Contacts of the helix formed by residues 2170 - 2181 (chain B) in PDB entry 1WUE
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 ASP2170 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2165B ILE* 3.2 29.4 - - + -
2167B PRO 3.1 18.3 - - - +
2168B GLY 5.2 0.3 - - - -
2169B TYR* 1.3 70.9 + - - +
2171B VAL* 1.3 84.8 + - - +
2172B GLU* 3.4 1.3 - - - +
2173B PRO* 3.2 7.0 - - - +
2174B VAL* 3.0 31.2 + - - +
2194B TYR* 2.7 25.1 + - + +
2201B GLN* 2.6 29.4 + - - +
2202B LEU* 5.4 0.7 - - - +
2205B LEU* 4.8 15.9 - - + -
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Residues in contact with VAL2171 (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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2170B ASP* 1.3 97.0 + - - +
2172B GLU* 1.3 81.1 + - + +
2174B VAL* 3.9 3.7 - - - +
2175B ALA* 2.9 27.1 + - - +
2201B GLN* 3.3 22.4 - - - +
2204B ARG* 3.5 47.3 - - + +
2205B LEU* 4.0 13.0 - - + -
2208B TYR* 4.6 13.0 - - + +
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Residues in contact with GLU2172 (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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2143B LEU* 4.6 16.3 - - + +
2169B TYR* 6.2 0.4 - - - -
2170B ASP 4.5 0.4 - - - +
2171B VAL* 1.3 93.2 - - + +
2173B PRO* 1.3 70.8 - - + +
2175B ALA* 3.5 14.4 - - - +
2176B LEU* 3.1 21.8 + - - +
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Residues in contact with PRO2173 (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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2143B LEU* 4.7 9.2 - - + -
2146B LEU* 3.9 12.4 - - + +
2163B LEU* 4.7 4.7 - - + -
2165B ILE* 4.0 7.6 - - + -
2169B TYR* 3.7 44.4 - - + +
2170B ASP* 3.2 33.4 - - - +
2172B GLU* 1.3 96.2 - - + +
2174B VAL* 1.3 60.2 + - - +
2176B LEU* 3.4 7.0 + - + +
2177B ILE* 3.2 28.7 + - - +
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Residues in contact with VAL2174 (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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2163B LEU* 4.5 14.6 - - + -
2165B ILE* 4.5 5.6 - - + -
2170B ASP 3.0 26.6 + - - +
2171B VAL* 4.0 3.8 - - - +
2173B PRO* 1.3 73.0 - - - +
2175B ALA* 1.3 66.7 + - - +
2177B ILE* 3.5 3.0 + - - +
2178B ARG* 3.0 22.3 + - - +
2186B LEU* 4.1 6.4 - - + +
2188B VAL* 3.8 26.5 - - + -
2205B LEU* 5.2 8.3 - - + -
2208B TYR* 3.7 31.0 - - + -
2210B LEU* 3.9 20.2 - - + -
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Residues in contact with ALA2175 (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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2171B VAL 2.9 19.5 + - - +
2172B GLU* 3.5 16.8 - - - +
2173B PRO 3.2 0.2 - - - -
2174B VAL* 1.3 77.3 - - - +
2176B LEU* 1.3 63.1 + - - +
2178B ARG* 3.2 2.3 + - - +
2179B GLN* 2.9 25.5 + - - +
2208B TYR* 3.4 33.0 - - + +
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Residues in contact with LEU2176 (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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2143B LEU* 3.5 50.9 - - + +
2144B PRO* 4.8 0.9 - - + -
2146B LEU* 5.4 4.3 - - + -
2147B LEU* 3.6 18.6 - - + +
2172B GLU 3.1 9.8 + - - +
2173B PRO* 3.7 9.4 - - + +
2175B ALA* 1.3 79.3 - - - +
2177B ILE* 1.3 61.7 + - + +
2179B GLN* 3.2 13.2 + - - +
2180B HIS* 3.2 54.4 + - + +
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Residues in contact with ILE2177 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2146B LEU* 3.9 16.2 - - + -
2147B LEU* 4.3 13.5 - - + -
2150B VAL* 3.4 35.4 - - + -
2163B LEU* 3.1 38.4 - - + -
2173B PRO 3.2 10.6 + - - +
2174B VAL 4.0 3.1 - - - +
2176B LEU* 1.3 74.6 - - + +
2178B ARG* 1.3 61.4 + - - +
2181B PHE* 2.8 44.5 + - + +
2184B LEU* 4.6 2.9 - - + -
2186B LEU* 4.2 22.2 - - + -
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Residues in contact with ARG2178 (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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2174B VAL 3.0 19.2 + - - +
2175B ALA 3.7 3.6 - - - +
2177B ILE* 1.3 78.2 - - - +
2179B GLN* 1.3 61.3 + - - +
2181B PHE 3.0 17.5 + - - -
2182B PRO* 3.1 42.7 + - - +
2183B ASN 4.1 0.6 - - - -
2184B LEU* 3.0 28.5 + - - +
2186B LEU* 3.6 26.1 - - + +
2207B HIS 5.7 0.4 - - - +
2208B TYR* 2.8 50.6 + - + +
2209B GLN* 3.2 23.1 + - - +
2210B LEU* 4.5 0.4 - - - +
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Residues in contact with GLN2179 (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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2175B ALA 2.9 17.3 + - - +
2176B LEU* 3.4 12.9 - - - +
2178B ARG* 1.3 81.5 - - - +
2180B HIS* 1.3 87.7 + - + +
2182B PRO* 4.3 6.4 - - - +
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Residues in contact with HIS2180 (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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2147B LEU* 3.3 29.1 - - + +
2151B GLN* 5.4 1.8 + - - +
2176B LEU* 3.2 37.4 + - + +
2179B GLN* 1.3 100.0 + - + +
2181B PHE* 1.3 88.7 + - + +
2182B PRO* 3.8 6.2 - - - +
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Residues in contact with PHE2181 (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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2147B LEU* 4.1 8.7 - - + -
2150B VAL* 3.5 31.6 - - + -
2151B GLN* 3.3 34.3 - - + -
2154B VAL* 3.7 31.9 - - + -
2177B ILE* 2.8 24.6 + - + +
2178B ARG* 3.0 24.5 + - - +
2180B HIS* 1.3 99.1 - - + +
2182B PRO* 1.3 62.9 - - - +
2183B ASN 3.4 2.6 + - - -
2184B LEU* 3.7 21.5 + - + +
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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