Contacts of the helix formed by residues 2170 - 2179 (chain B) in PDB entry 1WUF
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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2165B ILE* 3.4 22.4 - - + +
2166B ALA 3.0 2.1 - - - +
2167B PRO* 2.5 28.5 - - - +
2168B ASN 3.7 2.2 + - - -
2169B LYS* 1.3 74.3 + - - +
2171B ILE* 1.3 94.3 - - + +
2172B GLN* 3.3 5.2 + - - +
2173B PHE* 3.2 5.2 + - - +
2174B VAL* 3.0 26.5 + - - +
2194B TYR* 3.2 24.9 + - - +
2201B LEU* 4.0 13.9 - - - +
2205B LEU* 4.3 7.1 - - + +
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Residues in contact with ILE2171 (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 92.7 - - - +
2172B GLN* 1.3 63.7 + - - +
2174B VAL* 3.4 4.7 + - - +
2175B GLU* 3.2 28.4 + - - +
2201B LEU* 3.7 16.6 - - + +
2204B GLU* 3.0 53.8 - - + +
2205B LEU* 3.2 19.1 - - + -
2208B TYR* 3.9 27.6 - - + +
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Residues in contact with GLN2172 (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 VAL* 4.3 16.2 - - + +
2168B ASN 2.7 31.5 + - - -
2169B LYS* 4.1 1.0 - - - +
2170B ASP* 4.3 4.3 + - - +
2171B ILE* 1.3 77.1 - - - +
2173B PHE* 1.3 85.7 + - + +
2175B GLU* 4.0 13.0 - - - +
2176B ALA* 3.5 20.4 + - - +
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Residues in contact with PHE2173 (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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2140B GLN* 3.1 36.1 - - + -
2141B GLN 4.2 9.9 - - - -
2142B ASN 3.6 17.5 - - - -
2143B VAL* 4.3 13.0 - - + -
2146B LEU* 3.4 29.6 - - + -
2163B LEU* 4.9 3.4 - - + -
2164B LYS 6.1 0.2 - - - +
2165B ILE* 5.1 4.5 - - + -
2169B LYS* 3.5 42.8 - - + +
2170B ASP 3.2 5.5 + - - +
2172B GLN* 1.3 100.8 - - + +
2174B VAL* 1.3 67.9 + - + +
2176B ALA* 3.3 8.1 - - - +
2177B VAL* 3.0 25.9 + - - +
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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
----------------------------------------------------------
2163B LEU* 4.5 12.3 - - + +
2165B ILE* 3.9 17.3 - - + -
2170B ASP 3.0 22.1 + - - +
2171B ILE* 3.8 6.5 - - - +
2173B PHE* 1.3 76.5 - - - +
2175B GLU* 1.3 52.3 + - - +
2177B VAL* 3.1 3.3 + - - +
2178B ARG* 2.6 38.4 + - + +
2186B LEU* 4.6 5.6 - - + +
2188B ALA* 5.4 0.9 - - + -
2205B LEU* 4.3 13.2 - - + -
2208B TYR* 3.7 26.2 - - + -
2210B LEU* 3.6 33.2 - - + -
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Residues in contact with GLU2175 (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 ILE* 3.2 17.7 + - - +
2172B GLN* 4.0 13.3 - - - +
2174B VAL* 1.3 75.8 - - - +
2176B ALA* 1.3 55.6 + - - +
2178B ARG* 2.6 9.2 + - - -
2179B LYS* 2.5 68.0 + - + +
2208B TYR* 2.9 42.6 + - + +
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Residues in contact with ALA2176 (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 VAL* 3.2 35.7 - - + +
2146B LEU* 5.3 0.7 - - + -
2147B LEU* 3.3 14.7 - - + +
2172B GLN 3.5 5.3 + - - +
2173B PHE* 3.3 11.2 - - - +
2175B GLU* 1.3 78.9 - - - +
2177B VAL* 1.3 59.0 + - + +
2179B LYS* 3.4 5.6 - - - +
2180B SER* 3.1 25.5 - - - -
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Residues in contact with VAL2177 (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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2146B LEU* 3.5 25.1 - - + -
2147B LEU* 3.9 9.2 - - + -
2150B VAL* 3.8 36.3 - - + -
2163B LEU* 3.9 7.9 - - + -
2173B PHE 3.0 13.9 + - - +
2174B VAL 3.7 5.4 - - - +
2175B GLU 2.8 3.8 + - - -
2176B ALA* 1.3 74.4 - - + +
2178B ARG* 1.3 58.9 + - - +
2181B PHE* 3.0 31.8 + - + +
2184B LEU* 4.5 3.6 - - + -
2186B LEU* 3.3 33.2 - - + -
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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* 2.6 17.8 + - + +
2175B GLU 2.6 8.7 + - - +
2177B VAL* 1.3 72.7 - - - +
2179B LYS* 1.3 60.0 + - + +
2180B SER 2.8 8.1 + - - -
2181B PHE 3.0 17.2 + - - -
2182B PRO* 3.2 42.8 + - - +
2183B LYS 4.3 0.8 - - - -
2184B LEU* 2.8 31.0 + - - +
2185B SER* 4.6 0.4 - - - +
2186B LEU* 3.1 32.7 + - + +
2208B TYR* 3.0 47.8 + - + +
2209B ASP* 3.7 25.6 + - - +
2210B LEU* 4.9 0.6 - - - +
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Residues in contact with LYS2179 (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 GLU* 2.5 51.3 + - + +
2176B ALA* 3.4 5.7 - - - +
2178B ARG* 1.3 73.0 - - + +
2180B SER* 1.3 63.8 + - - +
2182B PRO* 5.6 0.7 - - - -
2208B TYR* 4.6 13.4 + - + -
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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