Contacts of the helix formed by residues 229 - 246 (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 GLY 229 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ASN* 4.6 0.4 - - - -
227C THR 3.2 0.6 + - - -
228C THR* 1.3 79.9 - - - +
230C ALA* 1.3 59.0 + - - +
231C GLY 3.3 2.5 - - - -
232C ASP* 3.3 21.9 + - - +
233C THR* 2.8 34.0 + - - -
264C THR* 3.8 3.8 - - - -
274C PHE* 4.0 14.8 - - - -
501C GOL 4.2 4.1 + - - -
900C ATP 3.7 8.8 + - - -
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Residues in contact with ALA 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C THR* 3.0 19.7 + - - +
228C THR 3.3 1.2 + - - -
229C GLY* 1.3 76.5 - - - +
231C GLY* 1.3 59.0 + - - +
233C THR* 3.2 4.9 + - - -
234C PHE* 2.9 28.8 + - - +
261C ALA* 3.8 4.7 - - - +
264C THR* 3.9 9.8 - - - +
265C VAL* 3.7 24.5 - - + -
900C ATP 3.4 31.0 + - + +
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Residues in contact with GLY 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LYS* 5.3 1.8 - - - -
43C GLN* 5.3 0.4 - - - -
161C ASN* 6.0 1.5 - - - -
180C VAL* 5.5 2.8 - - - +
200C THR* 5.8 2.0 - - - -
230C ALA* 1.3 77.0 - - - +
232C ASP* 1.3 59.3 + - - +
234C PHE* 3.3 2.0 + - - +
235C LEU* 2.9 30.1 + - - +
900C ATP 3.0 47.9 + - - -
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Residues in contact with ASP 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LYS* 2.8 35.5 + - - +
42C ASN* 3.0 45.5 + - + -
43C GLN* 2.9 27.6 - - + +
46C ILE* 4.3 3.3 - - + +
229C GLY* 3.3 12.0 + - - +
230C ALA 3.3 0.6 - - - -
231C GLY* 1.3 73.0 - - - +
233C THR* 1.3 66.1 + - - +
235C LEU* 3.5 1.2 + - - +
236C ALA* 3.0 26.7 + - - +
274C PHE* 5.2 0.2 - - + -
501C GOL 3.3 15.4 + - - -
900C ATP 4.2 1.5 + - - -
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Residues in contact with THR 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ILE* 3.3 26.3 - - + +
229C GLY 2.8 22.7 + - - -
230C ALA 3.5 4.9 - - - -
232C ASP* 1.3 78.0 - - - +
234C PHE* 1.3 62.2 + - - +
236C ALA* 3.8 0.5 - - - +
237C VAL* 2.9 29.2 + - + +
260C ALA* 3.6 34.1 - - + +
261C ALA* 3.7 3.4 - - - +
264C THR* 2.8 28.7 + - - +
274C PHE* 3.6 2.9 - - - -
275C PRO* 4.3 5.8 - - + -
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Residues in contact with PHE 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C VAL* 5.2 2.5 - - + -
198C VAL* 3.9 24.0 - - + -
200C THR* 3.9 13.0 - - + -
206C ALA* 3.7 21.8 - - + -
230C ALA 2.9 17.0 + - - +
231C GLY* 3.6 4.7 - - - +
232C ASP 3.3 0.2 - - - -
233C THR* 1.3 77.2 - - - +
235C LEU* 1.3 66.6 + - - +
238C MSE 3.0 34.7 + - + +
254C LEU* 3.9 20.4 - - + -
257C ALA* 3.3 39.7 - - + +
258C SER* 3.6 20.2 - - - -
261C ALA* 4.3 1.1 - - + +
900C ATP 3.6 35.2 - - - -
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Residues in contact with LEU 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C GLN* 3.6 29.2 - - + +
134C LEU* 4.0 23.1 - - + -
159C VAL* 4.9 6.1 - - + -
161C ASN* 3.5 34.8 - - + -
180C VAL* 3.9 32.8 - - + -
231C GLY 2.9 17.3 + - - +
232C ASP 3.9 2.5 - - - +
234C PHE* 1.3 80.4 - - - +
236C ALA* 1.3 70.2 + - - +
238C MSE 3.7 6.0 - - + +
239C LEU* 3.0 31.5 + - + +
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Residues in contact with ALA 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C GLN* 3.7 18.2 - - - +
46C ILE* 3.5 32.8 - - + -
47C LEU* 3.3 16.9 - - + +
232C ASP 3.0 18.7 + - - +
233C THR 3.8 0.2 - - - +
235C LEU* 1.3 84.0 - - - +
237C VAL* 1.3 57.8 + - - +
240C ALA* 2.9 29.3 + - - +
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Residues in contact with VAL 237 (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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46C ILE* 3.8 19.7 - - + -
50C CYS* 4.2 3.6 - - - -
233C THR* 2.9 19.1 + - + +
236C ALA* 1.3 73.3 - - - +
238C MSE 1.3 61.1 + - - +
240C ALA* 4.1 5.2 - - - -
241C SER* 2.8 29.1 + - - -
256C HIS* 3.9 15.0 - - + +
257C ALA* 3.9 22.9 - - - +
260C ALA* 3.5 23.8 - - + -
280C LEU* 3.8 14.8 - - + -
283C LEU* 5.5 2.0 - - + -
284C LEU* 4.1 12.6 - - + -
