Contacts of the helix formed by residues 231 - 241 (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 GLU 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A ILE 4.0 11.0 - - - +
170A SER 4.4 2.8 - - - +
171A LYS 4.5 0.9 - - - +
172A GLY* 3.6 32.0 + - - +
174A VAL* 5.6 1.9 - - - +
226A ALA* 3.3 12.2 + - - +
229A CYS* 3.5 33.6 - - + +
230A GLN* 1.3 75.0 - - - +
232A TYR* 1.3 60.7 + - - +
233A GLU 3.4 1.6 - - - +
234A ILE* 3.9 25.2 - - + +
235A VAL* 3.0 31.0 + - - +
284A ALA* 4.5 0.9 - - - +
874A LYS* 4.6 5.0 + - - +
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Residues in contact with TYR 232 (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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230A GLN* 3.5 13.8 + - - -
231A GLU* 1.3 72.4 - - - +
233A GLU* 1.3 58.5 + - - +
235A VAL* 3.5 1.3 + - - -
236A HIS* 3.0 29.1 + - - +
283A PRO* 3.8 19.6 - - - +
284A ALA* 3.7 28.7 - - + -
287A SER* 3.8 11.9 - - - -
288A LEU* 3.6 17.1 - - + +
866A TYR* 4.0 4.6 + + - -
867A VAL* 4.0 27.6 - - + -
870A ALA* 3.3 31.3 - - + +
871A GLN* 3.8 25.8 - - + +
874A LYS* 3.3 30.7 - - - +
131B TYR* 5.0 2.1 - - + -
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Residues in contact with GLU 233 (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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174A VAL* 3.6 38.1 - - + +
231A GLU* 3.4 0.4 - - - +
232A TYR* 1.3 77.0 - - - +
234A ILE* 1.3 60.4 - - + +
236A HIS* 3.4 5.0 + - - +
237A THR* 2.9 37.8 + - - +
871A GLN* 5.0 1.3 - - - +
107B GLU* 5.5 4.9 - - - +
108B TYR* 5.2 4.3 + - - -
131B TYR* 3.6 40.4 + - + +
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Residues in contact with ILE 234 (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* 3.9 33.7 - - + +
172A GLY* 4.4 16.6 - - - -
173A TYR 4.7 0.2 - - - +
174A VAL* 4.4 21.3 - - + -
177A VAL* 4.2 31.2 - - + -
226A ALA* 4.0 11.9 - - + -
231A GLU* 3.6 32.4 + - + +
232A TYR 3.4 0.2 - - - -
233A GLU* 1.3 74.4 - - + +
235A VAL* 1.3 60.7 + - - +
237A THR* 3.4 5.6 + - - -
238A LEU* 2.9 37.0 + - + +
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Residues in contact with VAL 235 (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* 4.4 11.6 - - + +
226A ALA* 3.3 33.9 - - + +
227A ALA* 3.9 11.2 - - + +
231A GLU 3.0 22.5 + - - +
232A TYR 3.8 2.9 - - - +
234A ILE* 1.3 76.6 - - - +
236A HIS* 1.3 57.3 + - - +
238A LEU* 3.4 0.7 + - - +
239A LEU* 2.9 45.6 + - + +
284A ALA* 3.4 30.1 - - + +
285A TYR* 4.6 5.4 - - + -
288A LEU* 3.8 9.0 - - + -
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Residues in contact with HIS 236 (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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232A TYR 3.0 18.3 + - - +
233A GLU 3.7 4.3 - - - +
234A ILE 3.3 0.2 - - - -
235A VAL* 1.3 78.5 - - - +
237A THR* 1.3 56.4 + - - +
239A LEU* 3.5 6.3 + - + +
240A ARG* 3.0 45.6 + - - +
288A LEU* 4.3 22.0 - - + -
87B MET* 3.8 22.3 - - + +
88B PHE* 2.9 30.8 + + - -
89B SER* 4.2 8.3 + - - -
131B TYR* 3.5 49.7 + + + +
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Residues in contact with THR 237 (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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174A VAL* 5.6 2.1 - - - +
177A VAL* 5.5 4.3 - - + -
178A GLU* 5.9 6.7 - - + -
181A LEU* 4.1 14.8 - - + -
233A GLU* 2.9 25.1 + - - +
234A ILE* 3.7 7.6 - - - -
235A VAL 3.3 0.2 - - - -
236A HIS* 1.3 77.5 + - - +
238A LEU* 1.3 60.7 + - - +
240A ARG* 3.3 36.2 + - - +
241A LYS* 3.4 35.2 + - - +
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Residues in contact with LEU 238 (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* 4.0 8.1 - - + -
181A LEU* 4.1 20.4 - - + -
192A LEU* 3.9 37.7 - - + -
222A PRO* 3.6 35.2 - - + +
223A ILE* 4.1 16.4 - - + +
226A ALA* 3.9 11.9 - - + -
234A ILE* 2.9 31.5 + - + +
237A THR* 1.3 73.6 - - - +
239A LEU* 1.3 64.2 + - - +
240A ARG 3.3 0.2 - - - -
241A LYS* 3.4 10.6 + - + +
242A GLY 3.7 0.2 + - - -
243A ALA* 3.3 28.0 + - + +
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Residues in contact with LEU 239 (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* 4.5 3.8 - - + -
235A VAL* 2.9 38.5 + - + +
236A HIS* 3.9 5.8 - - + +
238A LEU* 1.3 76.3 - - - +
240A ARG* 1.3 61.7 + - - +
242A GLY* 3.3 9.7 + - - -
243A ALA 3.4 21.1 - - - +
244A ARG* 3.6 39.4 + - - +
285A TYR* 4.1 15.5 - - + -
288A LEU* 3.8 33.9 - - + +
289A SER* 4.1 6.5 - - - -
87B MET* 3.3 24.8 - - + +
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Residues in contact with ARG 240 (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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236A HIS* 3.0 41.0 + - - +
237A THR* 3.5 31.3 + - - +
238A LEU 3.3 0.2 - - - -
239A LEU* 1.3 77.6 - - - +
241A LYS* 1.3 70.3 + - + +
242A GLY 3.4 1.1 - - - -
87B MET* 3.7 19.7 - - + -
131B TYR* 4.9 9.5 - - - +
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Residues in contact with LYS 241 (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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181A LEU* 3.8 37.3 + - + +
186A PHE 5.6 4.5 - - - +
188A GLU 4.7 3.6 - - - +
189A GLY* 4.2 20.4 - - - +
192A LEU* 3.8 30.3 - - + +
237A THR* 3.4 23.8 - - - +
238A LEU* 3.4 4.3 + - - +
239A LEU 3.2 1.2 - - - -
240A ARG* 1.3 90.7 - - + +
242A GLY* 1.3 63.4 + - - +
243A 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