Contacts of the helix formed by residues 166 - 173 (chain C) in PDB entry 2VWI
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 166 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63C GLU* 3.5 24.0 - - - +
67C MET* 3.8 13.0 - - - -
143C ILE 5.5 0.4 + - - -
144C HIS 5.0 0.6 + - - -
145C ARG* 5.9 0.3 - - - -
164C ASP 3.4 0.8 + - - -
165C PHE* 1.3 86.4 - - - +
167C VAL* 1.3 66.4 + - - -
168C SER 3.3 0.8 + - - -
169C ALA* 3.4 5.7 + - - +
170C PHE* 2.9 22.5 + - - +
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Residues in contact with VAL 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C ILE* 3.8 25.1 - - + -
60C LEU* 4.0 32.1 - - + -
63C GLU* 4.0 12.7 - - + +
64C ILE* 3.7 31.0 - - + -
67C MET* 3.5 17.0 - - - -
88C LEU* 4.4 3.1 - - + -
90C LEU* 4.2 13.9 - - + -
165C PHE 3.8 0.6 + - - -
166C GLY* 1.3 69.4 - - - -
168C SER* 1.3 64.7 + - - +
170C PHE* 3.2 8.1 - - - +
171C LEU* 3.0 27.9 + - + +
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Residues in contact with SER 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LYS* 2.9 33.8 + - - +
48C ILE* 5.1 3.8 - - - -
67C MET* 5.7 0.4 - - - +
90C LEU* 5.0 5.0 - - - +
146C ASP* 5.6 0.6 + - - -
164C ASP* 3.3 31.0 + - - -
165C PHE 4.9 1.0 + - - -
166C GLY 3.4 1.0 - - - -
167C VAL* 1.3 80.6 - - - +
169C ALA* 1.3 62.8 + - - +
171C LEU* 3.4 6.1 + - - +
172C ALA* 3.2 23.4 + - - +
1294C ANP 5.0 5.9 + - - -
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Residues in contact with ALA 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C HIS* 3.0 29.6 - - + +
145C ARG* 4.0 4.3 - - + -
146C ASP* 3.8 24.5 - - + -
164C ASP* 3.1 22.6 + - - +
166C GLY 3.4 6.0 + - - +
168C SER* 1.3 72.4 - - - +
170C PHE* 1.3 60.7 + - - +
172C ALA* 3.3 2.5 + - - +
173C THR* 2.6 36.2 + - - +
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Residues in contact with PHE 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C GLU* 3.9 39.0 - - + -
60C LEU* 3.7 23.1 - - + -
62C LYS* 4.7 1.1 - - - -
63C GLU* 3.5 29.6 - - + +
145C ARG* 3.5 25.0 - - - +
166C GLY 2.9 18.9 + - - +
167C VAL* 3.2 7.2 - - - +
169C ALA* 1.3 79.0 - - - +
171C LEU* 1.3 67.6 + - + +
172C ALA 3.4 0.3 + - - -
173C THR 3.6 3.1 + - - -
175C GLY* 3.0 49.2 + - - +
176C ASP* 3.4 35.7 - - + -
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Residues in contact with LEU 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C THR* 4.7 7.2 - - - +
48C ILE* 4.1 29.8 - - + -
53C CYS* 4.3 21.5 - - + +
55C THR* 3.9 31.9 - - + +
59C GLU* 4.4 1.8 - - - +
60C LEU* 4.1 4.0 - - + -
167C VAL* 3.0 31.4 + - + +
168C SER* 3.4 5.1 + - - +
169C ALA 3.3 0.2 - - - -
170C PHE* 1.3 96.0 - - + +
172C ALA* 1.3 58.5 + - - +
173C THR 3.4 0.2 - - - -
174C GLY 4.7 3.0 + - - -
175C GLY* 5.1 1.8 - - - +
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Residues in contact with ALA 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C THR* 6.5 0.4 - - + -
146C ASP* 4.0 22.9 - - - +
168C SER 3.2 16.6 + - - +
169C ALA 3.3 4.7 + - - +
170C PHE 3.3 0.4 - - - -
171C LEU* 1.3 78.3 - - - +
173C THR* 1.3 61.7 + - - +
174C GLY 3.8 1.9 + - - -
1294C ANP 4.8 11.9 - - - +
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Residues in contact with THR 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C ARG* 2.9 58.0 + - - +
146C ASP* 4.5 10.8 - - + +
169C ALA 2.6 21.7 + - - +
170C PHE 3.6 0.4 + - - -
171C LEU 3.4 0.4 - - - -
172C ALA* 1.3 85.7 - - + +
174C GLY* 1.3 56.7 + - - +
175C GLY 3.5 2.5 - - - -
177C ILE* 3.6 10.0 - - - +
204C TYR* 4.0 9.5 + - - -
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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