Contacts of the helix formed by residues 231 - 241 (chain B) 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 GLU 231 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169B ILE 4.0 11.7 - - - +
170B SER 4.4 3.1 - - - +
171B LYS 4.5 0.7 - - - +
172B GLY* 3.6 32.0 + - - +
174B VAL* 5.6 1.7 - - - +
226B ALA* 3.3 12.0 + - - +
229B CYS* 3.5 33.1 - - + +
230B GLN* 1.3 74.4 - - - +
232B TYR* 1.3 59.8 + - - +
233B GLU 3.4 1.6 - - - -
234B ILE* 3.9 24.7 - - + +
235B VAL* 3.0 31.6 + - - +
284B ALA* 4.5 1.1 - - - +
874B LYS* 4.6 6.3 + - - +
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Residues in contact with TYR 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B GLN* 3.5 14.8 + - + -
231B GLU* 1.3 72.8 - - - +
233B GLU* 1.3 58.4 + - - +
235B VAL* 3.5 1.3 + - - -
236B HIS* 3.0 28.9 + - - +
283B PRO* 3.8 19.8 - - - +
284B ALA* 3.7 26.7 - - + -
287B SER* 3.8 11.9 - - - -
288B LEU* 3.6 17.6 - - + +
866B TYR* 4.0 4.2 - + - -
867B VAL* 4.0 27.6 - - + -
870B ALA* 3.3 32.8 - - + +
871B GLN* 3.8 25.8 - - + +
874B LYS* 3.3 29.6 - - - +
131C TYR* 5.0 2.3 - - + +
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Residues in contact with GLU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B VAL* 3.6 37.9 - - + +
231B GLU* 3.4 0.4 - - - +
232B TYR* 1.3 77.0 - - - +
234B ILE* 1.3 60.4 + - + +
236B HIS* 3.4 5.3 + - - +
237B THR* 2.9 38.2 + - - +
871B GLN* 5.0 2.1 - - - +
107C GLU* 5.5 4.6 - - - +
108C TYR* 5.2 4.5 + - - -
131C TYR* 3.6 39.2 + - + +
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Residues in contact with ILE 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B ILE* 3.9 33.2 - - + +
172B GLY* 4.4 15.9 - - - -
173B TYR 4.7 0.2 - - - +
174B VAL* 4.4 21.3 - - + -
177B VAL* 4.2 32.8 - - + -
226B ALA* 4.0 11.7 - - + -
231B GLU* 3.6 32.6 + - + +
233B GLU* 1.3 73.1 - - + +
235B VAL* 1.3 60.6 + - - +
237B THR* 3.7 4.8 - - - -
238B LEU* 2.9 37.0 + - + +
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Residues in contact with VAL 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B ILE* 4.4 12.5 - - + +
226B ALA* 3.3 32.8 - - + +
227B ALA* 3.9 11.0 - - + +
231B GLU 3.0 21.9 + - - +
232B TYR* 3.8 3.8 - - - +
234B ILE* 1.3 77.0 - - - +
236B HIS* 1.3 58.0 + - - +
238B LEU* 3.8 0.9 - - - +
239B LEU* 2.9 44.5 + - + +
284B ALA* 3.4 30.3 - - + +
285B TYR* 4.6 4.9 - - + -
288B LEU* 3.8 7.9 - - + -
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Residues in contact with HIS 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232B TYR 3.0 18.6 + - - +
233B GLU 3.7 4.7 - - - +
235B VAL* 1.3 77.4 - - - +
237B THR* 1.3 56.6 + - - +
239B LEU* 3.5 6.7 + - + +
240B ARG* 3.0 44.2 + - - +
288B LEU* 4.2 22.2 - - + +
87C MET* 3.8 22.7 - - + +
88C PHE* 2.9 31.2 + + - -
89C SER* 4.2 8.5 + - - -
131C TYR* 3.5 49.2 + + + +
132C MET* 5.6 0.2 - - + -
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Residues in contact with THR 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174B VAL* 5.6 2.6 - - - +
177B VAL* 5.5 3.8 - - + -
178B GLU* 5.9 7.0 - - + -
181B LEU* 4.1 13.9 - - + -
233B GLU* 2.9 25.3 + - - +
234B ILE* 3.7 8.7 - - - -
236B HIS* 1.3 77.8 + - - +
238B LEU* 1.3 61.6 + - + +
240B ARG* 3.3 37.2 + - - +
241B LYS* 3.4 35.5 + - - +
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Residues in contact with LEU 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B LEU* 5.9 0.2 - - + -
169B ILE* 4.0 8.1 - - + -
181B LEU* 4.1 19.3 - - + -
192B LEU* 3.9 38.6 - - + -
222B PRO* 3.6 34.1 - - + +
223B ILE* 4.1 15.0 - - + -
226B ALA* 3.9 12.6 - - + -
234B ILE* 2.9 30.2 + - + +
237B THR* 1.3 73.1 - - - +
239B LEU* 1.3 65.1 + - - +
241B LYS* 3.4 10.0 + - + +
242B GLY 3.7 0.3 + - - -
243B ALA* 3.3 28.9 + - + +
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Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B ILE* 4.5 4.0 - - + -
235B VAL* 2.9 38.9 + - + +
236B HIS* 3.9 5.6 - - + +
238B LEU* 1.3 75.7 - - - +
240B ARG* 1.3 62.9 + - - +
242B GLY* 3.3 9.7 + - - -
243B ALA 3.4 20.9 - - - +
244B ARG* 3.6 39.3 + - - +
285B TYR* 4.1 14.8 - - + -
288B LEU* 3.8 33.2 - - + +
289B SER* 4.1 6.3 - - - +
87C MET* 3.3 24.0 - - + +
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Residues in contact with ARG 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B HIS* 3.0 40.4 + - - +
237B THR* 3.5 32.9 + - - +
238B LEU 3.3 0.2 - - - -
239B LEU* 1.3 78.5 - - - +
241B LYS* 1.3 68.8 + - + +
242B GLY 3.4 1.5 + - - -
87C MET* 3.7 18.6 - - + -
131C TYR* 4.9 9.1 - - - +
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Residues in contact with LYS 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181B LEU* 3.8 37.1 + - + +
186B PHE 5.6 4.5 - - - +
188B GLU 4.7 3.1 - - - +
189B GLY* 4.2 21.3 - - - +
192B LEU* 3.8 30.4 - - + +
237B THR* 3.4 23.3 - - - +
238B LEU* 3.4 4.4 + - - +
239B LEU 3.2 1.0 - - - -
240B ARG* 1.3 90.8 - - + +
242B GLY* 1.3 62.2 + - - +
243B ALA* 3.7 1.3 - - - -
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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