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Residues in contact with MSE 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C VAL* 6.0 1.1 - - + -
178C ILE* 4.2 11.2 - - + -
180C VAL* 4.2 20.4 - - + -
198C VAL* 3.6 33.4 - - + -
234C PHE* 3.0 23.5 + - + +
235C LEU* 3.7 7.6 - - + +
237C VAL* 1.3 77.4 - - - +
239C LEU* 1.3 79.4 + - + +
241C SER 3.4 0.2 + - - -
242C ALA* 3.1 21.3 + - - +
249C PRO* 3.9 26.0 - - + -
253C ALA* 3.5 33.9 - - + +
254C LEU* 4.1 15.9 - - + -
257C ALA* 3.8 8.6 - - + +
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Residues in contact with LEU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C VAL* 4.7 2.2 - - + -
47C LEU* 4.1 22.4 - - + -
132C ILE* 4.3 17.7 - - + -
134C LEU* 4.7 10.8 - - + -
159C VAL* 4.5 18.4 - - + -
178C ILE* 4.4 22.0 - - + -
235C LEU* 3.0 24.1 + - + +
236C ALA 3.8 3.6 - - - +
238C MSE 1.3 88.7 - - + +
240C ALA* 1.3 56.6 + - - +
242C ALA* 3.4 6.8 + - + +
243C LEU* 2.9 57.4 + - + +
249C PRO* 5.4 0.7 - - + -
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Residues in contact with ALA 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 4.0 4.2 - - + +
50C CYS* 3.5 37.9 - - + -
52C ILE* 3.9 20.2 - - + -
236C ALA 2.9 19.4 + - - +
237C VAL 3.7 2.2 - - - +
239C LEU* 1.3 76.3 - - - +
241C SER* 1.3 58.1 + - - +
243C LEU* 3.2 1.4 + - - +
244C LEU* 2.8 38.7 + - + +
284C LEU* 5.0 1.1 - - + -
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Residues in contact with SER 241 (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 2.8 21.5 + - - -
238C MSE 3.7 4.5 - - - -
240C ALA* 1.3 72.4 - - - +
242C ALA* 1.3 63.8 + - - +
244C LEU* 3.4 4.3 + - - +
245C ARG* 3.0 45.1 + - - +
253C ALA* 3.6 9.5 - - - -
256C HIS* 2.6 34.3 + - - -
284C LEU* 3.8 12.7 - - - +
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Residues in contact with ALA 242 (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 3.1 14.4 + - - +
239C LEU* 3.7 5.6 - - + +
241C SER* 1.3 77.5 - - - +
243C LEU* 1.3 61.6 + - + +
245C ARG* 3.2 5.4 + - - +
246C GLY 2.8 25.3 + - - -
247C VAL* 3.0 37.3 + - - +
248C ALA 4.1 1.1 - - - +
249C PRO* 3.9 28.7 - - + -
253C ALA* 4.6 1.1 - - + -
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Residues in contact with LEU 243 (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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-1C LEU* 4.5 21.3 - - + +
3C VAL* 3.9 25.4 - - + -
47C LEU* 5.0 0.7 - - + -
52C ILE* 3.8 24.7 - - + -
132C ILE* 3.7 21.1 - - + -
239C LEU* 2.9 42.2 + - + +
240C ALA* 3.5 4.0 - - - +
242C ALA* 1.3 78.6 - - + +
244C LEU* 1.3 61.5 + - - +
246C GLY* 3.1 13.8 + - - +
247C VAL 5.1 2.9 - - - +
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Residues in contact with LEU 244 (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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50C CYS 3.8 15.9 - - - +
51C GLY* 5.0 6.3 - - - +
52C ILE* 4.0 18.6 - - + -
240C ALA* 2.8 25.5 + - + +
241C SER* 3.8 4.9 - - - +
243C LEU* 1.3 74.5 - - - +
245C ARG* 1.3 63.3 + - + +
246C GLY 3.3 0.4 + - - -
284C LEU* 3.5 37.5 - - + -
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Residues in contact with ARG 245 (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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241C SER* 3.0 42.7 + - - +
242C ALA* 4.0 3.7 - - - +
244C LEU* 1.3 80.6 - - + +
246C GLY* 1.3 64.1 + - - +
247C VAL* 3.4 20.6 + - + +
250C ASP* 2.8 43.6 + - - -
252C LEU* 3.7 29.7 - - - +
253C ALA* 3.3 14.3 - - - +
256C HIS* 4.3 4.6 - - - -
284C LEU 5.8 1.6 - - - -
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Residues in contact with GLY 246 (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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242C ALA 2.8 7.1 + - - -
243C LEU* 3.1 13.2 + - - -
244C LEU 3.3 1.0 + - - -
245C ARG* 1.3 78.9 - - - +
247C VAL* 1.3 60.5 + - - +
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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
------------------------------------------------------------
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