Contacts of the helix formed by residues 250 - 266 (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 ASP 250 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208D LEU* 3.7 12.8 - - - -
210D GLN* 5.5 1.1 - - - +
215D GLN* 5.7 0.7 - - - +
245D ARG* 3.1 41.0 + - - -
247D VAL* 3.5 13.3 - - + +
248D ALA 3.9 6.7 - - - +
249D PRO* 1.3 75.4 - - - +
251D ALA* 1.3 66.2 + - - +
252D LEU* 3.5 5.2 + - - -
253D ALA* 3.0 15.2 + - - +
254D LEU* 3.3 13.2 + - - +
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Residues in contact with ALA 251 (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 LEU* 3.8 8.1 - - - +
215D GLN* 3.2 29.3 + - + +
217D CYS* 4.9 3.2 - - - +
250D ASP* 1.3 74.8 - - - +
252D LEU* 1.3 61.3 + - - +
254D LEU* 3.3 10.7 + - - +
255D ALA* 3.2 20.1 + - - +
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Residues in contact with LEU 252 (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 ARG* 3.8 31.9 - - - +
250D ASP* 3.3 9.2 + - - +
251D ALA* 1.3 76.6 - - - +
253D ALA* 1.3 65.9 + - - +
255D ALA* 3.2 11.2 + - + -
256D HIS* 3.0 50.8 + - + +
285D THR 5.8 2.0 - - - +
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Residues in contact with ALA 253 (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 3.5 35.7 - - + +
241D SER* 3.6 13.2 - - - +
242D ALA* 4.4 2.9 - - + +
245D ARG* 3.5 8.0 - - - +
249D PRO* 4.6 2.7 - - + -
250D ASP* 3.0 30.2 + - - +
252D LEU* 1.3 76.7 - - - +
254D LEU* 1.3 58.3 + - - +
256D HIS* 3.3 3.3 + - - +
257D ALA* 3.0 27.9 + - - +
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Residues in contact with LEU 254 (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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198D VAL* 4.3 11.0 - - + -
206D ALA* 4.2 6.5 - - + +
207D TRP 4.0 17.0 - - - +
208D LEU* 3.7 30.7 - - + +
215D GLN 4.8 1.3 - - - +
217D CYS* 3.6 26.5 - - + -
234D PHE* 3.8 14.2 - - + -
238D MSE 4.0 25.1 - - + -
249D PRO* 5.1 0.7 - - + -
250D ASP 3.3 17.4 + - - +
251D ALA* 3.6 10.8 - - - +
252D LEU 3.2 0.4 - - - -
253D ALA* 1.3 80.9 - - + +
255D ALA* 1.3 56.1 + - - +
257D ALA* 3.4 7.4 + - - +
258D SER* 2.9 32.4 + - - -
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Residues in contact with ALA 255 (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 CYS* 3.7 10.3 - - - -
251D ALA 3.2 13.2 + - - +
252D LEU* 3.2 21.3 + - + +
254D LEU* 1.3 77.2 - - - +
256D HIS* 1.3 61.9 + - + +
258D SER* 3.3 1.4 + - - -
259D ARG* 2.8 54.3 + - - +
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Residues in contact with HIS 256 (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* 3.7 5.8 - - + +
241D SER* 2.7 27.9 + - - +
245D ARG* 4.3 4.9 - - - -
252D LEU* 3.0 46.3 + - + +
253D ALA 3.6 7.2 - - - +
255D ALA* 1.3 75.3 - - + +
257D ALA* 1.3 65.9 + - - +
259D ARG* 3.2 7.3 + - + +
260D ALA 3.2 17.2 + - - -
283D LEU* 3.4 39.4 + - + +
284D LEU* 3.4 36.3 + - + +
285D THR 4.4 7.0 - - - -
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Residues in contact with ALA 257 (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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234D PHE* 3.2 50.4 - - + +
237D VAL* 3.7 13.1 - - - +
238D MSE 3.8 10.1 - - + +
253D ALA 3.0 16.8 + - - +
254D LEU 3.6 1.1 - - - +
256D HIS* 1.3 76.7 - - - +
258D SER* 1.3 56.5 + - - +
260D ALA* 3.3 1.7 + - - +
261D ALA* 2.9 31.0 + - - +
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Residues in contact with SER 258 (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 GLY* 5.8 0.2 - - - -
206D ALA* 5.8 0.2 - - - +
217D CYS* 3.5 15.0 + - - -
218D PRO 3.7 12.5 + - - -
219D ALA* 4.4 0.5 - - - -
220D VAL* 3.7 21.5 + - - +
234D PHE* 3.6 10.1 - - - -
254D LEU 2.9 17.3 + - - -
255D ALA 3.5 9.9 - - - -
256D HIS 3.2 0.2 - - - -
