Contacts of the helix formed by residues 2269 - 2283 (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 GLY2269 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2102B ALA* 3.7 12.2 - - - +
2105B GLU* 3.2 11.7 - - - -
2106B LEU* 4.4 4.7 - - - -
2264B LEU* 3.1 26.2 + - - +
2267B VAL* 3.5 2.8 - - - +
2268B GLY* 1.3 79.9 - - - +
2270B MET* 1.3 60.1 + - - -
2271B SER 3.7 1.3 - - - -
2272B SER 4.0 1.7 + - - -
2273B ALA* 3.1 20.9 + - - +
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Residues in contact with MET2270 (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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2105B GLU* 2.7 11.4 + - - +
2106B LEU* 3.7 15.7 - - + +
2109B TRP* 3.6 44.4 - - + +
2120B LEU* 4.6 11.0 - - - -
2124B ILE* 3.9 19.5 - - + -
2264B LEU* 3.9 10.1 - - + -
2269B GLY* 1.3 68.3 - - - -
2271B SER* 1.3 66.4 + - - +
2272B SER 3.1 1.6 - - - -
2273B ALA* 3.0 2.7 + - + -
2274B LEU* 2.9 50.7 + - + +
2301B HIS* 5.6 1.1 - - - +
2305B LEU* 3.3 39.9 - - + -
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Residues in contact with SER2271 (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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2084B PRO 4.3 0.2 + - - -
2085B GLU* 3.3 36.3 + - - +
2088B GLN* 3.8 23.0 - - - +
2105B GLU* 3.0 17.4 + - - -
2109B TRP* 3.6 11.9 - - - +
2270B MET* 1.3 79.0 - - - +
2272B SER* 1.3 62.8 + - - +
2274B LEU* 3.4 5.2 + - - +
2275B LYS* 3.1 30.7 + - - +
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Residues in contact with SER2272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2088B GLN* 3.5 26.9 + - - +
2105B GLU* 4.6 0.4 + - - -
2243B ARG 4.0 3.3 + - - -
2244B SER* 4.4 5.0 - - - -
2245B VAL* 4.5 1.4 + - - +
2267B VAL* 2.6 40.1 + - - +
2268B GLY 4.5 6.7 - - - -
2269B GLY 4.0 4.9 - - - -
2270B MET 3.1 0.4 - - - -
2271B SER* 1.3 77.8 - - - +
2273B ALA* 1.3 64.6 + - - +
2275B LYS* 3.4 7.5 + - - +
2276B ILE* 3.1 29.5 + - - +
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Residues in contact with ALA2273 (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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2262B LEU* 3.4 22.1 - - + +
2264B LEU* 3.4 21.5 - - + -
2267B VAL* 4.0 13.0 - - + +
2269B GLY 3.1 16.5 + - - +
2270B MET 3.0 4.8 + - - +
2272B SER* 1.3 78.1 - - - +
2274B LEU* 1.3 58.9 + - - +
2276B ILE* 3.3 2.5 + - - +
2277B ALA* 2.9 24.6 + - - +
2305B LEU* 3.8 15.3 - - + -
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Residues in contact with LEU2274 (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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2109B TRP* 4.1 16.6 - - + -
2124B ILE* 4.1 23.3 - - + +
2270B MET* 2.9 42.6 + - + +
2271B SER* 3.8 4.3 - - - +
2273B ALA* 1.3 72.5 - - - +
2275B LYS* 1.3 67.6 + - - +
2277B ALA* 3.1 5.9 + - + +
2278B GLU* 2.9 38.8 + - - +
2305B LEU* 4.2 4.5 - - + -
2308B ARG* 3.9 43.1 - - + +
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Residues in contact with LYS2275 (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* 3.3 29.2 + - - +
2245B VAL* 3.3 24.3 - - + +
2271B SER* 3.1 20.1 + - - +
2272B SER* 3.6 6.7 - - - +
2273B ALA 3.3 0.2 - - - -
2274B LEU* 1.3 78.3 - - - +
2276B ILE* 1.3 57.1 + - - +
2278B GLU* 3.6 11.3 + - - +
2279B TYR* 3.1 27.0 + - - +
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Residues in contact with ILE2276 (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* 4.7 5.2 - - + -
2243B ARG 4.7 0.2 - - - -
