Contacts of the helix formed by residues 221 - 229 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A LEU* 4.3 2.0 - - - +
191A ARG 5.9 0.2 - - - +
192A LEU 4.2 9.6 - - - -
193A ALA* 4.2 3.3 - - - -
194A THR* 3.6 33.9 - - - +
207A TYR* 5.7 2.7 - - + -
219A ASP 3.1 14.5 + - - +
220A VAL* 1.3 81.5 - - - +
222A PRO* 1.3 74.4 - - + +
223A ILE* 3.4 13.0 - - - +
224A ILE* 3.4 25.7 - - + +
225A LEU* 3.2 17.0 + - - +
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Residues in contact with PRO 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LEU* 3.8 20.6 - - + -
166A LEU* 4.0 17.3 - - + -
169A ILE* 3.7 22.5 - - + +
191A ARG 3.9 8.7 - - - +
192A LEU* 4.0 15.7 - - + +
207A TYR* 3.5 31.0 - - + +
221A THR* 1.3 86.5 - - - +
223A ILE* 1.3 57.1 + - - +
225A LEU* 3.6 1.4 + - + -
226A ALA* 2.9 30.0 + - - +
238A LEU* 3.6 10.1 - - + +
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Residues in contact with ILE 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A LEU 3.6 16.2 + - - +
193A ALA* 4.6 1.1 - - + -
221A THR* 3.4 13.9 - - - +
222A PRO* 1.3 75.7 - - - +
224A ILE* 1.3 63.9 + - + +
226A ALA 3.4 0.6 + - - +
227A ALA* 2.9 28.6 + - - +
235A VAL* 4.4 20.0 - - + +
238A LEU* 4.1 24.2 - - + +
239A LEU* 4.5 7.9 - - + -
243A ALA* 3.9 25.8 - - + +
244A ARG 3.8 20.0 - - - +
245A ILE* 3.9 21.5 - - + -
285A TYR* 4.3 11.7 - - + -
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Residues in contact with ILE 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A ASP* 4.2 16.6 - - + +
220A VAL* 4.7 11.4 - - + -
221A THR* 3.4 25.2 + - + +
222A PRO 3.4 0.2 - - - -
223A ILE* 1.3 77.4 - - + +
225A LEU* 1.3 57.4 + - - +
227A ALA* 3.3 1.6 + - - +
228A HIS* 2.9 61.4 + - + +
245A ILE* 4.0 37.7 - - + -
246A GLU 6.0 0.2 - - - +
275A ASN* 3.8 11.7 - - + +
276A ALA* 4.5 14.4 - - + +
279A GLY* 4.6 1.6 - - - -
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Residues in contact with LEU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A LEU* 3.3 43.7 - - + +
169A ILE* 3.9 10.7 - - + +
170A SER* 4.3 3.4 - - - +
216A PHE* 3.6 36.6 - - + -
220A VAL* 3.7 13.0 - - + -
221A THR 3.2 17.3 + - - +
222A PRO* 4.0 4.3 - - + +
224A ILE* 1.3 79.1 - - - +
226A ALA* 1.3 60.6 + - - +
228A HIS* 3.4 11.4 + - + +
229A CYS* 3.2 47.3 + - - -
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Residues in contact with ALA 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ILE* 3.7 16.1 - - + +
222A PRO 2.9 19.6 + - - +
223A ILE* 3.9 2.9 - - - +
225A LEU* 1.3 76.6 - - - +
227A ALA* 1.3 58.0 + - - +
229A CYS 4.8 0.2 - - - +
230A GLN 3.7 1.4 + - - -
231A GLU* 3.3 30.8 + - - +
234A ILE* 4.0 12.6 - - + -
235A VAL* 3.3 22.1 - - + +
238A LEU* 3.9 15.5 - - + -
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Residues in contact with ALA 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A ILE 2.9 17.1 + - - +
224A ILE 3.8 3.1 - - - +
226A ALA* 1.3 76.2 - - - +
228A HIS* 1.3 64.5 + - - +
229A CYS 3.4 0.4 - - - -
230A GLN* 3.7 9.0 + - - +
235A VAL* 3.9 9.2 - - + +
245A ILE* 4.2 6.1 - - + -
279A GLY* 3.6 24.7 - - - +
282A SER* 3.2 29.1 + - - +
284A ALA* 4.9 3.0 - - - +
285A TYR* 4.2 12.3 - - + -
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Residues in contact with HIS 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A VAL* 5.1 6.1 - - + +
224A ILE* 2.9 37.3 + - + +
225A LEU* 3.4 14.0 + - + +
227A ALA* 1.3 78.6 - - - +
229A CYS* 1.3 62.5 + - - +
230A GLN* 3.3 12.3 + - - +
275A ASN* 3.0 43.7 + - + -
278A LYS* 3.6 30.3 + - + +
279A GLY* 3.3 19.5 + - - -
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Residues in contact with CYS 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ILE 4.5 1.8 - - - +
170A SER* 4.2 23.3 - - - +
225A LEU* 3.2 37.2 + - - +
226A ALA 4.0 0.4 + - - -
227A ALA 3.4 0.2 - - - -
228A HIS* 1.3 77.9 - - - +
230A GLN* 1.3 69.6 + - - +
231A GLU* 3.3 30.6 + - + +
874A 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