Contacts of the helix formed by residues 188 - 196 (chain A) in PDB entry 1JUO
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 TYR 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A PRO* 1.3 70.9 - - - +
189A ASP* 1.3 70.1 + - + +
191A PHE* 3.2 2.3 + - - +
192A ILE* 2.9 51.1 + - + +
134B PHE* 3.7 16.8 - + - -
135B ARG 6.0 3.4 - - - -
136B LEU* 3.9 16.9 - - + +
170B THR* 2.7 44.4 + - + +
173B PHE* 3.4 47.7 - + + -
174B ARG* 5.9 3.4 - - + -
182B GLY* 2.9 16.2 + - - +
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Residues in contact with ASP 189 (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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187A PRO* 3.4 3.2 - - + +
188A TYR* 1.3 84.8 - - + +
190A ASP* 1.3 62.4 + - - +
192A ILE* 3.4 4.4 + - - +
193A GLN* 3.1 25.5 + - - +
135B ARG 4.3 3.3 - - - +
136B LEU* 3.6 9.9 - - - +
137B SER* 2.7 53.2 + - - -
139B GLN* 4.9 5.0 - - - +
140B ALA* 4.0 6.7 + - - +
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Residues in contact with ASP 190 (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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176A ARG* 2.8 42.4 + - - -
186A PHE* 3.4 10.7 - - - -
187A PRO* 3.1 28.4 + - + +
189A ASP* 1.3 76.0 + - - +
191A PHE* 1.3 66.1 + - - +
193A GLN* 3.2 17.2 - - - +
194A CYS* 3.0 27.2 + - - +
139B GLN* 5.5 0.7 + - - +
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Residues in contact with PHE 191 (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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186A PHE* 3.7 24.6 - + + -
187A PRO 2.9 15.5 + - - +
188A TYR 3.6 3.4 - - - +
190A ASP* 1.3 75.7 - - - +
192A ILE* 1.3 74.9 + - + +
194A CYS* 3.6 0.6 - - - +
195A VAL* 3.1 38.1 + - + +
169B LEU* 3.8 50.7 - - + -
173B PHE* 4.0 21.8 - + + -
186B PHE* 3.4 38.8 - + - -
191B PHE* 4.1 24.9 - + - -
194B CYS* 4.4 8.1 - - - -
195B VAL* 4.5 2.7 - - + -
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Residues in contact with ILE 192 (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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188A TYR* 2.9 58.9 + - + +
189A ASP* 3.7 4.3 - - - +
191A PHE* 1.3 85.4 - - + +
193A GLN* 1.3 68.2 + - - +
195A VAL* 4.6 1.1 - - - -
196A MET* 3.0 40.7 + - + +
136B LEU* 4.0 24.0 - - + -
140B ALA* 4.4 5.2 - - + -
144B ILE* 4.9 1.8 - - + -
166B LEU* 4.1 17.0 - - + -
169B LEU* 4.4 14.8 - - + -
170B THR* 4.1 7.4 - - - +
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Residues in contact with GLN 193 (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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176A ARG* 3.5 13.2 + - - -
189A ASP* 3.1 14.3 + - - +
190A ASP* 3.2 30.2 - - - +
192A ILE* 1.3 79.5 - - - +
194A CYS* 1.3 61.8 + - - +
196A MET* 4.8 0.7 - - - -
197A SER* 2.9 23.2 + - - -
139B GLN* 3.5 32.5 + - + +
140B ALA* 3.4 34.3 - - + +
143B SER* 3.2 21.2 + - - +
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Residues in contact with CYS 194 (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 LEU* 5.3 3.6 - - - -
172A SER* 3.6 34.7 + - - -
176A ARG* 3.9 20.9 - - - +
186A PHE* 4.5 11.4 - - + -
190A ASP 3.0 19.3 + - - +
191A PHE* 3.6 6.3 - - - +
192A ILE 3.1 0.2 - - - -
193A GLN* 1.3 87.1 - - - +
195A VAL* 1.3 68.7 + - + +
197A SER* 3.6 12.5 + - - -
198A VAL* 4.0 10.6 - - - +
191B PHE* 4.9 3.6 - - - -
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Residues in contact with VAL 195 (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 LEU* 4.4 8.3 - - + -
191A PHE* 3.1 36.3 + - + +
192A ILE* 4.1 4.5 - - - +
194A CYS* 1.3 75.0 - - + +
196A MET* 1.3 66.3 - - - +
197A SER 3.1 2.7 - - - -
198A VAL* 3.2 22.7 + - - +
165B LYS* 4.7 3.3 + - - -
169B LEU* 3.3 38.6 - - + +
191B PHE* 4.2 14.6 - - + -
195B VAL* 3.9 35.3 - - + +
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Residues in contact with MET 196 (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 ILE* 3.0 41.0 + - + +
193A GLN* 4.7 2.5 - - - +
195A VAL* 1.3 75.8 - - + +
197A SER* 1.3 61.4 + - - +
198A VAL 3.3 2.4 + - - +
143B SER 4.9 2.1 - - - +
144B ILE* 4.0 24.9 - - + +
147B ARG* 3.7 17.8 - - - +
148B TYR* 4.4 14.5 - - + -
162B CYS* 3.7 36.1 - - - +
165B LYS* 4.1 22.1 + - + +
166B LEU* 3.6 23.8 - - + -
169B LEU* 3.7 25.6 - - + -
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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