Contacts of the helix formed by residues 2244 - 2255 (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 SER2244 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1220A LYS* 5.1 1.9 + - - +
2088B GLN* 6.0 3.4 - - - -
2242B ILE 3.7 1.0 - - - -
2243B ARG* 1.3 81.1 - - - +
2245B VAL* 1.3 66.5 + - - +
2246B LYS* 3.7 11.6 + - - +
2247B ASP* 2.9 31.3 + - - +
2248B VAL* 3.0 15.4 + - - +
2267B VAL* 4.2 1.4 - - - +
2272B SER* 4.4 5.6 - - - -
2276B ILE* 3.7 13.2 - - - +
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Residues in contact with VAL2245 (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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2244B SER* 1.3 72.7 - - - +
2246B LYS* 1.3 52.5 + - - +
2248B VAL* 2.9 7.5 + - - +
2249B GLU* 2.8 43.8 + - - +
2272B SER* 4.5 2.0 + - - +
2275B LYS* 3.3 49.6 - - + +
2276B ILE* 3.6 11.7 - - + +
2279B TYR* 3.7 36.3 - - + -
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Residues in contact with LYS2246 (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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1218A GLY* 5.7 5.2 - - - +
1220A LYS* 5.7 4.5 - - + -
1221A ASP* 3.2 36.0 + - - +
1223A VAL* 5.7 0.4 - - - +
1224A ASP* 4.3 14.1 + - - -
2244B SER* 3.7 11.6 - - - +
2245B VAL* 1.3 79.4 - - - +
2247B ASP* 1.3 63.3 + - - +
2249B GLU* 3.3 23.4 + - - +
2250B GLN* 3.2 40.6 + - - +
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Residues in contact with ASP2247 (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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1220A LYS* 3.0 41.1 + - - +
2222B PHE* 4.2 10.8 - - + -
2241B ASN 3.6 17.3 - - - +
2242B ILE* 4.1 6.6 - - - +
2243B ARG* 2.9 31.7 + - - +
2244B SER* 2.9 17.9 + - - +
2246B LYS* 1.3 80.3 - - - +
2248B VAL* 1.3 61.3 + - - +
2250B GLN* 3.4 10.5 + - - +
2251B ALA* 3.2 21.5 + - - +
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Residues in contact with VAL2248 (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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2242B ILE* 3.9 23.3 - - + -
2244B SER 3.0 12.7 + - - +
2245B VAL* 2.9 9.7 + - - +
2247B ASP* 1.3 75.8 - - - +
2249B GLU* 1.3 53.4 + - - +
2251B ALA* 3.1 5.4 + - + +
2252B HIS* 2.8 33.1 + - - +
2257B CYS* 6.1 0.7 - - - -
2260B ILE* 4.4 13.0 - - + -
2276B ILE* 3.8 26.2 - - + -
2279B TYR* 3.7 28.3 - - + -
2280B CYS* 4.3 8.1 - - - -
2285B ILE* 3.9 15.5 - - + -
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Residues in contact with GLU2249 (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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1223A VAL* 6.2 0.4 - - - -
2245B VAL* 2.8 29.6 + - - +
2246B LYS* 3.4 27.1 + - + +
2248B VAL* 1.3 76.5 - - - +
2250B GLN* 1.3 62.3 + - + +
2252B HIS* 3.4 1.9 + - - +
2253B SER* 3.0 25.5 + - - -
2279B TYR* 3.4 36.3 + - + +
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Residues in contact with GLN2250 (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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1220A LYS* 3.4 16.5 - - - +
1221A ASP* 3.4 6.8 + - - -
1222A PHE* 2.5 46.8 - - - +
1223A VAL* 2.6 29.4 - - + +
2222B PHE* 4.0 17.1 - - + -
2246B LYS* 3.2 26.2 + - - +
2247B ASP* 3.7 12.6 - - - +
2249B GLU* 1.3 76.4 - - - +
2251B ALA* 1.3 68.5 + - - +
2252B HIS 3.1 0.2 + - - -
2253B SER* 3.3 6.4 + - - -
2254B ILE* 2.9 34.7 + - + +
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Residues in contact with ALA2251 (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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2222B PHE* 4.0 15.8 - - + -
2238B LEU* 3.9 28.3 - - + -
2242B ILE* 4.4 2.2 - - + -
2247B ASP 3.2 10.9 + - - +
2248B VAL* 3.1 11.1 + - + +
2250B GLN* 1.3 79.1 - - - +
2252B HIS* 1.3 57.5 + - - +
2254B ILE 3.8 0.2 - - - -
2255B GLY* 2.8 6.2 + - - -
2256B SER* 2.7 33.5 + - - -
2257B CYS* 3.9 15.6 + - - -
2260B ILE* 5.3 0.2 - - + -
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Residues in contact with HIS2252 (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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2248B VAL 2.8 16.9 + - - +
2249B GLU 3.5 5.4 - - - +
2251B ALA* 1.3 73.6 - - - +
2253B SER* 1.3 62.9 + - - +
2254B ILE 3.1 0.9 - - - -
2255B GLY* 2.8 21.8 + - - -
2257B CYS* 5.4 9.0 - - - -
2279B TYR* 2.9 23.0 + - - +
2283B ASN* 3.1 45.4 + - + +
2285B ILE* 3.9 20.2 - - + -
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Residues in contact with SER2253 (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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1223A VAL* 3.2 36.7 - - - +
2249B GLU 3.0 11.1 + - - -
2250B GLN 3.3 2.9 + - - -
2252B HIS* 1.3 79.0 - - - +
2254B ILE* 1.3 61.8 + - - +
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Residues in contact with ILE2254 (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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1223A VAL* 3.5 23.6 - - + -
1254A ILE* 3.6 35.0 - - + -
2222B PHE* 3.8 27.8 - - + +
2223B VAL* 4.7 6.1 - - + +
2226B ALA* 3.3 18.9 - - + +
2230B LYS* 3.9 12.6 + - - -
2250B GLN* 2.9 26.3 + - + +
2253B SER* 1.3 78.1 - - - +
2255B GLY* 1.3 59.7 - - - +
2256B SER* 3.7 16.4 - - - +
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Residues in contact with GLY2255 (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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2226B ALA* 2.9 20.5 - - - +
2229B GLN* 3.6 13.6 - - - +
2230B LYS* 4.4 7.4 - - - +
2251B ALA 2.8 1.4 + - - -
2252B HIS* 2.8 17.7 + - - -
2253B SER 3.3 0.2 - - - -
2254B ILE* 1.3 79.8 - - - +
2256B SER* 1.3 62.1 + - - +
2257B CYS 3.4 6.3 - - - -
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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