Contacts of the helix formed by residues 182 - 194 (chain B) in PDB entry 3VF0
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 LYS 182 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ALA* 3.9 6.2 - - - +
180B TYR* 3.5 9.5 - - - +
181B MET* 1.4 90.6 - - + +
183B LYS* 1.3 63.4 + - - +
184B ASP* 4.1 12.1 - - + +
185B SER* 3.3 31.9 + - - +
186B ALA 3.6 1.4 + - - -
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Residues in contact with LYS 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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131B ASP* 2.7 57.6 + - + +
132B ALA* 4.1 6.0 - - + +
182B LYS* 1.3 69.4 - - - +
184B ASP* 1.3 65.8 + - - +
186B ALA* 3.3 3.6 + - - +
187B ALA* 3.0 22.5 + - + +
207B TRP* 3.7 22.0 - - + -
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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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182B LYS* 3.3 10.6 - - + +
183B LYS* 1.3 78.4 - - - +
185B SER* 1.4 55.0 + - - +
187B ALA* 3.4 9.2 + - - +
188B ARG* 3.1 30.0 + - - +
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Residues in contact with SER 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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155B PHE* 3.1 28.1 + - - +
156B GLY* 3.7 8.2 - - - -
157B SER 4.7 1.0 + - - -
180B TYR* 3.6 23.0 - - - +
182B LYS* 3.3 28.6 + - - +
183B LYS 3.3 0.2 - - - -
184B ASP* 1.4 74.0 - - - +
186B ALA* 1.3 54.5 + - - +
188B ARG* 3.2 7.5 + - - +
189B ALA* 2.8 33.8 + - - +
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Residues in contact with ALA 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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132B ALA* 3.7 28.0 - - + +
134B LEU* 3.2 14.9 - - + +
180B TYR* 3.5 17.4 - - + -
182B LYS 3.6 1.0 + - - -
183B LYS 3.3 10.0 + - - +
185B SER* 1.3 76.8 - - - +
187B ALA* 1.3 52.5 + - - +
189B ALA 3.3 0.2 + - - -
190B LYS* 2.8 31.7 + - - +
207B TRP* 3.6 24.0 - - + -
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Residues in contact with ALA 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 LYS* 3.0 13.7 + - + +
184B ASP* 3.5 15.9 - - - +
186B ALA* 1.3 71.6 - - - +
188B ARG* 1.3 59.8 + - - +
190B LYS* 3.5 3.6 + - - +
191B SER* 3.0 29.8 + - - -
207B TRP* 3.8 18.8 - - + -
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Residues in contact with ARG 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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154B PRO* 3.2 28.2 + - - +
155B PHE* 3.6 35.9 + - + +
184B ASP* 3.1 15.9 + - - +
185B SER* 3.4 8.5 - - - +
187B ALA* 1.3 71.6 - - - +
189B ALA* 1.3 64.9 + - - +
191B SER* 3.4 7.5 + - - -
192B ASP* 3.1 29.8 + - - +
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Residues in contact with ALA 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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134B LEU* 3.8 11.4 - - + -
155B PHE* 3.5 20.8 - - + -
180B TYR* 3.4 27.4 - - + +
185B SER 2.8 13.4 + - - +
186B ALA 3.5 8.1 - - - +
188B ARG* 1.3 76.2 - - - +
190B LYS* 1.3 57.9 + - - +
192B ASP* 3.3 1.4 + - - -
193B LEU* 2.8 42.2 + - + +
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Residues in contact with LYS 190 (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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134B LEU* 3.9 4.2 - - + +
186B ALA 2.8 20.9 + - - +
187B ALA* 3.9 5.8 - - - +
189B ALA* 1.3 71.0 - - - +
191B SER* 1.3 58.6 + - - +
194B LEU* 2.9 56.6 + - + +
205B VAL* 3.9 48.9 - - + +
206B HIS* 5.2 0.2 - - - +
207B TRP* 3.3 40.7 - - + +
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Residues in contact with SER 191 (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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187B ALA 3.0 17.7 + - - -
188B ARG* 3.5 9.0 - - - -
190B LYS* 1.3 78.5 - - - +
192B ASP* 1.4 66.7 + - - +
194B LEU* 4.3 10.7 - - - +
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Residues in contact with ASP 192 (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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155B PHE* 3.5 34.8 - - + -
188B ARG* 3.1 17.7 + - - +
191B SER* 1.4 84.2 + - - +
193B LEU* 1.3 61.6 + - - +
194B LEU 3.7 1.0 - - - +
196B LYS* 3.6 19.9 + - - +
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Residues in contact with LEU 193 (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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134B LEU* 5.6 1.6 - - + -
136B VAL* 4.2 15.0 - - + -
151B LEU* 3.8 38.6 - - + +
152B VAL* 4.0 24.9 - - + -
155B PHE* 4.1 18.6 - - + -
189B ALA* 2.8 30.9 + - + +
192B ASP* 1.3 78.6 - - - +
194B LEU* 1.3 60.3 + - - +
195B GLY 3.1 1.2 + - - -
196B LYS* 3.0 34.7 + - + +
203B LEU* 3.5 20.0 - - + +
205B VAL* 3.6 13.9 - - + -
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Residues in contact with LEU 194 (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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190B LYS* 2.9 41.5 + - + +
191B SER* 4.3 9.2 - - - +
192B ASP 3.7 1.4 - - - +
193B LEU* 1.3 73.1 - - - +
195B GLY* 1.3 63.9 + - - +
196B LYS 3.7 0.3 + - - -
203B LEU 4.1 1.1 - - - +
204B TYR* 3.5 23.1 - - + -
205B VAL* 3.4 38.0 - - + +
313B ALA* 4.2 23.3 - - + +
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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