Contacts of the helix formed by residues 229 - 245 (chain D) in PDB entry 3IKH
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 GLY 229 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D ASN* 4.5 2.5 - - - -
227D THR 3.3 0.8 + - - -
228D THR* 1.3 79.3 - - - +
230D ALA* 1.3 58.1 + - - +
231D GLY 3.3 2.9 - - - -
232D ASP* 3.3 20.9 + - - +
233D THR* 2.8 34.3 + - - -
264D THR* 3.8 2.2 - - - -
274D PHE* 4.1 14.6 - - - -
501D GOL 4.0 5.2 + - - -
900D ATP 3.8 7.6 + - - -
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Residues in contact with ALA 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227D THR* 3.1 18.9 + - - +
228D THR 3.3 1.6 + - - -
229D GLY* 1.3 76.6 - - - +
231D GLY* 1.3 58.1 + - - +
233D THR* 3.3 5.5 + - - -
234D PHE* 2.9 28.8 + - - +
261D ALA* 3.9 3.4 - - - +
264D THR* 4.2 9.2 - - + -
265D VAL* 3.7 26.0 - - + -
900D ATP 3.5 29.9 + - + +
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Residues in contact with GLY 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D GLN* 5.4 0.2 - - - -
161D ASN* 5.8 2.2 + - - -
180D VAL* 5.5 2.4 - - - +
200D THR* 5.7 2.3 - - - +
230D ALA* 1.3 77.6 - - - +
232D ASP* 1.3 58.9 + - - +
234D PHE* 3.3 3.0 + - - +
235D LEU* 3.0 29.5 + - - +
900D ATP 3.2 47.4 + - - -
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Residues in contact with ASP 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D LYS* 3.5 24.1 + - - +
42D ASN* 2.9 40.6 + - + -
43D GLN* 2.9 39.0 - - + +
46D ILE* 4.3 3.0 - - + +
161D ASN* 4.1 2.8 + - - -
229D GLY* 3.3 9.2 + - - +
230D ALA 3.3 0.6 - - - -
231D GLY* 1.3 74.7 - - - +
233D THR* 1.3 64.6 + - - +
235D LEU 4.6 0.2 - - - +
236D ALA* 3.1 26.9 + - - +
501D GOL 3.0 16.4 + - - -
900D ATP 3.9 3.0 + - - -
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Residues in contact with THR 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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46D ILE* 3.3 25.9 - - + +
229D GLY 2.8 20.7 + - - -
230D ALA 3.5 5.2 - - - -
232D ASP* 1.3 77.4 - - - +
234D PHE* 1.3 63.0 + - - +
236D ALA* 3.9 0.5 - - - +
237D VAL* 3.1 29.4 + - + +
260D ALA* 3.7 33.4 - - + +
261D ALA* 3.7 3.6 - - - +
264D THR* 2.8 28.8 + - - +
274D PHE* 3.6 2.6 - - - -
275D PRO* 4.3 6.1 - - + -
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Residues in contact with PHE 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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180D VAL* 5.2 2.9 - - + -
198D VAL* 3.9 23.3 - - + -
200D THR* 3.9 13.9 - - + -
206D ALA* 3.8 19.3 - - + -
217D CYS* 5.7 0.2 - - - -
230D ALA 2.9 17.1 + - - +
231D GLY* 3.5 5.6 - - - +
233D THR* 1.3 78.1 - - - +
235D LEU* 1.3 67.2 + - - +
238D MSE 3.0 28.7 + - + +
254D LEU* 3.8 19.7 - - + -
257D ALA* 3.2 45.9 - - + +
258D SER* 3.6 20.2 - - - -
261D ALA* 4.4 1.7 - - + +
900D ATP 3.6 36.8 - - - -
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Residues in contact with LEU 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D GLN* 3.7 26.0 - - - +
134D LEU* 3.9 25.6 - - + -
159D VAL* 4.8 4.9 - - + -
161D ASN* 3.5 33.7 - - + -
180D VAL* 3.6 35.7 - - + -
231D GLY 3.0 16.3 + - - +
232D ASP 4.0 3.1 - - - +
234D PHE* 1.3 81.6 - - - +
236D ALA* 1.3 69.1 + - - +
238D MSE 3.7 9.2 - - + +
239D LEU* 3.1 29.3 + - + +
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Residues in contact with ALA 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D GLN* 3.6 27.4 - - - +
46D ILE* 3.6 22.2 - - + -
47D LEU* 3.3 21.8 - - + +
232D ASP 3.1 18.9 + - - +
235D LEU* 1.3 83.1 - - - +
237D VAL* 1.3 56.8 + - - +
239D LEU 3.4 1.0 + - - -
240D ALA* 2.9 26.5 + - - +
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Residues in contact with VAL 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D ILE* 3.7 20.6 - - + -
50D CYS* 4.2 3.6 - - - -
233D THR* 3.1 18.1 + - + +
236D ALA* 1.3 73.1 - - - +
238D MSE 1.3 61.0 + - - +
