Contacts of the helix formed by residues 4924 - 4955 (chain F) in PDB entry 6X34
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 VAL4924 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4919F PHE* 3.4 29.7 + - + +
4920F PHE* 3.2 23.8 - - + +
4921F PHE 3.9 0.6 + - - -
4923F ILE* 1.3 83.7 - - + +
4925F ILE* 1.3 72.7 + - + +
4928F ALA* 3.3 21.0 + - - +
4927H LEU* 5.9 7.9 - - + -
4930H ILE* 4.3 21.8 - - + -
4931H GLN* 3.6 39.6 - - + +
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Residues in contact with ILE4925 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4920F PHE 3.4 17.3 - - - +
4921F PHE* 3.0 25.1 + - + +
4924F VAL* 1.3 85.4 - - + +
4926F LEU* 1.3 67.1 + - - +
4928F ALA* 3.4 9.6 + - - +
4929F ILE* 3.2 28.1 + - + +
4824H ILE* 5.4 9.4 - - + -
4828H VAL* 4.3 19.5 - - + -
4930H ILE* 5.0 5.2 - - + +
4931H GLN* 6.0 0.7 - - - -
4934H ILE* 3.8 46.2 - - + -
----------------------------------------------------------
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Residues in contact with LEU4926 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4838F THR* 4.6 3.0 + - - +
4842F LEU* 4.6 22.7 - - + -
4845F VAL* 5.8 2.2 - - + -
4921F PHE 2.9 6.4 + - - +
4922F VAL* 3.3 30.5 + - + +
4924F VAL 3.6 0.2 - - - -
4925F ILE* 1.3 77.0 - - - +
4927F LEU* 1.3 63.6 + - - +
4929F ILE* 3.1 18.8 + - - +
4930F ILE* 3.4 16.2 + - - +
----------------------------------------------------------
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Residues in contact with LEU4927 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4919D PHE* 4.7 20.4 - - + -
4920D PHE* 6.0 1.8 - - + -
4924D VAL* 5.9 8.3 - - + -
4842F LEU* 4.7 12.1 - - + -
4889F VAL* 4.4 23.8 - - + +
4892F GLY* 6.0 3.8 - - - -
4922F VAL 3.4 20.9 + - - +
4923F ILE* 3.2 31.5 + - + +
4925F ILE 3.5 0.2 - - - -
4926F LEU* 1.3 80.0 - - - +
4928F ALA* 1.3 56.5 + - - +
4930F ILE* 3.2 11.7 + - + +
4931F GLN* 3.0 43.3 + - + +
----------------------------------------------------------
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Residues in contact with ALA4928 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4924F VAL 3.3 21.0 + - - +
4925F ILE* 3.4 6.6 + - - +
4926F LEU 3.2 0.8 - - - -
4927F LEU* 1.3 76.8 - - - +
4929F ILE* 1.3 57.9 + - + +
4931F GLN* 4.0 6.5 - - - +
4932F GLY* 2.7 33.8 + - - -
4931H GLN* 5.6 9.4 - - + +
4934H ILE* 6.3 0.9 - - + -
4935H ILE* 3.7 29.5 - - + +
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Residues in contact with ILE4929 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4838F THR* 4.1 25.4 - - + +
4925F ILE* 3.2 25.6 - - + +
4926F LEU* 3.1 8.9 + - - +
4928F ALA* 1.3 81.7 - - + +
4930F ILE* 1.3 64.0 + - - +
4932F GLY* 5.1 0.2 - - - -
4933F LEU* 3.3 42.0 + - + +
4824H ILE* 3.8 34.5 - - + -
4934H ILE* 5.5 6.7 - - + -
4935H ILE* 5.3 7.0 - - + -
4938H PHE* 4.9 22.2 - - + -
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Residues in contact with ILE4930 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4920D PHE* 6.1 5.8 - - + +
4924D VAL* 4.3 17.9 - - + -
4925D ILE* 5.0 6.7 - - + +
4835F LEU* 5.6 7.6 - - + -
4838F THR* 3.3 36.8 - - + +
4839F VAL* 4.3 17.7 - - + +
4842F LEU* 4.8 15.0 - - + -
4926F LEU 3.5 13.2 - - - +
4927F LEU* 3.2 16.0 + - + +
4929F ILE* 1.3 78.9 - - - +
4931F GLN* 1.3 61.4 + - - +
4933F LEU* 4.8 0.7 - - - +
4934F ILE* 3.3 25.5 + - + +
----------------------------------------------------------
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Residues in contact with GLN4931 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4924D VAL* 3.6 35.8 - - + +
4925D ILE* 6.0 0.4 - - - -
4928D ALA* 5.6 5.6 - - + +
4927F LEU* 3.0 27.2 + - + +
4928F ALA* 4.0 5.9 - - - +
4930F ILE* 1.3 76.2 - - - +
4932F GLY* 1.3 64.9 + - - +
4934F ILE* 3.4 3.2 + - - +
4935F ILE* 3.1 37.3 + - + +
----------------------------------------------------------
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Residues in contact with GLY4932 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4928F ALA 2.7 22.3 + - - -
