Contacts of the helix formed by residues 228 - 241 (chain C) in PDB entry 2ZXX
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 THR 228 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226C THR* 3.3 27.6 + - + -
227C VAL* 1.3 75.5 - - - +
229C PHE* 1.3 67.8 + - - +
230C ALA* 4.5 1.4 - - - +
231C LYS* 3.1 31.3 + - - +
232C VAL* 2.9 23.4 + - - +
267C ASN* 4.3 7.9 - - + +
281C GLN* 3.8 30.7 + - - +
282C LEU 3.8 3.8 - - - -
283C THR* 4.1 13.9 - - + +
284C ILE* 4.8 0.4 - - - -
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Residues in contact with PHE 229 (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 THR* 1.3 72.4 - - - +
230C ALA* 1.3 69.0 + - - +
232C VAL* 2.9 13.5 + - + +
233C LYS* 2.9 48.8 + - + +
244C PHE* 4.2 10.5 - + - -
245C GLU 4.0 2.2 - - - -
246C GLU* 3.4 49.4 - - + -
249C VAL* 3.6 29.6 - - + -
281C GLN* 4.3 2.8 + - + +
282C LEU* 2.7 40.6 + - + +
283C THR* 4.4 0.2 - - - +
284C ILE* 4.3 14.3 - - + +
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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
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228C THR* 3.3 2.0 - - - +
229C PHE* 1.3 87.2 - - - +
231C LYS* 1.3 62.9 - - + +
233C LYS* 3.6 8.2 + - - +
234C GLN* 3.2 22.6 + - - +
281C GLN* 3.2 26.7 + - - +
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Residues in contact with LYS 231 (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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216C ILE* 4.6 2.8 - - - +
220C LEU* 4.5 15.6 - - + +
225C GLU* 2.8 34.6 + - - +
226C THR* 2.9 32.2 + - - +
228C THR* 3.1 24.3 + - - +
229C PHE 3.0 1.0 - - - -
230C ALA* 1.3 79.4 - - + +
232C VAL* 1.3 64.7 + - - +
234C GLN* 3.5 14.7 + - - +
235C GLY* 3.2 17.0 + - - -
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Residues in contact with VAL 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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213C MSE 4.2 21.1 - - + -
216C ILE* 4.0 21.2 - - + +
217C VAL* 4.5 5.4 - - + -
220C LEU* 4.3 2.7 - - + -
227C VAL* 3.8 25.1 - - + -
228C THR 2.9 15.7 + - - +
229C PHE* 2.9 11.2 + - + +
231C LYS* 1.3 77.0 - - - +
233C LYS* 1.3 58.6 + - - +
235C GLY* 2.9 4.9 + - - -
236C VAL* 2.8 44.1 + - + +
244C PHE* 4.5 6.7 - - + -
284C ILE* 3.8 17.7 - - + -
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Residues in contact with LYS 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C PHE* 2.9 43.9 + - + +
230C ALA* 3.7 8.3 - - - +
232C VAL* 1.3 73.0 - - - +
234C GLN* 1.3 63.2 + - - +
236C VAL* 4.2 7.0 - - - -
237C GLN* 3.0 48.6 + - - +
244C PHE* 3.0 27.8 + - - +
245C GLU* 2.5 39.2 + - - +
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Residues in contact with GLN 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 ALA 3.2 15.3 + - - +
231C LYS* 3.7 18.0 - - - +
232C VAL 3.2 0.4 - - - -
233C LYS* 1.3 75.2 - - - +
235C GLY* 1.3 65.1 + - - +
237C GLN* 3.9 3.9 - - - +
238C GLU* 2.9 56.0 + - - +
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Residues in contact with GLY 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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216C ILE* 3.7 26.6 - - - +
231C LYS 3.2 8.3 + - - -
232C VAL 2.9 8.5 + - - -
234C GLN* 1.3 79.1 - - - +
236C VAL* 1.3 55.7 + - - -
238C GLU* 3.8 8.0 - - - +
239C MSE 3.0 28.1 + - - +
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Residues in contact with VAL 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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209C MSE 5.5 0.4 - - - +
212C SER* 3.8 14.6 - - - +
213C MSE 4.4 9.9 - - - +
216C ILE* 4.5 3.8 - - + -
232C VAL* 2.8 31.2 + - + +
233C LYS* 4.2 0.2 - - - -
235C GLY* 1.3 71.8 - - - +
237C GLN* 1.3 63.5 + - - +
239C MSE 3.0 6.4 + - - +
240C MSE 2.9 51.7 + - + +
244C PHE* 3.5 51.1 - - + -
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Residues in contact with GLN 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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233C LYS* 3.0 41.9 + - - +
234C GLN* 4.0 3.4 - - - +
236C VAL* 1.3 74.2 - - - +
238C GLU* 1.3 57.4 + - - +
241C ARG* 2.7 35.3 + - - -
242C LYS 3.3 21.1 - - - +
243C ARG* 3.8 5.0 - - - +
244C PHE* 2.9 39.5 + - + +
245C GLU* 4.2 2.3 - - - +
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Residues in contact with GLU 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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234C GLN* 2.9 51.1 + - - +
235C GLY* 3.8 6.7 - - - +
237C GLN* 1.3 77.8 - - - +
239C MSE 1.3 63.1 + - - +
241C ARG* 3.9 13.7 - - - +
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Residues in contact with MSE 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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211C ARG* 3.3 33.7 - - - +
212C SER* 3.1 24.7 - - - +
215C THR* 3.6 35.7 - - + +
216C ILE* 4.3 11.9 - - + -
235C GLY 3.0 17.1 + - - +
236C VAL 3.0 6.6 + - - +
238C GLU* 1.3 80.7 - - - +
240C MSE 1.3 60.9 + - + +
241C ARG* 3.8 5.0 + - - +
143E GLU* 5.5 0.4 - - - +
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Residues in contact with MSE 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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205C VAL* 5.8 0.7 - - + -
208C GLU* 4.0 25.4 - - + +
209C MSE 3.4 42.8 - - + -
212C SER* 4.0 11.2 - - - +
236C VAL* 2.9 40.5 + - + +
239C MSE 1.3 73.6 - - + +
241C ARG* 1.3 72.4 + - - +
242C LYS* 3.0 42.0 + - + +
243C ARG 4.2 10.3 - - - +
244C PHE* 4.3 1.8 - - + -
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Residues in contact with ARG 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 GLN 2.7 16.0 + - - +
238C GLU* 3.9 15.5 - - - +
239C MSE 4.6 4.3 - - - +
240C MSE 1.3 78.6 - - - +
242C LYS* 1.3 63.4 + - - +
127D GLU* 4.9 2.4 + - - -
130D ARG* 3.2 57.7 - - - +
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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