Contacts of the helix formed by residues 250 - 267 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208C LEU* 3.6 12.6 - - - -
210C GLN* 5.0 1.1 - - - +
215C GLN* 5.4 0.4 - - - -
245C ARG* 2.8 45.2 + - - -
247C VAL* 3.6 8.2 - - + +
248C ALA 3.8 8.0 - - - +
249C PRO* 1.3 75.4 - - - +
251C ALA* 1.3 65.2 + - - +
252C LEU* 3.9 6.8 - - - +
253C ALA* 3.0 15.9 + - - +
254C LEU* 3.1 16.1 - - - +
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Residues in contact with ALA 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C LEU* 3.9 8.4 - - - +
215C GLN* 4.3 26.7 + - + +
217C CYS* 4.8 3.7 - - - +
250C ASP* 1.3 76.2 - - - +
252C LEU* 1.3 63.9 + - - +
254C LEU* 3.2 9.1 + - - +
255C ALA* 3.1 20.4 + - - +
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Residues in contact with LEU 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245C ARG* 3.7 37.7 - - - +
250C ASP* 3.2 5.8 + - - +
251C ALA* 1.3 78.4 - - - +
253C ALA* 1.3 63.5 + - - +
255C ALA* 3.1 12.7 + - + +
256C HIS* 2.9 51.3 + - + +
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Residues in contact with ALA 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238C MSE 3.5 36.1 - - + +
241C SER* 3.6 8.7 - - - +
242C ALA 4.3 2.2 - - - +
245C ARG* 3.3 12.5 - - - +
249C PRO* 4.4 2.7 - - + -
250C ASP* 3.0 30.9 + - - +
252C LEU* 1.3 75.0 - - - +
254C LEU* 1.3 59.0 + - - +
256C HIS* 3.3 3.3 + - - +
257C ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C VAL* 4.8 2.9 - - + -
206C ALA* 4.1 8.1 - - + +
207C TRP 4.1 4.9 - - - +
208C LEU* 3.7 43.7 - - + +
215C GLN 4.9 0.7 - - - +
217C CYS* 3.7 25.4 - - + -
234C PHE* 3.8 21.5 - - + -
238C MSE 4.1 20.6 - - + -
249C PRO* 5.0 0.7 - - + -
250C ASP 3.1 27.5 + - - +
251C ALA* 3.7 8.5 - - - +
252C LEU 3.2 0.6 - - - -
253C ALA* 1.3 76.0 - - + +
255C ALA* 1.3 57.6 + - - +
257C ALA* 3.6 7.0 - - - +
258C SER* 2.7 37.2 + - - -
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Residues in contact with ALA 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217C CYS* 3.7 14.3 - - - -
220C VAL* 5.0 0.2 - - - +
251C ALA 3.1 12.2 + - - +
252C LEU* 3.1 19.7 + - + +
254C LEU* 1.3 74.8 - - - +
256C HIS* 1.3 67.2 + - + +
258C SER* 3.2 4.4 + - - -
259C ARG* 3.1 30.7 + - + +
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Residues in contact with HIS 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237C VAL* 3.9 6.8 - - + +
241C SER* 2.6 28.1 + - - +
245C ARG* 4.3 4.5 - - - -
252C LEU* 2.9 44.6 + - + +
253C ALA 3.6 7.0 - - - +
255C ALA* 1.3 77.8 - - + +
257C ALA* 1.3 62.3 + - - +
259C ARG* 3.1 17.0 + - - +
260C ALA* 3.0 21.8 + - - +
283C LEU* 3.5 25.3 + - + +
284C LEU* 3.5 44.2 + - + +
285C THR 4.5 5.6 + - - -
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Residues in contact with ALA 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C PHE* 3.3 49.7 - - + +
237C VAL* 3.9 12.7 - - - +
238C MSE 3.8 8.3 - - + +
253C ALA 2.9 18.3 + - - +
254C LEU 3.6 1.3 - - - +
256C HIS* 1.3 76.5 - - - +
258C SER* 1.3 56.6 + - - +
260C ALA* 3.3 1.7 + - - +
261C ALA* 2.9 32.2 + - - +
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Residues in contact with SER 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205C GLY* 5.9 0.3 - - - -
206C ALA* 5.7 0.5 - - - +
217C CYS* 3.4 15.0 + - - +
218C PRO 3.7 13.6 + - - -
220C VAL* 3.7 20.5 + - - +
234C PHE* 3.6 9.2 - - - -
254C LEU 2.7 24.3 + - - -
255C ALA* 3.2 8.0 + - - -
257C ALA* 1.3 76.7 - - - +
259C ARG* 1.3 62.8 + - - +
261C ALA* 3.5 1.6 + - - +
262C ALA* 3.1 23.9 + - - +
900C ATP 3.9 18.6 + - - -
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Residues in contact with ARG 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C VAL* 3.7 23.5 - - + +
255C ALA* 3.1 19.8 + - + +
256C HIS* 3.1 14.1 + - - +
