Contacts of the helix formed by residues 226 - 239 (chain C) in PDB entry 6D6U
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 TYR 226 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C PRO* 3.5 27.9 - - + +
222C ILE* 2.9 53.3 + - + +
225C THR* 1.3 98.2 + - - +
227C MET* 1.3 70.3 - - + +
228C PRO 3.2 0.9 - - - -
229C SER* 3.3 15.0 + - - -
230C ILE* 3.6 20.1 + - + +
281C ILE* 4.4 17.9 - - + +
284C TYR* 3.4 41.9 - + + -
285C LEU* 6.3 1.1 - - + -
335C TYR* 3.8 18.0 + + - -
336C TRP* 4.2 24.1 - + + -
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Residues in contact with MET 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B Y01 3.8 42.6 - - + +
222C ILE* 4.0 3.1 + - - +
223C LEU* 3.7 31.6 + - + +
226C TYR* 1.3 77.9 - - - +
228C PRO* 1.3 69.9 - - + +
230C ILE* 3.1 24.2 + - + +
231C LEU* 2.9 36.5 + - + +
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Residues in contact with PRO 228 (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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410B Y01 4.3 20.2 - - + -
223C LEU 4.5 0.2 - - - +
224C GLN 4.3 9.0 - - - +
225C THR 3.3 19.5 - - - +
227C MET* 1.3 93.2 - - + +
229C SER* 1.3 57.5 + - - +
231C LEU* 3.2 13.1 + - + +
232C ILE* 2.9 34.0 + - - +
264C ILE* 4.2 19.1 - - + -
407C Y01 4.0 30.2 - - + +
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Residues in contact with SER 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C THR 5.0 2.3 + - - -
226C TYR 3.3 8.9 + - - -
227C MET 3.3 0.6 - - - -
228C PRO* 1.3 76.0 - - - +
230C ILE* 1.3 61.5 + - - +
232C ILE* 3.2 2.1 + - - +
233C THR* 2.9 33.0 + - - -
261C MET* 3.2 22.6 - - - +
264C ILE* 4.7 5.8 - - - +
284C TYR* 4.7 4.5 - - - -
285C LEU* 3.1 29.7 - - - +
288C CYS* 3.9 24.0 - - - +
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Residues in contact with ILE 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C TYR* 3.8 22.0 - - + +
227C MET* 3.1 25.0 + - + +
229C SER* 1.3 76.2 - - - +
231C LEU* 1.3 59.5 + - + +
233C THR* 3.3 6.7 + - - +
234C ILE* 2.9 51.4 + - + +
284C TYR* 3.3 27.4 - - + +
288C CYS* 5.8 0.2 - - - -
328C PHE* 4.6 20.6 - - + -
332C ASN* 6.0 1.3 - - - +
336C TRP* 6.2 2.7 - - + +
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Residues in contact with LEU 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B Y01 3.6 45.8 - - + -
227C MET* 2.9 30.3 + - + +
228C PRO* 3.5 14.1 - - + +
230C ILE* 1.3 78.2 - - + +
232C ILE* 1.3 58.6 + - + +
234C ILE* 3.3 13.5 + - + +
235C LEU* 2.9 29.3 + - - +
407C Y01 4.3 25.8 - - + +
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Residues in contact with ILE 232 (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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228C PRO 2.9 21.4 + - - +
229C SER* 3.2 7.6 + - - +
231C LEU* 1.3 78.1 - - + +
233C THR* 1.3 59.0 + - - +
235C LEU* 3.3 15.3 + - + +
236C SER* 2.9 27.2 + - - -
257C THR* 3.8 31.9 - - + +
260C THR* 3.7 26.9 - - + -
261C MET* 4.1 17.3 - - + -
264C ILE* 3.7 18.6 - - + -
292C VAL* 4.5 7.4 - - + -
407C Y01 4.9 18.2 - - + -
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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
----------------------------------------------------------
229C SER 2.9 16.6 + - - -
230C ILE 3.7 4.3 - - - -
232C ILE* 1.3 77.4 - - - +
234C ILE* 1.3 56.7 + - - +
236C SER* 2.4 25.8 + - - +
237C TRP* 2.9 38.3 + - + +
261C MET* 6.0 0.2 - - - -
288C CYS* 4.0 22.5 - - - +
291C PHE* 4.7 11.7 - - + -
292C VAL* 4.4 9.4 - - + +
328C PHE* 3.8 30.1 - - + -
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Residues in contact with ILE 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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230C ILE* 2.9 40.9 + - + +
231C LEU* 3.8 13.2 - - + +
233C THR* 1.3 77.0 - - - +
235C LEU* 1.3 57.9 + - - +
237C TRP* 3.0 32.3 + - + +
238C VAL* 2.9 33.3 + - + +
328C PHE* 5.7 1.3 - - + -
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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
----------------------------------------------------------
409B Y01 4.0 42.0 - - + -
231C LEU 2.9 17.6 + - - +
232C ILE* 3.7 17.5 - - + +
234C ILE* 1.3 76.3 - - - +
236C SER* 1.3 63.1 + - - +
238C VAL* 3.1 34.9 + - + +
239C SER* 3.7 7.3 + - - -
253C LEU* 5.5 11.1 - - + +
256C THR* 6.4 2.0 - - + -
257C THR* 4.5 16.0 - - + +
407C Y01 5.5 9.6 - - + +
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Residues in contact with SER 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 ILE 2.9 13.5 + - - -
233C THR* 2.4 34.0 + - - +
235C LEU* 1.3 75.6 - - - +
237C TRP* 1.3 66.5 + - - +
239C SER* 3.4 19.1 + - - -
240C PHE* 3.8 9.8 - - - -
254C GLY* 6.3 1.3 - - - -
257C THR* 4.0 19.4 - - - +
292C VAL* 3.8 24.4 - - - +
295C ALA* 5.1 10.0 - - - +
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Residues in contact with TRP 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C THR* 2.9 26.8 + - + +
234C ILE* 3.0 37.0 + - + +
236C SER* 1.3 77.9 + - - +
238C VAL* 1.3 61.8 + - - +
239C SER 2.9 7.0 + - - -
240C PHE* 3.0 41.5 + + + +
241C TRP* 4.6 4.7 + - - -
291C PHE* 6.1 3.0 - + - +
295C ALA* 5.8 2.0 - - + -
324C PHE* 3.5 27.6 - + + +
325C PRO* 3.5 37.7 - - + -
328C PHE* 3.4 48.5 - + + -
329C SER* 5.6 0.7 - - - -
409C Y01 6.4 0.2 - - + -
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Residues in contact with VAL 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B Y01 4.8 17.7 - - + -
234C ILE* 2.9 28.4 + - + +
235C LEU* 3.1 31.8 + - + +
237C TRP* 1.3 75.9 - - - +
239C SER* 1.3 61.2 + - - +
240C PHE 3.2 0.7 + - - -
241C TRP* 3.7 31.3 + - + +
242C ILE* 4.4 8.2 - - + +
253C LEU* 5.6 4.7 - - + -
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Residues in contact with SER 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C LEU 3.9 5.5 + - - -
236C SER* 3.4 15.5 + - - -
237C TRP 2.9 1.2 + - - -
238C VAL* 1.3 79.3 - - - +
240C PHE* 1.3 54.7 + - - +
241C TRP 3.4 0.2 - - - -
242C ILE* 3.4 17.4 + - - +
250C ARG* 2.4 54.5 + - - +
253C LEU* 3.2 33.3 - - - +
254C GLY* 5.3 2.1 - - - -
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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
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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