Contacts of the helix formed by residues 2198 - 2207 (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 ASP2198 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2167B PRO* 4.9 5.7 - - - +
2193B ALA 4.7 1.0 - - - +
2194B TYR* 3.5 31.4 - - + -
2195B ASN* 2.9 45.5 + - - +
2196B ARG 2.8 2.4 + - - -
2197B GLU* 1.3 81.3 - - - +
2199B PHE* 1.3 64.6 + - - +
2200B LEU* 3.0 4.6 + - - +
2201B LEU* 3.0 27.1 + - + +
2202B LEU* 3.0 14.2 - - + +
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Residues in contact with PHE2199 (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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2195B ASN 4.2 0.6 + - - -
2196B ARG 2.9 20.5 + - - +
2197B GLU* 4.3 9.6 - - - -
2198B ASP* 1.3 78.3 - - - +
2200B LEU* 1.3 86.1 + - + +
2202B LEU* 3.4 8.7 + - - +
2203B LYS* 2.8 62.0 + - + +
2217B PHE* 5.5 1.8 - - + -
2227B TRP* 3.6 28.3 - + + -
2228B LEU* 5.1 7.9 - - + -
2231B GLN* 3.9 19.7 - - - +
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Residues in contact with LEU2200 (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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2197B GLU 5.1 5.8 - - - +
2198B ASP* 3.0 1.7 - - - -
2199B PHE* 1.3 107.6 - - + +
2201B LEU* 1.3 69.9 + - + +
2203B LYS* 3.1 9.6 + - + +
2204B GLU* 3.1 34.5 + - - +
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Residues in contact with LEU2201 (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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2167B PRO* 3.7 28.9 - - + +
2170B ASP* 4.0 11.0 - - - +
2171B ILE* 3.7 16.3 - - + +
2194B TYR* 3.8 19.7 - - + -
2198B ASP* 3.0 23.6 + - + +
2200B LEU* 1.3 81.9 - - + +
2202B LEU* 1.3 66.4 + - + +
2204B GLU* 3.1 18.8 + - - +
2205B LEU* 3.1 23.6 - - - +
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Residues in contact with LEU2202 (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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2165B ILE* 5.8 0.7 - - + -
2190B ALA* 5.4 0.2 - - + -
2194B TYR* 3.4 48.0 - - + -
2198B ASP 3.0 26.3 + - - +
2199B PHE* 3.8 9.9 - - - +
2201B LEU* 1.3 81.0 - - - +
2203B LYS* 1.3 61.6 + - - +
2205B LEU* 3.3 28.6 + - + +
2206B ASP 3.8 3.3 + - - -
2213B ILE* 4.3 32.2 - - + +
2216B PRO* 4.5 11.2 - - + -
2217B PHE* 5.1 3.4 - - + -
2228B LEU* 4.4 26.2 - - + -
2232B LEU* 3.9 8.2 - - + +
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Residues in contact with LYS2203 (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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2199B PHE* 2.8 45.2 + - + +
2200B LEU* 3.1 9.8 + - + +
2202B LEU* 1.3 73.8 - - - +
2204B GLU* 1.3 61.2 + - + +
2205B LEU 3.1 1.8 + - - -
2206B ASP* 3.1 18.9 + - - +
2207B GLN* 4.3 3.3 + - - +
2228B LEU* 5.3 1.8 - - + -
2231B GLN* 2.7 61.5 + - - +
2232B LEU* 3.7 19.7 - - + -
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Residues in contact with GLU2204 (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* 3.0 35.5 - - + +
2200B LEU* 3.1 23.8 + - + +
2201B LEU* 3.1 16.9 + - - +
2203B LYS* 1.3 76.5 - - + +
2205B LEU* 1.3 58.1 + - - +
2206B ASP 3.4 0.2 - - - -
2207B GLN* 3.4 17.3 + - - +
2208B TYR* 3.0 23.2 + - - -
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Residues in contact with LEU2205 (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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2165B ILE* 4.9 18.6 - - + -
2170B ASP* 4.3 4.3 - - + +
2171B ILE* 3.2 32.5 - - + -
2174B VAL* 4.3 20.0 - - + -
2188B ALA* 5.0 1.6 - - + -
2194B TYR* 5.6 0.2 - - - +
2201B LEU 3.1 19.3 - - - +
2202B LEU* 3.6 21.8 - - + +
2203B LYS 3.1 1.0 - - - -
2204B GLU* 1.3 77.3 - - - +
2206B ASP* 1.3 66.7 + - - +
2207B GLN 3.1 2.9 - - - -
2208B TYR* 3.0 24.1 + - + +
2210B LEU* 4.2 21.9 - - + +
2213B ILE* 4.2 24.5 - - + -
2234B THR* 4.7 0.9 - - - -
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Residues in contact with ASP2206 (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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2202B LEU 3.8 2.2 + - - -
2203B LYS* 3.1 17.3 + - + +
2205B LEU* 1.3 78.9 - - - +
2207B GLN* 1.3 57.7 + - - +
2208B TYR 3.2 4.2 + - - -
2209B ASP* 3.7 8.0 + - - -
2213B ILE* 5.4 1.3 - - - +
2231B GLN 4.0 2.3 - - - +
2232B LEU* 3.1 23.1 - - + +
2233B LYS* 2.6 50.0 + - - +
2234B THR* 2.6 45.1 + - - -
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Residues in contact with GLN2207 (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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2203B LYS 4.7 3.1 - - - +
2204B GLU* 3.4 24.5 + - - +
2206B ASP* 1.3 77.0 - - + +
2208B TYR* 1.3 95.5 + - - +
2209B ASP* 3.4 7.6 + - - +
2233B LYS* 4.2 15.0 - - - +
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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