Contacts of the helix formed by residues 231 - 241 (chain C) in PDB entry 5UHO
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 SER 231 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218C GLU* 2.8 28.1 + - - -
224C CYS* 4.3 5.2 - - - -
225C TYR 3.0 19.4 + - - -
227C ASN 2.8 20.9 + - - -
228C VAL 3.6 8.1 + - - -
230C GLN* 1.4 71.3 - - - +
232C PRO* 1.4 63.2 - - - +
233C TYR* 3.2 7.3 + - - +
234C LEU* 3.6 9.4 + - - -
235C ARG* 3.2 28.9 + - - +
270C ILE* 3.9 2.9 - - - +
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Residues in contact with PRO 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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190C SER* 5.1 1.7 + - - -
192C ALA* 5.0 0.2 - - - +
225C TYR 3.6 11.4 - - - +
226C PRO* 4.0 5.2 - - + -
230C GLN 3.7 5.8 - - - +
231C SER* 1.4 85.8 - - - +
233C TYR* 1.4 62.5 + - + +
235C ARG* 3.4 25.4 - - + +
236C THR* 3.1 27.9 + - - -
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Residues in contact with TYR 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C HIS* 4.0 17.9 - + - +
190C SER* 5.6 1.1 - - - -
191C PHE* 4.3 13.9 - + + -
192C ALA* 3.5 32.5 - - + +
195C GLN* 2.7 29.0 + - - -
214C PHE* 4.3 1.2 - - - -
216C PRO* 3.4 25.5 - - + +
217C THR* 2.8 24.1 + - - -
218C GLU* 3.6 44.4 - - + +
231C SER* 3.2 1.5 - - - +
232C PRO* 1.4 81.1 - - + +
234C LEU* 1.4 68.7 + - + +
236C THR 3.4 2.6 + - - -
237C VAL* 3.2 36.6 + - + +
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Residues in contact with LEU 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C PRO* 4.9 6.7 - - + -
218C GLU 3.8 20.0 - - - +
224C CYS* 3.6 27.8 - - - -
228C VAL* 3.8 19.1 - - + +
231C SER* 3.6 10.9 + - - +
233C TYR* 1.4 86.6 - - + +
235C ARG* 1.3 56.1 + - - +
237C VAL* 3.5 6.9 - - + +
238C GLY* 2.8 31.9 + - - -
249C TRP* 4.4 10.5 - - + -
267C VAL* 4.4 1.1 - - + -
270C ILE* 3.7 39.6 - - + +
271C ILE* 3.9 19.4 - - + -
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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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229C SER 4.1 2.0 + - - -
230C GLN* 3.1 45.3 + - - +
231C SER 3.2 24.1 + - - +
232C PRO* 3.4 29.8 - - - +
233C TYR 3.2 0.2 - - - -
234C LEU* 1.3 76.4 - - - +
236C THR* 1.4 51.3 + - - +
238C GLY* 3.4 0.7 + - - -
239C GLU* 2.8 60.6 + - - +
270C ILE* 3.5 23.2 - - - +
272C LYS* 4.3 9.1 + - - +
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Residues in contact with THR 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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190C SER* 4.4 1.4 + - - -
192C ALA* 3.7 17.7 - - + +
193C HIS* 3.4 53.0 + - + +
196C VAL* 4.2 2.0 - - + +
232C PRO 3.1 17.1 + - - -
233C TYR 3.4 4.7 + - - -
235C ARG* 1.4 73.1 - - - +
237C VAL* 1.4 57.2 + - - +
239C GLU* 4.5 5.6 - - - -
240C LYS* 2.8 41.0 + - + +
241C LEU 3.9 0.3 + - - -
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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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192C ALA* 4.3 8.3 - - + -
195C GLN* 5.5 0.4 - - + +
196C VAL* 4.0 11.4 - - + -
214C PHE* 3.7 31.6 - - + -
216C PRO* 4.9 2.7 - - + -
233C TYR* 3.2 40.1 + - + +
234C LEU* 3.5 11.2 - - + +
235C ARG 3.3 0.2 - - - -
236C THR* 1.4 74.4 - - - +
238C GLY* 1.3 59.2 + - - +
241C LEU* 2.9 45.8 + - + +
247C VAL* 4.3 13.0 - - + -
271C ILE* 5.0 9.2 - - + -
273C ARG* 4.8 0.4 + - - +
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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 LEU 2.8 15.1 + - - -
235C ARG 3.8 0.2 - - - -
237C VAL* 1.3 74.4 - - - +
239C GLU* 1.4 59.2 + - - +
241C LEU 4.1 0.3 - - - +
270C ILE 3.5 15.9 - - - -
271C ILE* 3.4 25.2 - - - +
272C LYS* 4.1 14.2 - - - +
273C ARG* 3.8 16.2 + - - -
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Residues in contact with GLU 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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235C ARG* 2.8 45.0 + - - +
236C THR* 4.1 3.4 - - - +
238C GLY* 1.4 74.8 - - - +
240C LYS* 1.3 91.9 + - - +
241C LEU 3.8 3.5 + - - +
272C LYS* 3.7 19.3 + - + +
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Residues in contact with LYS 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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193C HIS* 4.9 11.9 - - + +
196C VAL* 3.6 22.2 - - + +
200C ASN* 3.8 6.6 + - - +
236C THR* 2.8 32.4 + - + +
239C GLU* 1.3 108.3 + - + +
241C LEU* 1.3 61.7 + - - +
242C LEU 3.6 1.7 + - - -
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Residues in contact with LEU 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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196C VAL* 3.8 18.8 - - + +
199C THR* 3.8 26.5 - - + -
200C ASN* 3.6 18.2 - - - +
214C PHE* 3.7 28.0 - - + -
237C VAL* 2.9 24.5 + - + +
238C GLY 4.1 4.2 - - - +
239C GLU 4.1 3.1 - - - +
240C LYS* 1.3 76.7 - - - +
242C LEU* 1.4 59.7 + - - +
243C PRO* 3.6 2.3 - - - +
245C ILE* 3.8 17.0 - - + -
247C VAL* 3.8 10.5 - - + -
273C ARG* 2.8 44.4 + - - +
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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