240D ALA* 3.8 6.6 - - - +
241D SER* 2.9 28.1 + - - -
256D HIS* 3.7 25.1 - - + +
257D ALA* 3.7 10.8 - - - +
260D ALA* 3.5 20.4 - - + -
280D LEU* 3.8 12.8 - - + -
283D LEU* 4.2 3.8 - - + -
284D LEU* 4.1 18.6 - - + -
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Residues in contact with MSE 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D VAL* 5.7 1.6 - - + -
178D ILE* 4.3 9.6 - - + -
180D VAL* 3.9 23.1 - - + -
198D VAL* 3.6 33.0 - - - -
234D PHE* 3.0 24.8 + - + +
235D LEU* 3.7 9.9 - - + +
237D VAL* 1.3 76.7 - - - +
239D LEU* 1.3 77.4 + - + +
241D SER 3.5 0.2 + - - -
242D ALA* 3.1 20.6 + - - +
249D PRO* 4.2 24.7 - - + -
253D ALA* 3.5 32.9 - - + +
254D LEU* 4.0 14.8 - - + -
257D ALA* 3.8 10.0 - - + +
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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
----------------------------------------------------------
3D VAL* 4.9 3.1 - - + -
47D LEU* 4.2 22.0 - - + -
132D ILE* 3.6 33.0 - - + -
134D LEU* 4.5 13.5 - - + -
159D VAL* 4.5 21.5 - - + -
178D ILE* 4.7 12.1 - - + -
235D LEU* 3.1 22.9 + - + +
236D ALA 3.6 3.6 - - - +
238D MSE 1.3 85.8 - - + +
240D ALA* 1.3 59.6 + - - +
242D ALA* 3.3 7.0 + - + +
243D LEU* 2.9 46.2 + - + +
249D PRO* 5.5 1.3 - - + -
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Residues in contact with ALA 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D LEU* 4.0 4.2 - - + +
50D CYS* 3.5 37.5 - - + -
52D ILE* 3.8 22.0 - - + -
236D ALA 2.9 17.4 + - - +
237D VAL 3.8 2.7 - - - +
239D LEU* 1.3 76.4 - - - +
241D SER* 1.3 57.9 + - - +
243D LEU* 3.2 1.3 + - - +
244D LEU* 2.8 39.3 + - + +
284D LEU* 5.0 1.1 - - + -
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Residues in contact with SER 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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237D VAL 2.9 19.5 + - - -
238D MSE 3.6 5.2 - - - -
240D ALA* 1.3 78.5 - - - +
242D ALA* 1.3 62.2 + - - +
244D LEU* 3.5 3.9 + - - +
245D ARG* 3.1 43.6 + - - +
253D ALA* 3.6 9.7 - - - -
256D HIS* 2.7 33.8 + - - -
284D LEU* 3.9 12.5 - - - +
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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 MSE 3.1 15.0 + - - +
239D LEU* 3.3 6.9 + - + +
241D SER* 1.3 78.4 - - - +
243D LEU* 1.3 63.5 + - + +
245D ARG* 3.3 4.7 + - - +
246D GLY 3.0 4.7 + - - -
247D VAL* 3.0 53.4 + - + +
248D ALA 4.1 1.3 - - - -
249D PRO* 4.0 28.5 - - + -
253D ALA* 4.6 1.8 - - + -
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Residues in contact with LEU 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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-1D LEU* 4.0 33.0 - - + +
3D VAL* 3.8 27.8 - - + -
47D LEU* 4.8 0.9 - - + -
52D ILE* 3.9 26.9 - - + -
132D ILE* 3.9 18.6 - - + -
239D LEU* 2.9 40.4 + - + +
240D ALA 3.5 3.8 - - - +
242D ALA* 1.3 77.6 - - + +
244D LEU* 1.3 64.4 + - - +
246D GLY* 2.9 15.7 + - - -
247D VAL 5.1 1.8 - - - +
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Residues in contact with LEU 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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50D CYS 3.8 15.5 - - - +
51D GLY* 5.2 4.9 - - - +
52D ILE* 3.9 18.2 - - + -
240D ALA* 2.8 26.6 + - + +
241D SER* 3.9 4.7 - - - +
243D LEU* 1.3 73.8 - - - +
245D ARG* 1.3 64.1 + - + +
246D GLY 3.7 0.3 + - - -
284D LEU* 3.6 35.2 - - + -
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Residues in contact with ARG 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 SER* 3.1 39.8 + - - +
242D ALA* 4.1 4.1 - - - +
243D LEU 3.1 0.8 - - - -
244D LEU* 1.3 81.5 - - + +
246D GLY* 1.3 62.5 + - - +
247D VAL* 3.4 19.3 + - + +
250D ASP* 3.1 39.2 + - - -
252D LEU* 3.8 28.8 - - - +
253D ALA* 3.5 14.1 - - - +
256D HIS* 4.3 5.6 - - - -
284D LEU 5.5 2.7 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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