Contacts of the helix formed by residues 2192 - 2212 (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 LEU2192 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2187B LYS* 4.2 9.9 - - + +
2190B GLU* 3.1 33.7 + - + +
2191B ASP* 1.3 72.1 + - - +
2193B ARG* 1.3 58.7 + - - +
2194B GLN 3.3 2.2 - - - -
2195B ASP* 3.3 13.8 + - + +
2196B GLU* 3.0 23.6 + - - +
2227B VAL* 3.4 16.3 - - + +
2228B ILE 4.7 0.4 - - - +
2229B PRO* 4.4 12.1 - - + +
2231B SER 5.5 1.0 + - - -
2234B SER 4.6 2.8 + - - +
2235B GLY* 3.4 41.3 - - - +
2236B LEU 3.8 8.1 - - - +
2237B ILE* 3.6 33.4 - - + -
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Residues in contact with ARG2193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1978B VAL* 5.8 5.8 - - - -
2191B ASP* 2.7 35.9 + - - +
2192B LEU* 1.3 74.8 - - - +
2194B GLN* 1.3 65.1 + - - +
2196B GLU* 3.3 21.8 + - - +
2197B ARG* 3.4 28.7 + - - +
2229B PRO* 4.0 22.4 - - + +
2231B SER 5.0 7.0 - - - +
2232B THR* 3.7 30.7 - - - +
2426B LEU* 3.7 48.4 + - - +
2427B LEU* 3.8 15.7 - - + -
2429B TRP* 4.9 7.5 - - - +
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Residues in contact with GLN2194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2191B ASP* 4.1 10.2 + - - +
2192B LEU 3.3 0.4 - - - -
2193B ARG* 1.3 76.5 - - - +
2195B ASP* 1.3 64.6 + - - +
2197B ARG* 3.2 6.2 + - - +
2198B VAL* 3.1 27.6 + - - +
2358B PHE 3.8 9.8 - - - +
2359B GLY* 3.0 29.4 + - - +
2427B LEU* 3.9 16.6 - - + -
2429B TRP* 3.3 32.9 - - - +
2430B ARG* 3.3 54.5 + - - +
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Residues in contact with ASP2195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2191B ASP 4.5 6.9 - - - +
2192B LEU* 3.3 21.2 + - + +
2194B GLN* 1.3 77.0 - - - +
2196B GLU* 1.3 62.3 + - - +
2198B VAL* 3.8 7.9 - - - +
2199B MET* 3.2 28.4 + - - +
2225B TYR* 3.8 9.6 + - - +
2227B VAL* 4.1 15.7 - - + -
2237B ILE* 4.4 8.4 - - + +
2357B ASP* 3.8 6.6 + - - -
2358B PHE* 3.3 49.1 + - + -
2359B GLY* 4.1 1.9 + - - -
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Residues in contact with GLU2196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1940B PRO* 4.2 18.1 - - + +
1975B PRO* 5.7 4.9 - - - +
2192B LEU 3.0 13.3 + - - +
2193B ARG* 3.3 11.6 - - - +
2194B GLN 3.2 0.4 - - - -
2195B ASP* 1.3 76.1 - - - +
2197B ARG* 1.3 86.3 + - - +
2199B MET* 3.2 6.6 + - - +
2200B GLN* 3.1 18.8 + - - +
2227B VAL* 3.7 28.9 - - + +
2229B PRO* 3.7 25.1 - - + +
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Residues in contact with ARG2197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1940B PRO* 3.5 38.9 + - - +
1941B GLN* 3.6 21.8 + - - -
1944B ALA* 5.1 2.6 - - - +
2193B ARG* 3.6 23.6 + - - +
2194B GLN 3.2 5.9 + - - +
2196B GLU* 1.3 89.2 + - - +
2198B VAL* 1.3 59.5 + - - +
2200B GLN* 3.3 16.0 - - - +
2201B LEU 3.1 20.8 + - - -
2421B PHE* 3.4 39.1 - - + +
2424B ASP* 2.5 37.2 + - - -
2426B LEU* 5.6 5.5 - - - +
2427B LEU* 3.5 21.4 - - + +
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Residues in contact with VAL2198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2194B GLN 3.1 17.5 + - - +
2195B ASP 3.8 5.4 - - - +
2196B GLU 3.2 0.4 - - - -
2197B ARG* 1.3 76.0 - - - +
2199B MET* 1.3 59.1 + - - +
2201B LEU* 3.2 8.5 + - + +
2202B PHE* 3.0 55.6 + - + -
2334B LEU* 3.7 17.0 - - + -
2358B PHE* 3.6 35.9 - - + +
2361B CYS* 3.9 17.3 - - - -
2421B PHE* 4.9 8.7 - - + -
2430B ARG* 5.3 2.2 - - - +