257D ALA* 1.3 77.2 - - - +
259D ARG* 1.3 63.4 + - - +
261D ALA* 3.4 2.1 + - - +
262D ALA* 3.0 24.3 + - - +
900D ATP 3.8 18.4 + - - -
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Residues in contact with ARG 259 (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 CYS* 5.1 1.0 - - - -
218D PRO 4.9 5.1 + - - -
220D VAL* 3.5 31.4 - - + +
255D ALA* 2.8 44.8 + - - +
256D HIS* 3.2 10.7 + - + +
258D SER* 1.3 80.0 - - - +
260D ALA* 1.3 62.2 + - - +
262D ALA* 3.3 15.6 + - - +
263D ILE* 3.4 13.0 + - - +
283D LEU* 3.9 20.6 - - + +
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Residues in contact with ALA 260 (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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233D THR* 3.7 9.3 - - + +
237D VAL* 3.5 32.1 - - + -
256D HIS 3.2 5.5 + - - +
257D ALA 3.8 4.5 - - - +
259D ARG* 1.3 76.8 - - - +
261D ALA* 1.3 65.9 + - - +
263D ILE* 2.9 20.3 + - - +
264D THR* 3.2 12.6 + - - -
275D PRO* 4.3 3.3 - - + +
280D LEU* 4.2 5.8 - - + -
283D LEU* 3.4 20.4 - - + +
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Residues in contact with ALA 261 (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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230D ALA* 3.9 13.0 - - - +
233D THR* 3.7 13.4 - - - +
234D PHE* 4.4 3.4 - - + +
257D ALA 2.9 17.5 + - - +
258D SER 3.8 2.9 - - - +
260D ALA* 1.3 76.0 - - - +
262D ALA* 1.3 63.2 + - - +
264D THR* 3.1 5.1 + - - -
265D VAL* 2.9 29.0 + - - +
900D ATP 3.2 37.5 - - - +
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Residues in contact with ALA 262 (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 VAL* 3.7 35.9 - - + +
221D PRO 5.1 0.2 - - - +
222D ALA* 3.7 8.3 - - + +
258D SER 3.0 13.7 + - - +
259D ARG 3.3 11.0 - - - +
261D ALA* 1.3 77.6 - - - +
263D ILE* 1.3 60.5 + - + +
265D VAL* 2.9 26.8 - - - +
266D SER* 3.2 11.6 + - - -
900D ATP 4.4 3.8 + - + -
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Residues in contact with ILE 263 (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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259D ARG 3.6 15.3 - - - +
260D ALA* 2.9 13.2 + - - +
262D ALA* 1.3 78.8 - - + +
264D THR* 1.3 61.6 + - - +
266D SER* 2.6 22.9 + - - +
267D ARG* 3.3 48.2 + - - +
273D ALA 4.6 0.2 - - - +
275D PRO* 3.8 30.1 - - + -
279D GLU* 4.0 20.4 - - + +
283D LEU* 4.6 8.7 - - + -
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Residues in contact with THR 264 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226D ASP 3.2 3.3 - - - +
228D THR 3.3 24.7 - - - +
229D GLY 3.8 9.2 - - - -
230D ALA* 3.9 3.4 - - - +
233D THR* 2.8 37.1 + - - +
260D ALA 3.2 0.6 + - - -
261D ALA 3.1 9.5 + - - -
263D ILE* 1.3 79.6 - - - +
265D VAL* 1.3 61.9 + - - +
267D ARG* 3.1 22.0 + - - +
273D ALA* 3.6 14.5 - - + +
274D PHE* 3.9 13.2 - - + -
275D PRO* 3.5 13.2 - - - +
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Residues in contact with VAL 265 (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 ALA* 3.6 17.5 - - + -
224D ALA* 3.4 5.5 - - - -
225D LEU 2.7 30.1 + - - -
226D ASP 3.1 18.1 + - - +
227D THR* 4.2 13.9 - - + -
230D ALA* 3.7 25.6 - - + -
261D ALA 2.9 16.3 + - - +
262D ALA* 2.9 34.8 - - - +
264D THR* 1.3 74.7 - - - +
266D SER* 1.3 49.7 + - - +
267D ARG 3.2 0.4 - - - -
900D ATP 3.7 32.8 - - + +
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Residues in contact with SER 266 (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 ALA* 4.9 1.3 - - - -
223D GLU* 4.8 18.5 - - - +
224D ALA 4.3 5.2 - - - +
225D LEU* 3.6 24.0 - - - +
262D ALA 3.2 13.2 + - - -
263D ILE* 2.6 23.4 + - - +
265D VAL* 1.3 77.9 - - - +
267D ARG* 1.3 67.5 + - - +
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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