Contacts of the helix formed by residues 221 - 229 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166D LEU* 4.3 1.8 - - - -
191D ARG 5.9 0.2 - - - +
192D LEU 4.2 8.7 - - - -
193D ALA* 4.2 2.6 - - - +
194D THR* 3.6 34.3 - - - +
207D TYR* 5.7 2.7 - - + -
219D ASP 3.1 14.5 + - - +
220D VAL* 1.3 80.6 - - - +
222D PRO* 1.3 75.1 - - + +
223D ILE* 3.4 11.4 - - - +
224D ILE* 3.4 26.5 - - + +
225D LEU* 3.2 17.2 + - - +
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Residues in contact with PRO 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D LEU* 3.8 19.5 - - + -
166D LEU* 4.0 16.8 - - + -
169D ILE* 3.7 21.6 - - + +
191D ARG 3.9 9.4 - - - +
192D LEU* 4.0 15.7 - - + +
207D TYR* 3.5 30.3 - - + +
221D THR* 1.3 86.9 - - + +
223D ILE* 1.3 58.1 + - - +
225D LEU* 4.0 0.6 - - + +
226D ALA* 2.9 30.1 + - - +
238D LEU* 3.6 10.6 - - + +
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Residues in contact with ILE 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D LEU 3.6 17.4 + - - +
193D ALA* 4.6 1.1 - - + -
221D THR* 3.4 13.5 - - - +
222D PRO* 1.3 76.5 - - - +
224D ILE* 1.3 63.0 + - + +
226D ALA 3.8 0.3 - - - -
227D ALA* 2.9 28.2 + - - +
235D VAL* 4.4 20.0 - - + +
238D LEU* 4.1 24.7 - - + +
239D LEU* 4.5 7.9 - - + -
243D ALA* 3.9 25.4 - - + +
244D ARG 3.8 19.7 - - - +
245D ILE* 3.9 19.5 - - + -
285D TYR* 4.3 13.2 - - + -
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Residues in contact with ILE 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D ASP* 4.2 17.3 - - + +
220D VAL* 4.7 12.1 - - + -
221D THR* 3.4 24.3 + - + +
222D PRO 3.4 0.2 - - - -
223D ILE* 1.3 78.7 - - + +
225D LEU* 1.3 56.3 + - - +
227D ALA* 3.3 1.6 + - - +
228D HIS* 2.9 62.0 + - + +
245D ILE* 4.0 38.1 - - + -
275D ASN* 3.8 11.0 - - + +
276D ALA* 4.5 14.6 - - + +
279D GLY* 4.6 2.0 - - - -
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Residues in contact with LEU 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D LEU* 3.3 43.1 - - + +
169D ILE* 3.9 10.5 - - + +
170D SER* 4.3 3.1 - - - +
216D PHE* 3.6 37.2 - - + -
220D VAL* 3.7 14.1 - - + +
221D THR 3.2 17.2 + - - +
222D PRO* 4.0 4.5 - - + +
224D ILE* 1.3 78.5 - - - +
226D ALA* 1.3 60.4 + - - +
228D HIS* 3.4 11.0 + - + +
229D CYS* 3.2 46.6 + - - -
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Residues in contact with ALA 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D ILE* 3.7 16.8 - - + +
222D PRO 2.9 20.6 + - - +
223D ILE* 3.4 2.9 + - - +
225D LEU* 1.3 76.3 - - - +
227D ALA* 1.3 57.6 + - - +
229D CYS 4.0 0.6 + - - -
230D GLN 3.7 1.6 + - - -
231D GLU* 3.3 29.8 + - - +
234D ILE* 4.0 12.6 - - + -
235D VAL* 3.3 21.8 - - + +
238D LEU* 3.9 15.5 - - + -
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Residues in contact with ALA 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D ILE 2.9 17.7 + - - +
224D ILE 3.8 3.4 - - - +
225D LEU 3.2 0.2 - - - -
226D ALA* 1.3 76.4 - - - +
228D HIS* 1.3 64.7 + - - +
229D CYS 3.4 0.2 - - - -
230D GLN* 3.7 8.4 + - - +
235D VAL* 3.9 8.5 - - + +
245D ILE* 4.2 6.1 - - + -
279D GLY* 3.6 24.7 - - - +
282D SER* 3.2 29.0 + - - +
284D ALA* 4.9 2.6 - - - +
285D TYR* 4.2 12.6 - - + -
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Residues in contact with HIS 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220D VAL* 5.1 6.7 - - + +
224D ILE* 2.9 36.8 + - + +
225D LEU* 3.4 13.6 + - + +
227D ALA* 1.3 78.3 - - - +
229D CYS* 1.3 64.0 + - - +
230D GLN* 3.3 11.8 + - - +
275D ASN* 3.0 43.0 + - + -
278D LYS* 3.6 30.8 - - + +
279D GLY* 3.3 20.1 + - - -
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Residues in contact with CYS 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D ILE 4.5 1.6 - - - +
170D SER* 4.2 24.0 - - - +
225D LEU* 3.2 37.0 + - - +
227D ALA 3.4 0.2 - - - -
228D HIS* 1.3 77.9 - - - +
230D GLN* 1.3 70.9 + - - +
231D GLU* 3.3 29.9 + - + +
874D LYS* 5.4 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