4931F GLN* 1.3 75.2 - - - +
4933F LEU* 1.3 59.5 + - - +
4935F ILE* 3.4 11.8 - - - +
4936F ASP* 3.0 33.0 + - - +
4935H ILE* 6.4 2.9 - - - -
----------------------------------------------------------
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Residues in contact with LEU4933 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4830F HIS 5.6 0.3 - - - +
4831F ASN* 5.6 13.8 - - + +
4834F GLN* 4.9 26.0 - - + +
4835F LEU* 6.4 3.1 - - + +
4838F THR* 5.9 3.1 - - + -
4929F ILE* 3.3 39.0 + - + +
4930F ILE* 4.8 1.6 - - - +
4932F GLY* 1.3 78.1 - - - +
4934F ILE* 1.3 66.2 + - + +
4936F ASP* 4.2 6.1 - - + +
4937F ALA* 3.3 21.1 + - - +
4938H PHE* 3.5 39.3 - - + -
----------------------------------------------------------
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Residues in contact with ILE4934 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4925D ILE* 3.8 43.1 - - + -
4928D ALA* 6.3 0.4 - - + -
4929D ILE* 5.5 6.7 - - + -
4827F SER* 3.1 44.7 + - - +
4828F VAL* 4.2 11.4 - - + +
4830F HIS 5.5 1.8 - - - +
4835F LEU* 4.1 28.5 - - + -
4930F ILE* 3.3 21.3 + - + +
4931F GLN* 3.4 3.7 + - - +
4932F GLY 3.2 0.2 - - - -
4933F LEU* 1.3 80.7 - - + +
4935F ILE* 1.3 69.3 + - + +
4937F ALA* 3.2 2.4 + - - -
4938F PHE* 3.2 9.5 + - - +
----------------------------------------------------------
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Residues in contact with ILE4935 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4928D ALA* 3.7 34.5 - - + +
4929D ILE* 5.3 5.8 - - + -
4932D GLY* 6.4 2.2 - - - -
4931F GLN* 3.1 23.0 + - + +
4932F GLY* 3.4 12.6 - - - +
4934F ILE* 1.3 81.6 - - + +
4936F ASP* 1.3 61.5 + - + +
4938F PHE* 3.5 9.0 + - - +
4939F GLY* 3.1 22.3 + - - -
----------------------------------------------------------
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Residues in contact with ASP4936 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4932F GLY 3.0 20.4 + - - +
4933F LEU* 4.2 8.1 - - + +
4935F ILE* 1.3 78.6 - - + +
4937F ALA* 1.3 59.2 + - - +
4939F GLY* 3.7 1.5 - - - +
4940F GLU* 2.8 33.5 + - - +
----------------------------------------------------------
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Residues in contact with ALA4937 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4827F SER* 3.5 29.6 - - - +
4830F HIS* 4.1 28.1 - - + +
4831F ASN* 5.1 4.3 - - + -
4933F LEU 3.3 15.4 + - - +
4934F ILE 3.2 1.6 + - - +
4936F ASP* 1.3 80.5 - - - +
4938F PHE* 1.3 56.6 + - - +
4940F GLU* 4.1 4.3 - - - +
4941F LEU* 3.0 31.9 + - - +
----------------------------------------------------------
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Residues in contact with PHE4938 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4834D GLN* 6.1 4.3 - - + -
4929D ILE* 4.9 14.6 - - + -
4933D LEU* 3.5 41.5 - - + -
4820F THR 5.5 0.2 - - - -
4823F THR* 3.1 37.5 - - + -
4824F ILE* 4.6 17.9 - - + -
4827F SER* 3.6 11.1 + - - +
4934F ILE* 3.2 10.3 + - + +
4935F ILE* 3.8 11.2 - - - +
4936F ASP 3.3 0.2 - - - -
4937F ALA* 1.3 78.9 - - - +
4939F GLY* 1.3 61.8 + - - +
4941F LEU* 3.8 3.6 - - - +
4942F ARG* 2.8 44.8 + - + +
----------------------------------------------------------
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Residues in contact with GLY4939 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4935F ILE 3.1 14.8 + - - -
4936F ASP* 3.8 2.7 - - - -
4938F PHE* 1.3 82.6 - - - +
4940F GLU* 1.3 57.3 + - - +
4942F ARG* 3.9 4.1 - - - +
4943F ASP* 2.9 30.5 + - - +
----------------------------------------------------------
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Residues in contact with GLU4940 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4830F HIS* 6.1 3.1 - - + +
4936F ASP 2.8 22.8 + - - +
4937F ALA* 4.1 4.0 - - - +
4939F GLY* 1.3 75.2 - - - +
4941F LEU* 1.3 57.4 + - - +
4943F ASP* 3.4 5.3 + - - +
4944F GLN* 2.8 28.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU4941 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4823F THR* 5.3 15.7 - - + +
4826F SER* 4.2 26.2 - - - +
