Contacts of the helix formed by residues 226 - 240 (chain C) in PDB entry 4IXU
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 226 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A ASP 6.1 0.7 - - - -
222C ILE* 2.8 19.9 + - - -
223C ASP 4.6 1.0 + - - -
224C ARG 3.5 1.2 - - - -
225C LEU* 1.3 83.2 - - - +
227C ILE* 1.3 65.0 + - - -
228C GLN 3.2 4.1 + - - -
229C LYS 3.3 0.6 + - - -
230C VAL* 3.1 21.2 + - - +
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Residues in contact with ILE 227 (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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223A ASP* 4.8 16.4 + - + +
196C ILE* 4.4 0.9 - - + -
222C ILE* 4.1 30.9 - - + +
226C GLY* 1.3 69.8 - - - -
228C GLN* 1.3 67.4 + - - +
230C VAL* 3.6 16.6 - - + +
231C MET* 2.9 25.6 + - + +
271C LEU* 4.8 0.2 - - + -
275C GLU* 4.0 32.9 + - + +
278C TYR* 3.8 29.4 - - + -
279C ILE* 3.8 35.7 - - + -
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Residues in contact with GLN 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ASP 5.0 2.3 + - - +
224A ARG* 3.1 67.9 - - - +
225A LEU* 5.9 0.3 - - - +
226C GLY 3.2 1.4 - - - -
227C ILE* 1.3 82.4 - - - +
229C LYS* 1.3 68.9 + - + +
231C MET* 3.2 2.8 + - - +
232C GLU* 2.9 48.3 + - + +
278C TYR* 3.6 27.7 + - + +
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Residues in contact with LYS 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C LEU* 3.6 44.6 + - + +
226C GLY 3.3 2.4 + - - +
228C GLN* 1.3 81.4 - - + +
230C VAL* 1.3 67.4 + - - +
232C GLU* 3.5 20.7 - - - +
233C ARG* 2.9 43.3 + - + +
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Residues in contact with VAL 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C ILE* 4.2 22.4 - - + -
217C PHE* 3.7 46.0 - - + -
221C ASP 4.3 0.2 - - - +
222C ILE* 4.0 24.0 - - + -
225C LEU* 4.1 14.6 - - + -
226C GLY 3.1 17.8 + - - +
227C ILE* 3.6 14.8 - - + +
228C GLN 3.3 0.2 - - - -
229C LYS* 1.3 77.7 - - - +
231C MET* 1.3 56.6 + - - +
233C ARG* 3.4 1.6 + - - +
234C THR* 2.8 36.2 + - - +
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Residues in contact with MET 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C VAL* 5.2 0.7 - - + -
196C ILE* 3.5 31.2 - - + -
227C ILE* 2.9 23.4 + - + +
228C GLN 3.8 3.4 - - - +
230C VAL* 1.3 79.7 - - - +
232C GLU* 1.3 63.2 + - - +
234C THR* 3.3 5.1 + - + -
235C PHE* 3.0 60.2 + - + -
278C TYR* 3.9 18.4 - - + +
279C ILE* 3.9 37.5 - - + +
282C GLU* 3.9 20.6 - - + +
283C ILE* 4.6 5.4 - - + -
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Residues in contact with GLU 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A ARG* 5.4 0.5 + - - -
228C GLN* 2.9 52.3 + - + +
229C LYS* 3.2 22.1 + - - +
231C MET* 1.3 77.8 - - - +
233C ARG* 1.3 59.6 + - + +
235C PHE* 3.4 5.0 + - - +
236C ASP* 3.0 27.0 + - - +
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Residues in contact with ARG 233 (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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217C PHE* 3.6 30.8 - - + -
225C LEU* 3.7 36.0 - - - +
229C LYS* 2.9 32.7 + - - +
232C GLU* 1.3 76.1 - - + +
234C THR* 1.3 65.9 + - - +
236C ASP* 3.2 8.2 + - - +
237C LEU* 2.9 30.2 + - + +
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Residues in contact with THR 234 (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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140C VAL* 4.1 22.2 - - + -
194C VAL* 3.6 24.8 - - + +
196C ILE* 3.8 14.3 - - + +
217C PHE* 3.4 24.1 - - - -
230C VAL 2.8 23.7 + - - -
231C MET* 3.5 9.9 - - + -
232C GLU 3.3 0.2 - - - -
233C ARG* 1.3 77.5 - - - +
235C PHE* 1.3 67.6 + - + +
237C LEU* 3.3 5.0 + - - +
238C LEU* 3.0 30.0 + - + +
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Residues in contact with PHE 235 (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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140C VAL* 4.8 3.6 - - + -
231C MET* 3.0 42.9 + - + +
232C GLU* 4.0 5.2 - - - +
234C THR* 1.3 82.3 - - + +
236C ASP* 1.3 60.5 + - - +
238C LEU* 4.3 4.3 - - + +
239C ILE* 2.7 53.5 + - + +
240C GLY 3.0 5.0 + - - -
246C ILE* 4.2 9.0 - - + -
282C GLU* 3.6 41.5 - - + -
283C ILE* 3.9 18.2 - - + -
286C THR* 3.5 26.2 - - + -
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Residues in contact with ASP 236 (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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232C GLU 3.0 17.4 + - - +
233C ARG* 3.2 8.9 + - - +
235C PHE* 1.3 77.2 - - - +
237C LEU* 1.3 61.9 + - + +
240C GLY* 3.1 32.6 + - - +
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Residues in contact with LEU 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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191C ALA 4.4 7.9 - - - +
194C VAL* 4.1 15.5 - - + -
215C GLN* 3.7 46.2 - - + +
217C PHE* 4.2 19.3 - - + -
233C ARG* 2.9 19.5 + - + +
234C THR 3.5 6.5 - - - +
235C PHE 3.2 0.2 - - - -
236C ASP* 1.3 79.9 - - + +
238C LEU* 1.3 62.7 + - + +
244C ARG* 5.1 1.7 + - - -
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Residues in contact with LEU 238 (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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138C CYS* 3.8 26.0 - - + -
139C VAL 3.8 11.7 - - - +
140C VAL* 3.7 30.1 - - + -
191C ALA 3.7 12.6 - - - +
192C SER* 3.7 31.2 - - - +
194C VAL* 3.7 22.2 - - + -
234C THR* 3.0 19.6 + - + +
235C PHE* 4.3 5.2 - - + +
237C LEU* 1.3 80.2 - - - +
239C ILE* 1.3 62.2 + - + +
240C GLY 3.7 0.7 - - - -
241C LYS 5.5 0.2 + - - -
242C ARG* 5.5 0.9 + - - +
244C ARG* 3.1 31.7 + - - +
246C ILE* 6.1 0.2 - - + -
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Residues in contact with ILE 239 (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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138C CYS* 4.3 9.6 - - - -
235C PHE* 2.7 48.5 + - + +
238C LEU* 1.3 79.1 - - + +
240C GLY* 1.3 62.3 + - - +
241C LYS 3.2 4.0 + - - +
242C ARG 3.3 27.2 + - - +
243C GLN* 4.8 9.2 + - - +
244C ARG* 3.8 30.3 - - + +
246C ILE* 4.6 4.3 - - + -
286C THR* 4.2 13.0 - - + -
288C LEU* 3.9 21.1 - - + -
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Residues in contact with GLY 240 (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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235C PHE 3.0 6.9 + - - -
236C ASP* 3.1 35.5 + - - +
238C LEU 3.7 1.0 - - - -
239C ILE* 1.3 78.4 - - - +
241C LYS* 1.3 64.5 + - - +
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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