Contacts of the helix formed by residues 181 - 189 (chain B) in PDB entry 1HJV
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 GLY 181 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B SER* 3.1 5.7 + - - -
180B ALA* 1.3 78.2 - - - +
182B LYS* 1.3 55.3 + - - -
183B VAL* 3.4 3.8 - - - -
184B THR* 3.1 6.8 + - - -
185B ILE* 2.7 35.1 + - - +
208B PHE* 4.6 1.1 - - - -
234B PHE 5.7 0.4 - - - -
1H NAG 3.6 35.3 + - - +
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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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246A ARG* 4.3 8.3 - - - +
1385A SO4 4.3 4.7 - - - -
180B ALA 3.5 5.5 + - - -
181B GLY* 1.3 70.7 - - - -
183B VAL* 1.3 56.6 + - + +
185B ILE* 3.5 9.5 - - - +
186B ASP* 2.3 72.9 + - - +
233B ARG* 4.2 5.2 - - - +
234B PHE* 3.4 49.3 + - + +
239B TYR* 3.4 24.0 - - + +
243B TYR* 3.2 28.9 + - + -
1385D SO4 4.1 18.8 - - - -
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B ARG* 6.0 2.2 - - - +
181B GLY* 5.2 1.3 - - - -
182B LYS* 1.3 79.5 - - + +
184B THR* 1.3 65.4 - - - +
186B ASP* 3.4 9.0 + - - +
187B SER* 3.1 24.3 + - - -
234B PHE* 5.0 17.3 - - + -
231D PRO* 4.2 31.4 - - + +
1H NAG 5.8 3.1 - - - +
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Residues in contact with THR 184 (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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141B TYR* 3.8 35.9 - - + -
179B SER* 3.7 25.5 + - - -
181B GLY 3.1 7.3 + - - -
183B VAL* 1.3 78.1 - - - +
185B ILE* 1.3 67.6 + - - +
187B SER* 3.0 16.1 + - - +
188B SER* 3.0 20.2 + - - +
189B TYR* 4.7 3.6 - - + -
1H NAG 3.9 16.1 + - - -
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Residues in contact with ILE 185 (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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179B SER 3.2 28.5 - - - +
180B ALA* 3.8 15.3 - - - +
181B GLY 2.7 25.2 + - - +
182B LYS* 3.5 8.3 - - - +
184B THR* 1.3 71.6 - - - +
186B ASP* 1.3 63.2 + - - +
189B TYR* 3.1 41.1 + - + +
191B ILE* 4.4 7.6 - - + -
203B ILE* 4.8 2.9 - - + -
240B ALA* 5.2 3.6 - - + +
243B TYR* 4.2 13.2 - - + -
244B MET* 3.3 26.7 - - + -
247B LEU* 4.2 24.9 - - + -
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Residues in contact with ASP 186 (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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246A ARG* 3.9 15.7 - - - +
144B ARG* 5.5 2.8 + - - +
147B LYS* 3.0 23.8 + - - +
182B LYS* 2.3 54.8 + - - +
183B VAL* 3.6 7.4 + - - +
185B ILE* 1.3 75.2 - - - +
187B SER* 1.3 57.1 + - - +
188B SER 3.5 0.2 - - - -
243B TYR* 2.6 24.9 + - - -
247B LEU* 5.1 1.0 - - - +
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Residues in contact with SER 187 (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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142B PRO 4.8 0.2 + - - -
143B GLY 2.9 18.5 - - - +
144B ARG* 3.3 53.5 + - - +
147B LYS* 4.1 7.4 - - - +
183B VAL 3.1 15.0 + - - -
184B THR* 3.0 7.6 + - - +
186B ASP* 1.3 78.7 - - - +
188B SER* 1.3 65.3 + - - +
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Residues in contact with SER 188 (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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142B PRO* 2.3 49.1 + - - +
143B GLY 4.0 3.1 - - - -
147B LYS* 3.5 23.9 - - - +
150B PHE* 4.0 10.4 - - - -
184B THR* 3.0 20.9 + - - +
186B ASP 3.5 0.2 - - - -
187B SER* 1.3 84.5 + - - +
189B TYR* 1.3 74.4 + - - +
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Residues in contact with TYR 189 (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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139B TRP 4.6 2.1 + - - -
141B TYR* 3.8 17.7 - + - -
142B PRO* 4.3 17.4 - - + +
147B LYS* 3.5 14.7 + - - +
150B PHE* 3.5 30.3 - + - -
177B ALA 4.1 2.8 + - - -
178B LEU* 3.2 34.3 - - + -
179B SER* 2.9 42.9 + - - -
184B THR* 4.4 3.8 - - + -
185B ILE* 3.1 45.4 + - + +
188B SER* 1.3 82.4 - - - +
190B ASP* 1.3 59.3 + - - +
191B ILE* 3.3 25.8 + - + +
194B ILE* 4.6 1.6 - - + -
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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