Contacts of the helix formed by residues 187 - 193 (chain Q) in PDB entry 3J7Y
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 LEU 187 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113Q VAL* 3.6 10.3 - - + -
114Q GLY* 3.5 33.2 - - - +
136Q ILE* 4.2 10.3 - - + -
137Q CYS 3.8 4.9 - - - +
138Q ILE* 2.8 25.3 + - - +
182Q ARG* 3.9 23.8 - - + +
184Q ASP* 3.6 18.2 - - + +
186Q SER* 1.3 76.6 - - - +
188Q LEU* 1.3 64.9 + - - +
189Q TYR* 3.1 31.2 - - + +
190Q LEU* 2.9 38.9 + - + +
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Residues in contact with LEU 188 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3153A U 5.4 0.2 - - - +
138Q ILE* 3.4 19.1 - - + -
139Q GLN* 3.6 34.8 - - + +
150Q ILE* 6.0 0.4 - - + -
186Q SER* 3.4 20.9 - - - -
187Q LEU* 1.3 77.2 - - - +
189Q TYR* 1.3 55.5 + - - +
191Q ARG* 2.9 71.5 + - - +
233Q TRP* 3.9 24.3 - - + -
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Residues in contact with TYR 189 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182Q ARG* 3.7 13.6 + - - +
183Q LEU 5.5 0.7 + - - -
184Q ASP* 4.6 7.6 + - + +
186Q SER* 3.4 25.8 - - - -
187Q LEU* 3.0 25.5 + - + +
188Q LEU* 1.3 77.6 - - - +
190Q LEU* 1.3 67.6 + - + +
191Q ARG 3.2 0.4 - - - -
192Q ASP* 3.2 14.7 + - - +
193Q ALA* 3.3 9.5 + - - +
222Q VAL* 3.7 27.6 - - + -
224Q MET* 4.1 3.7 - - - +
233Q TRP* 3.8 31.6 - + + +
240Q ILE* 3.8 23.3 - - + -
242Q GLY* 3.8 20.0 + - - -
243Q ILE* 3.4 37.0 - - + -
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Residues in contact with LEU 190 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136Q ILE* 4.7 20.2 - - + -
138Q ILE* 5.7 3.4 - - + -
152Q ARG* 4.1 25.7 + - + +
182Q ARG* 4.5 13.9 - - - +
187Q LEU* 2.9 44.6 + - + +
189Q TYR* 1.3 77.7 - - + +
191Q ARG* 1.3 65.9 + - - +
192Q ASP 3.1 2.2 - - - -
193Q ALA* 3.1 20.6 + - - +
197Q TYR* 4.0 29.4 - - + +
222Q VAL* 4.0 30.3 - - + -
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Residues in contact with ARG 191 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2469A A 4.5 8.7 + - - -
3153A U 4.8 9.5 + - - -
99L ARG* 3.3 38.3 - - - +
101L ASP* 5.2 2.0 - - - +
138Q ILE* 4.7 1.5 - - - +
139Q GLN* 5.4 0.2 - - - +
150Q ILE* 6.0 2.0 - - - +
152Q ARG* 3.9 21.4 + - - +
161Q GLU* 2.9 40.8 + - - +
188Q LEU* 2.9 53.9 + - - +
190Q LEU* 1.3 77.4 - - - +
192Q ASP* 1.3 70.3 + - - +
193Q ALA 3.4 5.4 + - - +
225Q LYS* 3.8 13.2 + - - -
230Q SER* 5.1 11.4 + - - +
233Q TRP* 5.7 0.9 - - - -
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Residues in contact with ASP 192 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188Q LEU 4.3 0.2 - - - +
189Q TYR 3.2 4.5 + - - +
190Q LEU 3.1 0.8 - - - -
191Q ARG* 1.3 85.2 - - - +
193Q ALA* 1.3 53.8 + - - +
224Q MET* 3.6 25.0 - - + +
225Q LYS* 2.8 42.2 + - + +
229Q TRP* 3.9 14.7 - - + -
230Q SER* 2.7 48.8 + - - -
233Q TRP* 3.0 14.3 + - - -
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Residues in contact with ALA 193 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152Q ARG* 5.8 0.5 + - - -
189Q TYR 3.3 4.4 + - - +
190Q LEU* 3.1 27.3 + - - +
191Q ARG 3.8 5.2 - - - +
192Q ASP* 1.3 81.0 - - - +
194Q LEU* 1.3 69.2 + - - +
195Q PRO* 3.7 2.4 - - - +
197Q TYR* 4.2 6.1 - - + -
222Q VAL* 3.3 34.1 - - + -
223Q LYS 3.8 6.1 - - - +
224Q MET* 4.2 2.5 - - - +
225Q LYS* 4.2 9.1 + - - +
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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