Contacts of the helix formed by residues 2264 - 2268 (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 LEU2264 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2102B ALA* 4.4 1.3 - - - -
2106B LEU* 3.8 29.4 - - + -
2262B LEU* 4.2 3.0 + - - +
2263B LYS* 1.3 68.4 - - - +
2265B ALA* 1.3 62.6 + - - +
2267B VAL* 3.1 11.1 - - - +
2268B GLY 3.2 0.2 + - - -
2269B GLY 3.1 52.7 + - - +
2270B MET* 3.9 12.8 - - + -
2273B ALA* 3.4 19.1 - - + -
2294B GLU* 6.0 1.8 - - - +
2298B GLY 5.5 0.4 - - - +
2301B HIS* 3.9 31.2 - - + +
2302B ASN* 4.2 10.4 + - + +
2305B LEU* 3.6 21.9 - - + +
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Residues in contact with ALA2265 (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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2047B GLU 5.7 0.7 - - - +
2049B GLU* 3.8 36.3 - - + +
2098B GLU 3.3 20.1 - - - +
2099B MET* 3.3 15.8 - - + +
2102B ALA* 3.6 14.8 - - + -
2106B LEU* 5.3 0.8 - - - +
2263B LYS* 3.3 1.0 - - - +
2264B LEU* 1.3 77.9 - - - +
2266B ARG* 1.3 63.2 + - - +
2267B VAL 3.1 1.4 + - - -
2268B GLY 3.2 9.9 + - - -
2292B MET* 4.2 10.5 - - + -
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Residues in contact with ARG2266 (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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2056B TYR* 3.6 15.9 - - - +
2057B THR* 4.4 6.3 - - + -
2098B GLU* 3.5 7.9 - - - +
2099B MET* 3.9 24.4 - - + +
2239B ASP* 2.8 40.8 + - - -
2240B GLU* 3.7 11.2 - - - +
2242B ILE* 2.7 43.8 + - - +
2243B ARG* 3.2 31.2 - - - +
2261B ASN 2.8 31.5 + - - -
2262B LEU* 4.0 6.9 - - - +
2263B LYS* 3.1 38.2 + - + +
2265B ALA* 1.3 78.0 - - - +
2267B VAL* 1.3 59.6 + - - +
2268B GLY 3.5 0.4 - - - -
2292B MET* 4.9 0.2 - - - -
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Residues in contact with VAL2267 (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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2098B GLU* 4.1 3.0 - - - +
2242B ILE 4.6 4.7 - - - +
2243B ARG* 3.2 24.2 - - - +
2262B LEU* 3.6 19.5 - - + -
2263B LYS 3.2 13.4 + - - +
2264B LEU* 3.1 19.5 - - - +
2265B ALA 3.1 0.8 - - - -
2266B ARG* 1.3 80.3 - - - +
2268B GLY* 1.3 55.8 + - - +
2269B GLY 3.6 15.9 - - - +
2272B SER* 2.6 34.6 + - - +
2273B ALA* 4.0 3.6 - - + -
2276B ILE* 3.0 36.8 - - + -
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Residues in contact with GLY2268 (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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2088B GLN* 5.7 5.2 + - - +
2098B GLU* 3.4 28.3 - - - +
2101B LYS* 4.1 13.3 - - - +
2102B ALA* 3.8 14.4 + - - -
2105B GLU* 4.3 8.1 - - - +
2265B ALA 3.2 7.9 + - - -
2266B ARG 3.5 0.8 - - - -
2267B VAL* 1.3 78.9 - - - +
2269B GLY* 1.3 56.8 + - - +
2272B SER* 4.5 5.6 - - - -
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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