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Residues in contact with MET2199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2195B ASP 3.2 14.6 + - - +
2196B GLU* 3.2 9.1 + - - +
2198B VAL* 1.3 72.7 - - - +
2200B GLN* 1.3 57.3 + - - +
2202B PHE* 3.4 12.7 + - + +
2203B GLY 3.0 14.9 + - - -
2223B GLN 4.9 1.6 - - - +
2224B ARG* 2.8 61.6 + - - +
2225B TYR* 3.4 58.8 - - + +
2227B VAL* 3.7 10.1 - - + +
2355B HIS 4.8 0.7 - - - +
2358B PHE* 3.5 25.6 - - + -
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Residues in contact with GLN2200 (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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1900B LEU* 4.3 20.9 - - + +
1904B LEU* 5.2 2.4 - - - +
1937B GLN 2.9 27.3 + - - +
1938B VAL* 4.3 0.6 - - - +
1940B PRO* 3.8 10.5 - - - +
1941B GLN* 3.1 37.9 + - - +
2196B GLU 3.1 9.2 + - - +
2197B ARG* 3.3 25.3 - - - +
2199B MET* 1.3 76.3 - - - +
2201B LEU* 1.3 60.8 + - - +
2203B GLY* 3.4 2.3 + - - -
2204B LEU* 3.3 19.8 + - - +
2224B ARG* 4.6 3.4 - - - +
2417B VAL* 4.8 8.7 - - + +
2421B PHE* 6.3 0.7 - - - -
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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
----------------------------------------------------------
2197B ARG 3.1 11.4 + - - +
2198B VAL* 3.2 8.7 + - - +
2200B GLN* 1.3 76.2 - - - +
2202B PHE* 1.3 70.9 + - + +
2204B LEU* 3.1 8.4 + - + +
2205B VAL* 3.0 34.3 + - + +
2330B VAL* 5.3 4.3 - - + +
2333B ILE* 6.4 0.7 - - + -
2334B LEU* 4.0 40.8 - - + +
2407B LEU* 6.3 0.2 - - + -
2414B VAL* 4.4 24.0 - - + +
2417B VAL* 3.9 28.4 - - + +
2418B LEU* 4.0 15.7 - - + -
2421B PHE* 4.6 2.7 - - + -
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Residues in contact with PHE2202 (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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2198B VAL* 3.0 40.0 + - + +
2199B MET* 3.8 22.7 - - + +
2200B GLN 3.4 0.2 - - - -
2201B LEU* 1.3 80.4 - - + +
2203B GLY* 1.3 56.6 + - - +
2205B VAL* 3.2 2.8 + - - +
2206B ASN* 2.9 35.8 + - - -
2222B ILE* 3.7 43.0 - - + +
2223B GLN 5.1 0.9 - - - -
2224B ARG* 4.1 8.3 - - + +
2327B MET* 3.6 17.0 - - + -
2330B VAL* 3.9 21.5 - - + -
2334B LEU* 4.2 11.2 - - + -
2355B HIS* 5.7 0.9 - - + -
2358B PHE* 3.5 36.1 - + - -
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Residues in contact with GLY2203 (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 MET 3.0 10.5 + - - -
2200B GLN 3.4 3.8 + - - -
2201B LEU 3.2 0.2 - - - -
2202B PHE* 1.3 77.6 - - - +
2204B LEU* 1.3 58.9 + - - +
2206B ASN* 3.4 7.5 + - - +
2207B THR* 2.9 27.3 + - - -
2224B ARG* 3.5 26.4 - - - +
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Residues in contact with LEU2204 (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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1898B ASN* 5.1 9.4 - - - +
1900B LEU* 3.9 28.4 - - + +
2200B GLN 3.3 7.4 + - - +
2201B LEU* 3.1 12.6 + - + +
2203B GLY* 1.3 75.8 - - - +
2205B VAL* 1.3 58.5 + - + +
2207B THR* 3.0 14.8 + - - -
2208B LEU* 2.9 51.2 + - + +
2413B SER* 3.5 42.6 - - - +
2414B VAL* 4.1 9.0 - - + +
2417B VAL* 3.5 18.2 - - + -
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Residues in contact with VAL2205 (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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2201B LEU* 3.0 33.1 + - + +
2202B PHE* 3.7 7.4 - - - +
2204B LEU* 1.3 74.6 - - + +
2206B ASN* 1.3 56.6 + - - +
2208B LEU* 3.2 11.0 + - + +
2209B LEU* 2.9 44.7 + - + +
