Contacts of the helix formed by residues 175 - 182 (chain B) in PDB entry 1JS6
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 175 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A GLU* 3.0 32.7 + - - +
168B GLN* 4.1 1.3 - - - +
173B GLY 3.6 3.8 + - - -
174B LEU* 1.3 75.5 - - - +
176B GLN* 1.3 67.8 + - - +
177B GLY 3.3 5.9 + - - -
178B ALA* 3.1 37.1 - - + +
179B VAL* 3.3 9.5 + - - +
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Residues in contact with GLN 176 (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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180A LEU* 5.4 1.8 - - - +
203A GLY* 3.6 34.8 + - - -
160B ARG* 5.4 9.1 + - - -
164B VAL* 4.2 36.9 - - + +
168B GLN* 3.9 6.0 - - - +
174B LEU 3.9 1.2 + - - -
175B THR* 1.3 69.9 + - - +
177B GLY* 1.3 68.7 + - - +
178B ALA 2.9 2.0 - - - -
179B VAL* 2.9 15.4 + - - +
180B LEU* 3.0 33.3 + - + +
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Residues in contact with GLY 177 (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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177A GLY* 3.9 26.6 - - - -
180A LEU* 5.4 3.8 - - - -
181A GLU* 4.0 14.9 - - - +
175B THR* 3.3 5.7 + - - -
176B GLN* 1.3 81.8 - - - +
178B ALA* 1.3 62.1 + - - +
180B LEU* 3.5 7.3 + - - +
181B GLU* 3.4 25.3 + - - +
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Residues in contact with ALA 178 (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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181A GLU* 4.1 1.3 + - - +
174B LEU* 4.6 12.1 - - + -
175B THR* 3.1 35.7 + - + +
176B GLN 2.9 0.6 + - - -
177B GLY* 1.3 78.0 - - - +
179B VAL* 1.3 62.1 - - - +
181B GLU* 3.4 25.2 + - - +
182B LYS* 4.0 12.4 + - - +
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Residues in contact with VAL 179 (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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163B VAL* 4.8 0.4 - - + -
164B VAL* 4.0 28.9 - - + +
167B LEU* 3.4 38.4 - - + -
168B GLN* 5.4 0.9 - - + -
174B LEU* 4.0 20.4 - - + -
175B THR 3.5 14.8 - - - +
176B GLN* 2.9 9.4 + - - +
178B ALA* 1.3 73.1 - - - +
180B LEU* 1.3 64.3 + - - +
182B LYS* 3.2 12.5 + - - +
183B LEU* 3.3 28.4 + - + +
235B ILE* 4.9 4.8 - - + +
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Residues in contact with LEU 180 (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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160A ARG* 6.3 0.2 - - - +
176A GLN* 5.4 1.6 - - - +
177A GLY* 5.4 4.9 - - - -
180A LEU* 4.0 26.9 - - + -
203A GLY* 6.1 0.2 - - - -
160B ARG* 3.6 28.9 - - + +
164B VAL* 4.7 3.4 - - + -
176B GLN* 3.0 34.0 + - + +
177B GLY* 3.9 10.3 - - - +
178B ALA 3.4 0.2 - - - -
179B VAL* 1.3 75.0 - - - +
181B GLU* 1.3 64.9 + - - +
182B LYS 3.0 1.4 + - - -
183B LEU* 3.0 43.1 + - + +
202B GLY 4.3 8.5 - - - +
203B GLY* 4.1 23.3 - - - +
204B VAL* 4.3 6.1 - - + -
205B LYS* 4.9 2.4 + - - +
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Residues in contact with GLU 181 (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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175A THR* 3.0 38.9 + - - +
177A GLY* 4.0 14.8 - - - +
178A ALA* 4.1 3.3 + - - -
177B GLY 3.4 15.2 + - - +
178B ALA* 3.5 17.5 - - - +
179B VAL 3.3 0.6 - - - -
180B LEU* 1.3 78.1 - - - +
182B LYS* 1.3 65.9 + - + +
205B LYS* 3.0 33.9 + - - +
234B LEU* 4.4 1.6 - - - +
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Residues in contact with LYS 182 (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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178B ALA* 4.3 12.1 - - - +
179B VAL* 3.2 5.1 + - - +
180B LEU 3.1 0.8 - - - -
181B GLU* 1.3 85.5 - - + +
183B LEU* 1.3 59.6 + - - +
184B VAL 3.5 0.3 + - - -
233B GLY* 3.2 26.3 + - - +
234B LEU* 3.4 18.4 - - + +
235B ILE* 2.5 54.2 + - + +
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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