Contacts of the helix formed by residues 181 - 189 (chain B) in PDB entry 5JKC
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 181 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140B TRP* 3.6 9.1 - - - -
179B PHE 3.7 1.4 - - - +
180B PRO* 1.3 86.0 - - + +
182B PRO* 1.3 75.5 - - + +
183B ALA* 3.5 12.0 + - - +
184B ASP* 2.5 50.3 + - - +
185B LEU 3.3 3.3 + - - -
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Residues in contact with PRO 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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136B CYS* 3.6 29.2 - - + +
137B GLU* 4.1 20.6 - - + +
140B TRP* 3.5 42.1 - - + -
180B PRO 4.5 0.9 - - - +
181B THR* 1.3 86.3 - - + +
183B ALA* 1.3 62.1 + - - +
185B LEU* 3.0 13.5 + - - +
186B CYS* 3.0 16.8 + - - +
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Residues in contact with ALA 183 (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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181B THR* 3.1 12.4 + - - +
182B PRO* 1.3 78.8 - - - +
184B ASP* 1.3 63.3 + - - +
186B CYS* 3.9 0.2 - - - +
187B GLU* 3.1 39.2 + - - +
196B ALA* 3.6 26.2 - - + +
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Residues in contact with ASP 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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178B TYR 4.9 0.9 - - - +
179B PHE* 3.7 21.7 - - + -
180B PRO* 3.3 16.7 - - + +
181B THR* 2.5 42.2 + - - +
183B ALA* 1.3 77.5 - - - +
185B LEU* 1.3 57.6 + - - +
187B GLU* 5.3 0.7 - - - -
188B LYS* 3.0 63.1 + - + +
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Residues in contact with LEU 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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90B PHE* 4.3 6.3 - - + -
136B CYS 5.2 0.2 - - - +
139B TRP* 3.7 25.7 - - + +
140B TRP* 3.4 42.0 - - + +
143B CYS* 4.4 8.7 - - + -
175B PHE* 4.2 14.4 - - + -
179B PHE* 3.7 31.8 - - + -
181B THR 3.3 3.5 + - - +
182B PRO 3.0 9.7 + - - +
184B ASP* 1.3 79.5 - - - +
186B CYS* 1.3 62.6 + - - +
187B GLU 3.3 0.5 + - - -
189B THR* 2.9 50.3 + - + +
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Residues in contact with CYS 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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131B LEU* 4.0 9.6 - - - -
136B CYS* 2.0 57.4 - - - -
139B TRP* 3.8 24.2 - - - -
182B PRO 3.0 7.5 + - - +
183B ALA 3.9 3.6 - - - +
185B LEU* 1.3 79.9 - - - +
187B GLU* 1.3 64.9 + - + +
189B THR* 4.1 4.3 + - - -
190B TRP* 4.7 0.9 - - - +
194B PHE* 3.5 30.9 - - + +
196B ALA* 4.3 9.2 - - + +
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Residues in contact with GLU 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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183B ALA* 3.1 26.8 + - - +
184B ASP* 4.2 1.8 - - - +
186B CYS* 1.3 80.9 - - + +
188B LYS* 1.3 70.4 + - + +
189B THR 3.7 0.3 + - - -
190B TRP 3.8 1.9 + - - -
191B SER 3.8 1.4 + - - -
192B ASN* 2.8 42.3 + - - +
194B PHE 3.3 20.4 - - - +
195B LYS* 3.2 33.6 + - - +
196B ALA* 2.9 31.3 + - - +
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Residues in contact with LYS 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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151B SER* 3.3 26.9 + - - +
152B ASN* 3.4 29.3 + - - +
153B TRP 3.6 15.0 + - - -
154B ARG* 3.9 6.4 + - - +
178B TYR 6.0 0.2 - - - +
179B PHE* 4.3 2.0 - - + -
184B ASP* 3.0 44.9 + - + +
187B GLU* 1.3 83.6 - - + +
189B THR* 1.3 64.6 + - - +
190B TRP 3.2 3.2 + - - -
191B SER* 3.5 9.5 + - - +
192B ASN* 4.8 9.6 - - - +
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Residues in contact with THR 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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74B PHE* 5.5 1.2 - - - -
90B PHE* 4.1 6.3 - - + -
139B TRP* 4.1 6.9 - - - -
153B TRP* 3.7 51.6 - - + +
154B ARG* 4.8 0.7 + - - -
179B PHE* 3.8 14.4 - - + -
185B LEU* 2.9 43.8 + - + +
186B CYS 4.1 3.8 + - - -
188B LYS* 1.3 77.6 - - - +
190B TRP* 1.3 79.3 + - - +
191B SER 3.5 1.1 + - - -
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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