2244B SER* 3.7 17.7 - - - +
2245B VAL* 3.6 22.9 - - + +
2248B VAL* 3.8 22.0 - - + -
2260B ILE* 4.6 8.3 - - + -
2262B LEU* 4.1 16.2 - - + -
2267B VAL* 3.0 37.0 - - + -
2272B SER 3.1 10.5 + - - +
2273B ALA 3.5 6.7 - - - +
2274B LEU 3.1 0.4 - - - -
2275B LYS* 1.3 75.8 - - - +
2277B ALA* 1.3 59.9 + - - +
2279B TYR* 3.2 5.0 + - - +
2280B CYS* 2.9 37.8 + - - -
2287B VAL* 5.1 0.4 - - + -
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Residues in contact with ALA2277 (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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2273B ALA 2.9 14.0 + - - +
2274B LEU* 3.1 12.3 + - + +
2276B ILE* 1.3 75.1 - - - +
2278B GLU* 1.3 64.4 + - - +
2280B CYS* 3.3 2.9 + - - +
2281B ALA 3.0 18.4 + - - -
2287B VAL* 4.5 12.6 - - - -
2308B ARG* 5.2 1.8 - - - +
2310B GLU* 3.4 29.3 - - + +
2311B PHE* 3.7 28.7 - - + -
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Residues in contact with GLU2278 (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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2274B LEU* 2.9 23.8 + - - +
2275B LYS* 3.8 10.2 - - - +
2277B ALA* 1.3 78.4 - - - +
2279B TYR* 1.3 61.7 + - - +
2281B ALA* 3.2 7.0 + - - +
2282B LEU* 3.1 30.0 + - + +
2308B ARG* 3.3 24.0 + - - +
2310B GLU* 3.8 18.2 - - - +
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Residues in contact with TYR2279 (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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2245B VAL* 3.7 22.0 - - + -
2248B VAL* 3.7 28.5 - - + -
2249B GLU* 3.4 39.2 + - + +
2252B HIS* 2.9 21.5 + + - +
2275B LYS 3.1 18.6 + - - +
2276B ILE* 3.2 4.5 + - - +
2278B GLU* 1.3 73.9 - - - +
2280B CYS* 1.3 69.6 + - - +
2282B LEU* 3.2 7.8 + - + -
2283B ASN* 3.0 44.9 + - - +
2285B ILE* 3.8 14.1 - - + -
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Residues in contact with CYS2280 (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* 4.3 9.2 - - - -
2260B ILE* 4.2 12.1 - - - -
2276B ILE* 2.9 34.4 + - - +
2277B ALA 3.3 4.2 + - - +
2279B TYR* 1.3 77.2 - - - +
2281B ALA* 1.3 63.0 + - - +
2283B ASN 3.2 4.7 + - - -
2284B GLU* 3.2 1.4 + - - -
2285B ILE* 2.9 67.1 + - + +
2287B VAL* 3.9 21.3 - - + -
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Residues in contact with ALA2281 (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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2277B ALA 3.0 12.4 + - - +
2278B GLU* 3.3 10.5 - - - +
2279B TYR 3.2 0.2 - - - -
2280B CYS* 1.3 79.2 - - - +
2282B LEU* 1.3 65.5 + - + +
2283B ASN 3.4 0.9 + - - -
2284B GLU* 3.8 8.7 + - - +
2285B ILE 5.0 0.7 - - - -
2287B VAL* 5.4 0.8 - - - +
2310B GLU* 3.7 22.4 - - + +
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Residues in contact with LEU2282 (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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2278B GLU* 3.1 21.0 + - + +
2279B TYR* 3.2 8.0 + - + +
2281B ALA* 1.3 79.7 - - + +
2283B ASN* 1.3 72.1 + - - +
2284B GLU 3.7 1.1 + - - -
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Residues in contact with ASN2283 (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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2252B HIS* 3.1 39.5 + - + +
2279B TYR* 3.0 38.2 + - - +
2280B CYS 3.2 0.8 + - - -
2282B LEU* 1.3 90.5 + - - +
2284B GLU* 1.3 62.3 + - - +
2285B ILE* 2.9 27.2 + - + +
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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