Contacts of the helix formed by residues 182 - 187 (chain B) in PDB entry 2VN9
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 SER 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180B TYR 3.7 1.0 + - - -
181B LEU* 1.3 76.8 - - - +
183B PRO* 1.3 75.9 - - - +
184B GLU* 3.0 29.2 + - - -
185B VAL* 3.3 21.3 + - - +
186B LEU* 3.1 21.8 + - - +
195B VAL* 3.4 11.6 + - - +
198B TRP* 3.7 22.4 - - - -
226B ILE* 4.0 1.6 - - - -
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Residues in contact with PRO 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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182B SER* 1.3 88.4 - - - +
184B GLU* 1.3 61.9 + - - +
186B LEU* 3.4 2.1 + - - +
187B ARG* 2.8 39.7 + - - +
198B TRP* 3.6 36.8 - - + -
226B ILE* 3.6 24.2 - - + +
227B LYS* 4.2 16.5 - - + +
255B ILE* 4.0 30.5 - - + +
260B ARG* 4.3 0.2 - - - +
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Residues in contact with GLU 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 SER* 3.0 22.7 + - - +
183B PRO* 1.3 71.8 - - - +
185B VAL* 1.3 67.4 + - - +
187B ARG* 3.3 7.9 + - - +
188B LYS 3.3 2.9 + - - -
189B ASP* 3.0 46.7 + - + +
190B PRO 4.2 4.5 - - - +
191B TYR* 3.6 23.1 - - + +
194B PRO* 4.4 0.5 - - - +
195B VAL* 3.1 14.4 + - - +
255B ILE 4.1 2.1 - - - +
257B PRO* 3.9 24.5 - - + +
260B ARG* 2.9 41.7 + - - -
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Residues in contact with VAL 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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173B GLY 4.4 12.6 - - - +
174B PHE* 3.9 28.8 - - + -
175B ALA 4.5 6.5 - - - +
181B LEU* 4.0 22.9 - - + -
182B SER* 3.3 25.9 + - - +
184B GLU* 1.3 77.6 - - - +
186B LEU* 1.3 62.0 + - - +
188B LYS* 3.2 14.7 + - - +
189B ASP 5.1 0.2 - - - -
191B TYR* 3.7 38.8 - - + -
195B VAL* 3.9 8.5 - - + -
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Residues in contact with LEU 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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174B PHE* 3.8 16.2 - - + -
181B LEU* 3.7 21.8 - - + +
182B SER 3.1 10.4 + - - +
183B PRO 3.7 5.8 - - - +
185B VAL* 1.3 76.1 - - - +
187B ARG* 1.3 59.8 + - - +
188B LYS* 3.2 6.3 + - - +
223B TYR* 3.4 52.5 - - + +
226B ILE* 3.3 43.7 - - + -
227B LYS* 3.8 23.0 + - + +
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Residues in contact with ARG 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 PRO* 2.8 30.1 + - - +
184B GLU* 3.7 3.6 - - - +
185B VAL 3.3 0.6 - - - -
186B LEU* 1.3 73.3 - - - +
188B LYS* 1.3 69.1 + - - +
189B ASP* 3.3 34.9 + - - +
227B LYS* 4.3 19.3 + - + +
255B ILE* 5.6 7.4 - - - +
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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