Contacts of the helix formed by residues 2246 - 2257 (chain B) in PDB entry 5WBY
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 LEU2246 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2244B ASP 3.8 1.0 + - - -
2245B THR* 1.3 72.0 - - - +
2247B HIS* 1.3 62.5 + - - +
2249B LEU* 3.4 7.2 + - - +
2250B ILE* 3.0 43.5 + - + +
2299B LEU* 3.7 40.2 - - + -
2341B PRO* 3.3 21.2 + - + +
2344B LEU* 3.3 20.7 + - + +
2345B MET* 4.2 2.0 - - - +
2346B LEU* 4.2 8.5 - - + -
2378B ARG* 3.3 33.7 - - - +
2380B THR* 5.3 0.7 - - + -
2382B MET* 6.0 0.7 - - + -
2383B LEU* 3.9 18.4 - - + -
2549B TRP* 5.0 2.5 - - + -
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Residues in contact with HIS2247 (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 THR* 3.9 4.0 - - - +
2246B LEU* 1.3 80.0 - - - +
2248B ALA* 1.3 54.6 + - - +
2250B ILE* 3.4 1.4 + - - +
2251B ARG* 2.7 60.2 + - - +
2261B LEU* 4.4 15.8 - - + +
2262B ASN* 5.6 2.7 - - - -
2341B PRO* 3.2 14.8 + - + +
2342B SER* 3.8 24.5 + - - +
2546B CYS* 5.8 0.4 - - - -
2549B TRP* 3.4 36.2 - + - -
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Residues in contact with ALA2248 (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 ASP* 4.5 9.9 - - + -
2245B THR* 3.0 31.4 + - - +
2247B HIS* 1.3 77.3 - - + +
2249B LEU* 1.3 57.3 + - - +
2251B ARG* 3.3 28.0 + - - +
2252B ASP* 3.0 38.0 + - - +
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Residues in contact with LEU2249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2244B ASP* 3.6 37.0 - - - +
2245B THR 3.0 19.6 + - - +
2246B LEU* 3.7 6.7 - - - +
2248B ALA* 1.3 76.8 - - - +
2250B ILE* 1.3 57.7 + - + +
2252B ASP* 3.4 10.5 + - - +
2253B TYR* 3.0 28.8 + - - +
2299B LEU* 4.5 7.0 - - + -
2302B LEU* 3.7 22.5 - - + +
2303B LEU* 5.8 1.8 - - + -
2306B LYS* 3.7 29.2 - - + +
2346B LEU* 3.6 34.1 - - + -
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Residues in contact with ILE2250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2246B LEU* 3.0 39.0 + - + +
2247B HIS 3.9 2.0 - - - +
2249B LEU* 1.3 73.0 - - + +
2251B ARG* 1.3 65.3 + - - +
2253B TYR* 3.9 5.1 - - - -
2254B ARG* 2.9 51.6 + - + +
2261B LEU* 4.5 0.7 - - + -
2298B ASP* 4.3 12.8 - - + +
2299B LEU* 5.1 3.8 - - + +
2302B LEU* 4.6 6.1 - - + -
2382B MET* 3.6 29.8 - - + -
2549B TRP* 3.9 47.1 - - + -
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Residues in contact with ARG2251 (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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2247B HIS* 2.7 37.5 + - + +
2248B ALA* 3.4 31.6 - - - +
2250B ILE* 1.3 73.9 - - - +
2252B ASP* 1.3 86.8 + - - +
2254B ARG* 3.8 1.4 - - - +
2255B GLU* 3.1 38.7 + - + +
2261B LEU* 3.8 30.4 - - + +
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Residues in contact with ASP2252 (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 ALA* 3.0 18.1 + - - +
2249B LEU* 3.6 9.3 - - - +
2251B ARG* 1.3 108.3 + - - +
2253B TYR* 1.3 58.2 + - - +
2254B ARG 3.3 0.2 + - - -
2255B GLU* 3.4 10.8 + - - +
2256B LYS* 2.9 34.8 + - + +
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Residues in contact with TYR2253 (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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2249B LEU 3.0 16.3 + - - +
2250B ILE* 3.9 3.6 - - - +
2252B ASP* 1.3 76.0 - - - +
2254B ARG* 1.3 60.4 + - - +
2256B LYS* 3.5 9.7 + - + +
2257B LYS* 2.9 64.6 + - + +
2259B ILE* 4.3 11.1 - - + +
2297B ASP* 4.7 3.5 + - - -
2298B ASP* 3.3 54.1 + - + -
2301B LYS* 4.0 25.1 - - + +
2302B LEU* 3.7 39.7 - - + -
2305B LEU* 5.3 4.5 - - + -
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Residues in contact with ARG2254 (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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2250B ILE* 2.9 35.1 + - + +
2251B ARG 3.8 2.9 - - - +
2253B TYR* 1.3 75.3 - - - +
2255B GLU* 1.3 59.8 + - - +
2257B LYS 3.5 1.0 + - - -
2258B LYS 3.0 6.9 + - - -
2259B ILE* 2.7 66.1 + - - +
2260B LEU 3.9 4.3 + - - -
2261B LEU* 3.4 29.2 + - + -
2263B ILE* 3.8 9.3 - - - +
2264B GLU* 2.8 39.8 + - - -
2294B THR* 5.8 1.2 - - - -
2295B ALA 4.2 4.4 + - - +
2298B ASP* 2.7 41.9 + - - +
2382B MET* 3.6 10.7 - - - +
2549B TRP* 3.1 18.5 - - - +
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Residues in contact with GLU2255 (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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2251B ARG* 3.1 30.0 + - + +
2252B ASP* 3.4 17.3 - - - +
2254B ARG* 1.3 75.7 - - - +
2256B LYS* 1.3 65.8 - - + +
2258B LYS* 3.4 23.6 + - - +
2259B ILE 4.1 3.1 + - - -
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Residues in contact with LYS2256 (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 ASP* 2.9 21.6 + - + +
2253B TYR* 3.6 11.4 - - + +
2255B GLU* 1.3 80.4 - - + +
2257B LYS* 1.3 73.8 + - + +
2258B LYS* 3.3 11.9 + - - +
2305B LEU* 4.1 23.6 - - - +
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Residues in contact with LYS2257 (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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2253B TYR* 2.9 50.1 + - + +
2256B LYS* 1.3 90.0 - - + +
2258B LYS* 1.3 71.9 + - - +
2259B ILE* 3.2 25.0 + - + +
2305B LEU* 3.8 26.7 - - - +
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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