Contacts of the helix formed by residues 221 - 229 (chain C) in PDB entry 6UZA
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 221 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166C LEU* 4.3 1.8 - - - -
191C ARG 5.9 0.2 - - - +
192C LEU 4.2 9.2 - - - -
193C ALA* 4.2 3.1 - - - -
194C THR* 3.6 34.7 + - - +
207C TYR* 5.7 2.9 - - + -
219C ASP 3.1 14.0 + - - +
220C VAL* 1.3 80.3 - - - +
222C PRO* 1.3 75.0 - - + +
223C ILE* 3.4 12.3 - - - +
224C ILE* 3.4 26.6 - - + +
225C LEU* 3.2 16.3 + - - +
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Residues in contact with PRO 222 (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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165C LEU* 3.8 21.5 - - + -
166C LEU* 4.0 16.4 - - + -
169C ILE* 3.7 22.0 - - + +
191C ARG 3.9 9.2 - - - +
192C LEU* 4.0 16.4 - - + +
207C TYR* 3.5 29.6 - - + +
221C THR* 1.3 88.4 - - - +
223C ILE* 1.3 57.4 + - - +
225C LEU* 3.6 1.3 + - + +
226C ALA* 2.9 29.6 + - - +
238C LEU* 3.6 10.8 - - + +
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Residues in contact with ILE 223 (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 LEU 3.6 15.1 + - - +
193C ALA* 4.6 1.3 - - + -
221C THR* 3.4 13.5 - - - +
222C PRO* 1.3 76.9 - - - +
224C ILE* 1.3 64.1 + - + +
226C ALA* 3.8 0.4 - - - -
227C ALA* 2.9 28.1 + - - +
235C VAL* 4.4 20.4 - - + +
238C LEU* 4.1 25.1 - - + +
239C LEU* 4.5 7.2 - - + -
243C ALA* 3.9 26.0 - - + +
244C ARG 3.8 20.2 - - - +
245C ILE* 3.9 20.6 - - + -
285C TYR* 4.3 11.9 - - + -
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Residues in contact with ILE 224 (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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219C ASP* 4.2 17.7 - - + +
220C VAL* 4.7 11.4 - - + -
221C THR* 3.4 25.5 + - + +
222C PRO 3.4 0.2 - - - -
223C ILE* 1.3 79.1 - - + +
225C LEU* 1.3 56.2 + - - +
227C ALA* 3.3 1.0 + - - +
228C HIS* 2.9 62.9 + - + +
245C ILE* 4.0 37.5 - - + -
246C GLU 6.0 0.2 - - - +
275C ASN* 3.8 11.4 - - + +
276C ALA* 4.5 14.6 - - + +
279C GLY* 4.6 2.0 - - - -
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Residues in contact with LEU 225 (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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166C LEU* 3.3 42.4 - - + +
169C ILE* 3.9 10.9 - - + +
170C SER* 4.3 3.1 - - - +
216C PHE* 3.6 38.1 - - + -
220C VAL* 3.7 13.8 - - + +
221C THR 3.2 16.8 + - - +
222C PRO* 4.0 3.8 - - + +
224C ILE* 1.3 78.9 - - - +
226C ALA* 1.3 60.5 + - - +
228C HIS* 3.4 10.6 + - + +
229C CYS* 3.2 46.9 + - - -
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Residues in contact with ALA 226 (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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169C ILE* 3.7 16.5 - - + +
222C PRO 2.9 18.8 + - - +
223C ILE 3.9 2.7 - - - +
224C ILE 3.4 0.2 - - - -
225C LEU* 1.3 76.7 - - - +
227C ALA* 1.3 58.6 + - - +
229C CYS 4.0 0.4 + - - -
230C GLN 3.7 1.6 + - - -
231C GLU* 3.3 31.0 + - - +
234C ILE* 4.0 13.5 - - + -
235C VAL* 3.3 21.5 - - + +
238C LEU* 3.9 15.0 - - + -
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Residues in contact with ALA 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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223C ILE 2.9 18.1 + - - +
224C ILE 3.8 3.4 - - - +
226C ALA* 1.3 77.3 - - - +
228C HIS* 1.3 65.0 + - - +
229C CYS 3.4 0.2 - - - -
230C GLN* 3.7 8.2 + - - +
235C VAL* 4.1 9.0 - - + -
245C ILE* 4.2 6.1 - - + -
279C GLY* 3.6 24.0 - - - +
282C SER* 3.2 29.6 + - - +
284C ALA* 4.9 2.4 - - - +
285C TYR* 4.2 12.6 - - + -
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Residues in contact with HIS 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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220C VAL* 5.1 5.8 - - + +
224C ILE* 2.9 36.8 + - + +
225C LEU* 3.4 14.7 + - + +
227C ALA* 1.3 78.8 - - - +
229C CYS* 1.3 63.7 + - - +
230C GLN* 3.3 12.2 + - - +
275C ASN* 3.0 42.0 + - + -
278C LYS* 3.6 31.6 - - + +
279C GLY* 3.3 19.4 + - - -
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Residues in contact with CYS 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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169C ILE 4.5 1.1 - - - +
170C SER* 4.2 23.3 - - - +
225C LEU* 3.2 37.0 + - - +
226C ALA 4.0 0.2 + - - -
227C ALA 3.4 0.2 - - - -
228C HIS* 1.3 78.5 - - - +
230C GLN* 1.3 69.4 + - - +
231C GLU* 3.3 30.0 + - + +
874C LYS* 5.4 2.3 - - - +
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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