 + - + +
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Residues in contact with VAL 245 (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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241D LEU* 2.8 32.9 + - + +
242D ALA* 4.2 1.8 - - - +
244D PHE* 1.3 73.1 - - + +
246D ALA* 1.3 63.0 + - - +
248D ARG* 3.3 11.5 + - + +
249D ILE* 2.9 42.9 + - + +
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Residues in contact with ALA 246 (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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242D ALA 2.8 21.0 + - - +
243D VAL* 3.7 7.9 - - - +
245D VAL* 1.3 78.0 - - - +
247D LEU* 1.3 62.9 + - + +
249D ILE* 3.1 14.9 + - - +
250D ILE* 2.9 31.8 + - + +
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Residues in contact with LEU 247 (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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190D ILE* 3.6 47.1 - - + -
193D TRP* 5.2 6.1 - - + -
243D VAL* 3.2 25.1 + - + +
244D PHE* 2.9 19.1 + - + +
246D ALA* 1.3 80.3 - - + +
248D ARG* 1.3 60.2 + - - +
250D ILE* 3.1 23.1 + - + +
251D VAL* 3.4 22.4 - - + +
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Residues in contact with ARG 248 (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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85C SER* 3.7 22.6 + - - +
88C GLU* 4.3 13.5 + - - +
89C GLY* 3.9 14.3 - - - +
92C ASP* 3.4 27.1 + - - +
244D PHE 2.8 17.8 + - - +
245D VAL* 3.6 13.5 - - + +
247D LEU* 1.3 68.2 - - + +
249D ILE* 1.3 59.4 - - + +
250D ILE 3.0 4.5 - - - -
251D VAL* 3.1 5.4 + - - -
252D GLY* 2.8 31.9 + - - +
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Residues in contact with ILE 249 (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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245D VAL* 2.9 36.3 + - + +
246D ALA* 3.1 7.4 + - - +
248D ARG* 1.3 76.9 - - + +
250D ILE* 1.3 59.9 + - + +
251D VAL 3.3 2.6 + - - -
252D GLY 4.4 9.5 + - - +
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Residues in contact with ILE 250 (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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246D ALA* 2.9 29.8 + - + +
247D LEU* 3.6 18.2 - - + +
248D ARG 3.0 1.2 - - - -
249D ILE* 1.3 82.7 - - + +
251D VAL* 1.3 68.1 + - + +
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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