258C SER* 1.3 76.0 - - - +
260C ALA* 1.3 62.5 + - - +
262C ALA* 3.5 4.0 + - - +
263C ILE* 3.5 24.4 + - - +
282C ALA 5.3 2.0 + - - -
283C LEU* 3.2 53.1 + - + +
285C THR 5.9 0.8 + - - -
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Residues in contact with ALA 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233C THR* 3.6 8.6 - - + +
237C VAL* 3.5 32.8 - - + -
256C HIS 3.0 11.1 + - - +
257C ALA 3.7 6.1 - - - +
259C ARG* 1.3 76.3 - - - +
261C ALA* 1.3 65.1 + - - +
263C ILE* 3.1 15.7 + - - +
264C THR 3.2 8.8 + - - -
275C PRO* 3.6 9.5 - - + +
280C LEU* 4.3 5.4 - - + -
283C LEU* 3.6 19.2 - - + +
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Residues in contact with ALA 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C ALA* 3.8 15.7 - - - +
233C THR* 3.7 11.1 - - - +
234C PHE* 4.3 5.2 - - + +
257C ALA 2.9 18.1 + - - +
258C SER 4.0 2.0 - - - +
260C ALA* 1.3 76.2 - - - +
262C ALA* 1.3 62.0 + - - +
264C THR* 3.3 3.6 + - - -
265C VAL* 3.0 29.0 + - - +
900C ATP 3.2 34.8 - - - +
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Residues in contact with ALA 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C VAL* 3.8 34.1 - - + +
221C PRO 4.7 0.7 - - - +
222C ALA* 3.8 8.9 - - + +
258C SER 3.1 18.3 + - - +
259C ARG 3.6 6.7 - - - +
261C ALA* 1.3 73.4 - - - +
263C ILE* 1.3 67.5 + - + +
265C VAL* 3.0 25.5 - - - +
266C SER* 3.1 11.1 + - - -
900C ATP 4.5 4.5 + - + -
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Residues in contact with ILE 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C ARG 3.5 15.9 + - - +
260C ALA 3.1 6.4 + - - +
262C ALA* 1.3 77.6 - - + +
264C THR* 1.3 63.8 + - - +
266C SER* 2.6 24.9 + - - +
267C ARG* 3.2 51.2 + - - +
273C ALA 4.4 1.3 - - - +
275C PRO* 3.8 27.4 - - + -
279C GLU* 4.8 13.2 - - + +
283C LEU* 4.3 18.4 - - + -
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Residues in contact with THR 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C ASP 3.2 2.9 - - - +
228C THR 3.4 24.9 - - - +
229C GLY 3.8 9.9 - - - -
230C ALA* 3.9 4.0 - - + +
233C THR* 2.8 30.8 + - - +
260C ALA 3.2 2.9 + - - -
261C ALA* 3.3 8.9 + - - -
263C ILE* 1.3 79.5 - - - +
265C VAL* 1.3 62.2 + - - +
267C ARG* 3.1 21.1 + - - +
273C ALA* 3.6 14.1 - - + +
274C PHE* 3.6 13.2 - - + -
275C PRO* 3.5 18.0 - - - +
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Residues in contact with VAL 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C ALA* 3.6 21.8 - - + -
223C GLU 3.8 2.5 - - - +
224C ALA* 4.4 7.9 - - - -
225C LEU 2.9 23.7 + - - -
226C ASP 3.1 19.4 + - - +
227C THR* 4.2 12.1 - - + -
230C ALA* 3.7 26.0 - - + -
261C ALA 3.0 15.6 + - - +
262C ALA* 3.0 22.0 - - - +
264C THR* 1.3 76.0 - - - +
266C SER* 1.3 58.2 + - - +
267C ARG 3.2 0.4 - - - -
900C ATP 3.9 30.3 - - + +
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Residues in contact with SER 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C ALA* 4.9 2.2 - - - -
223C GLU* 3.2 23.3 - - - -
225C LEU* 3.2 24.5 - - - +
262C ALA 3.1 11.6 + - - -
263C ILE* 2.6 25.2 + - - +
265C VAL* 1.3 78.1 - - - +
267C ARG* 1.3 66.0 + - - +
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Residues in contact with ARG 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C LEU* 5.0 0.9 - - - -
226C ASP* 3.2 17.1 - - - +
263C ILE* 3.3 31.9 - - - +
264C THR 3.1 13.3 + - - +
265C VAL 3.2 0.6 - - - -
266C SER* 1.3 87.7 + - - +
268C ARG* 1.3 65.4 + - - +
272C SER 4.8 5.4 + - - +
273C ALA* 3.4 34.9 - - + +
274C PHE 3.8 12.7 + - - -
279C GLU* 2.6 44.1 + - - -
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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
------------------------------------------------------------
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