2222B ILE* 3.6 23.3 - - + -
2330B VAL* 3.8 19.5 - - + -
2403B VAL* 5.7 0.4 - - + -
2406B VAL* 6.2 1.3 - - + -
2407B LEU* 4.2 24.2 - - + -
2414B VAL* 4.8 6.1 - - + -
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Residues in contact with ASN2206 (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 PHE 2.9 23.5 + - - +
2203B GLY* 3.6 6.0 - - - +
2205B VAL* 1.3 73.2 - - - +
2207B THR* 1.3 59.9 + - - +
2209B LEU* 3.7 6.4 - - - +
2210B ALA* 2.8 30.1 + - - +
2220B LEU 5.3 0.7 - - - +
2221B SER* 3.4 12.9 - - - +
2222B ILE* 2.6 42.6 + - - +
2224B ARG* 3.1 30.5 - - - +
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Residues in contact with THR2207 (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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1897B GLY 5.7 3.1 - - - +
1898B ASN* 4.7 14.4 - - + +
2203B GLY 2.9 17.1 + - - -
2204B LEU* 3.0 15.4 + - + -
2206B ASN* 1.3 75.1 - - - +
2208B LEU* 1.3 63.2 + - + +
2210B ALA* 3.2 7.0 + - + +
2211B ASN* 3.0 45.6 + - - +
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Residues in contact with LEU2208 (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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1898B ASN* 5.4 7.6 - - - +
2204B LEU* 2.9 40.0 + - + +
2205B VAL* 3.5 13.5 - - + +
2207B THR* 1.3 75.9 - - - +
2209B LEU* 1.3 57.6 + - - +
2211B ASN* 3.3 11.6 + - - +
2212B ASP* 3.0 28.9 + - - +
2406B VAL* 3.8 21.9 - - + +
2407B LEU* 5.4 3.4 - - + -
2410B HIS* 3.6 50.6 + - + +
2413B SER* 5.2 4.5 - - - +
2414B VAL* 4.3 20.6 - - + -
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Residues in contact with LEU2209 (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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2205B VAL* 2.9 40.0 + - + +
2206B ASN* 3.8 5.4 - - - +
2208B LEU* 1.3 73.3 - - - +
2210B ALA* 1.3 63.0 + - - +
2212B ASP* 3.2 8.3 - - - +
2215B SER* 3.1 43.3 - - - +
2216B LEU* 3.5 4.5 + - - -
2220B LEU* 3.6 29.4 - - + +
2221B SER* 4.4 5.4 - - - -
2222B ILE* 5.0 0.7 - - + -
2326B VAL* 4.2 22.2 - - + -
2403B VAL* 4.2 23.8 - - + -
2406B VAL* 4.2 17.5 - - + -
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Residues in contact with ALA2210 (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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2206B ASN 2.8 17.8 + - - +
2207B THR* 3.5 8.7 - - + +
2209B LEU* 1.3 76.2 - - - +
2211B ASN* 1.3 64.3 + - - +
2216B LEU* 3.5 43.3 - - + +
2220B LEU 5.1 1.0 + - - -
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Residues in contact with ASN2211 (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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1898B ASN* 3.7 18.8 - - - +
2207B THR* 3.0 40.6 + - - +
2208B LEU* 3.7 9.9 - - + +
2209B LEU 3.2 0.4 - - - -
2210B ALA* 1.3 80.7 - - - +
2212B ASP* 1.3 62.0 + - - +
2213B PRO* 3.4 9.2 - - - +
2410B HIS* 5.9 5.1 - - + +
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Residues in contact with ASP2212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2208B LEU 3.0 13.3 + - - +
2209B LEU 3.2 4.0 - - - +
2210B ALA 3.5 0.4 - - - -
2211B ASN* 1.3 74.7 - - - +
2213B PRO* 1.4 68.7 - - - +
2214B THR* 4.0 11.7 + - - -
2215B SER* 3.0 29.3 + - - +
2216B LEU* 2.9 25.5 + - - +
2402B THR* 4.0 3.6 - - - +
2406B VAL* 3.3 29.8 - - + +
2409B GLU* 5.0 8.7 - - - +
2410B HIS* 6.0 1.8 + - - +
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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