Contacts of the helix formed by residues 226 - 238 (chain C) in PDB entry 1X1O
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 PRO 226 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204C ARG 5.9 2.0 - - - +
224C ASN 3.7 8.3 - - - +
225C PHE* 1.3 86.8 - - + +
227C LEU* 1.3 55.3 + - - +
228C GLU* 3.2 15.9 - - + +
229C ALA* 2.6 41.4 + - + +
230C LEU 3.0 6.9 + - - -
253C ARG* 5.8 0.4 - - - +
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Residues in contact with LEU 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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225C PHE 3.3 2.4 + - - -
226C PRO* 1.3 72.0 - - - +
228C GLU* 1.3 68.6 + - - +
229C ALA 2.8 1.4 + - - -
230C LEU* 3.6 24.0 - - + -
231C ARG* 2.8 77.7 + - + +
256C ALA* 5.0 15.3 - - + +
260C ALA* 4.5 9.9 - - + -
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Residues in contact with GLU 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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226C PRO* 3.8 19.7 - - + +
227C LEU* 1.3 78.3 + - - +
229C ALA* 1.3 58.2 + - - +
231C ARG* 4.2 26.0 + - - +
232C GLU* 3.2 22.6 + - - +
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Residues in contact with ALA 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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206C LEU* 3.8 16.4 - - + -
225C PHE* 3.3 28.5 - - + -
226C PRO* 2.6 28.2 + - + +
228C GLU* 1.3 73.7 - - - +
230C LEU* 1.3 55.9 + - - +
231C ARG 3.3 1.3 - - - -
232C GLU* 3.5 9.1 - - - +
233C ALA* 2.6 37.6 + - - +
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Residues in contact with LEU 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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222C LEU* 4.9 10.3 - - + +
225C PHE* 4.2 19.5 - - + +
226C PRO 3.0 7.0 + - - +
227C LEU* 3.6 28.9 - - + +
229C ALA* 1.3 79.5 - - - +
231C ARG* 1.3 62.1 + - - +
233C ALA* 4.0 4.4 - - - +
234C VAL* 3.6 16.6 + - - +
245C ALA* 5.0 6.5 - - + -
249C MET* 6.3 1.8 - - + -
253C ARG 4.9 4.9 - - - +
256C ALA* 5.4 1.6 - - + -
257C ALA* 3.8 25.8 - - + +
260C ALA* 3.3 20.4 - - + -
262C VAL* 3.6 26.0 - - + -
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Residues in contact with ARG 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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227C LEU* 2.8 56.9 + - + +
228C GLU* 4.2 25.8 + - - +
230C LEU* 1.3 76.7 - - - +
232C GLU* 1.3 64.1 + - - +
234C VAL* 3.8 3.7 + - - +
235C ARG* 3.5 15.2 + - - +
260C ALA* 3.8 26.3 - - + +
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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
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206C LEU* 3.5 31.2 - - - +
228C GLU 3.2 20.0 + - - +
229C ALA* 3.1 8.1 + - - +
231C ARG* 1.3 76.4 - - - +
233C ALA* 1.3 56.2 + - - +
235C ARG* 2.6 60.8 + - - +
236C ARG* 2.7 44.6 + - - +
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Residues in contact with ALA 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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206C LEU* 4.8 4.0 - - + -
209C LEU* 3.8 27.4 - - + -
222C LEU* 4.1 22.4 - - + -
225C PHE* 5.1 2.2 - - + -
229C ALA 2.6 21.3 + - - +
230C LEU 4.0 4.5 - - - +
232C GLU* 1.3 73.6 + - - +
234C VAL* 1.4 64.0 + - - +
236C ARG* 3.1 5.9 + - - +
237C VAL* 3.0 31.1 + - + +
243C LEU* 4.6 3.4 - - + -
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Residues in contact with VAL 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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132C LYS* 5.7 3.8 - - - +
222C LEU* 6.5 0.4 - - + -
230C LEU 3.6 15.1 + - - +
231C ARG 4.2 3.1 - - - +
232C GLU 3.2 1.0 - - - -
233C ALA* 1.4 78.1 - - - +
235C ARG* 1.3 63.0 + - - +
237C VAL* 3.9 0.9 - - - +
238C GLY* 3.2 18.1 + - - -
239C GLY* 4.3 7.1 + - - +
243C LEU* 3.5 28.6 - - + +
260C ALA 3.1 31.4 - - - +
261C GLY* 4.0 20.0 - - - +
262C VAL* 4.1 5.6 - - + +
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Residues in contact with ARG 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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231C ARG 3.5 9.0 + - - +
232C GLU* 2.6 57.8 + - - +
234C VAL* 1.3 75.2 - - - +
236C ARG* 1.3 78.3 + - - +
237C VAL 3.1 1.5 + - - -
238C GLY* 3.3 11.7 + - - -
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Residues in contact with ARG 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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206C LEU* 3.9 30.7 + - - +
209C LEU* 5.1 6.3 - - + +
210C GLU* 2.9 44.4 + - - +
213C LEU* 4.8 10.0 - - + +
232C GLU* 2.7 43.6 + - - +
233C ALA* 3.1 8.7 + - - +
235C ARG* 1.3 89.4 - - - +
237C VAL* 1.3 60.8 + - + +
240C ARG* 5.7 4.3 + - - -
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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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209C LEU* 4.8 6.7 - - + -
213C LEU* 4.1 25.6 - - + -
233C ALA* 3.0 20.9 + - - +
234C VAL 4.1 2.5 - - - +
236C ARG* 1.3 79.6 - - - +
238C GLY* 1.3 64.0 + - - +
239C GLY* 2.9 6.2 + - - +
240C ARG* 2.9 41.6 - - + +
241C VAL* 3.7 31.0 - - + +
243C LEU* 3.7 24.0 - - + -
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Residues in contact with GLY 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 VAL* 3.2 12.3 + - - -
235C ARG 3.3 9.1 + - - -
237C VAL* 1.3 76.9 - - - +
239C GLY* 1.3 61.1 + - - +
240C ARG* 3.4 8.2 - - - +
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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