4827F SER* 5.1 6.5 - - - +
4830F HIS* 5.3 19.5 - - + +
4937F ALA 3.0 20.7 + - - +
4938F PHE* 4.0 4.0 - - + +
4940F GLU* 1.3 73.2 - - - +
4942F ARG* 1.3 60.6 + - - +
4944F GLN* 3.2 13.0 + - + +
4945F GLN* 2.8 50.6 + - + +
----------------------------------------------------------
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Residues in contact with ARG4942 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4823F THR* 6.5 1.6 - - + -
4938F PHE* 2.8 36.9 + - + +
4939F GLY* 3.9 4.9 - - - +
4941F LEU* 1.3 77.7 - - - +
4943F ASP* 1.3 57.4 + - - +
4945F GLN* 3.4 7.1 + - - +
4946F GLU* 2.9 28.9 + - - +
----------------------------------------------------------
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Residues in contact with ASP4943 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4939F GLY 2.9 19.6 + - - +
4940F GLU* 3.8 6.3 - - - +
4942F ARG* 1.3 73.6 - - - +
4944F GLN* 1.3 56.2 + - - +
4946F GLU* 3.6 6.9 - - - +
4947F GLN* 2.7 35.7 + - - +
----------------------------------------------------------
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Residues in contact with GLN4944 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4940F GLU 2.8 18.9 + - - +
4941F LEU* 3.2 17.9 + - + +
4943F ASP* 1.3 76.6 - - - +
4945F GLN* 1.3 61.2 + - + +
4947F GLN* 3.7 6.3 - - - +
4948F VAL* 3.1 26.4 + - - +
----------------------------------------------------------
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Residues in contact with GLN4945 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4214F PHE* 4.9 11.8 - - - +
4823F THR* 6.2 4.0 - - + -
4941F LEU* 2.8 36.7 + - + +
4942F ARG* 3.9 6.3 - - - +
4944F GLN* 1.3 76.8 - - + +
4946F GLU* 1.3 61.1 + - - +
4948F VAL* 3.3 13.6 - - - +
4949F ARG* 3.3 22.5 + - - +
----------------------------------------------------------
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Residues in contact with GLU4946 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4942F ARG 2.9 18.6 + - - +
4943F ASP* 3.8 7.6 - - - +
4945F GLN* 1.3 75.5 - - - +
4947F GLN* 1.3 60.6 + - - +
4949F ARG* 3.8 5.5 - - - +
4950F GLU* 3.0 28.6 + - - +
----------------------------------------------------------
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Residues in contact with GLN4947 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4943F ASP 2.7 21.9 + - - +
4944F GLN* 3.3 7.8 + - - +
4946F GLU* 1.3 72.0 - - - +
4948F VAL* 1.3 54.6 + - - +
4950F GLU* 3.1 7.4 + - - +
4951F ASP* 2.5 51.0 + - + +
4954F THR* 4.7 8.9 - - - +
----------------------------------------------------------
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Residues in contact with VAL4948 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4213F ILE* 4.2 13.5 - - + +
4214F PHE* 4.4 14.4 - - + -
4217F VAL* 3.7 29.2 - - + -
4944F GLN 3.1 19.1 + - - +
4945F GLN* 3.3 23.3 - - - +
4947F GLN* 1.3 77.8 - - - +
4949F ARG* 1.3 65.9 + - - +
4951F ASP* 3.2 19.3 + - + +
4952F MET* 3.5 9.0 + - - +
----------------------------------------------------------
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Residues in contact with ARG4949 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4945F GLN 3.3 15.4 + - - +
4946F GLU* 3.8 7.0 - - - +
4947F GLN 3.2 0.4 - - - -
4948F VAL* 1.3 84.2 - - - +
4950F GLU* 1.3 59.1 + - - +
4952F MET* 3.7 14.5 + - - +
4953F GLU* 4.8 0.9 + - - +
----------------------------------------------------------
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Residues in contact with GLU4950 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4946F GLU 3.0 19.3 + - - +
4947F GLN* 3.8 10.1 - - - +
4949F ARG* 1.3 72.3 - - - +
4951F ASP* 1.3 63.1 + - - +
4952F MET 3.2 2.5 - - - -
4953F GLU* 3.3 16.8 + - - +
4954F THR* 3.3 16.3 + - + +
----------------------------------------------------------
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Residues in contact with ASP4951 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4217F VAL* 6.4 0.2 - - + -
4947F GLN* 2.5 29.4 + - + +
4948F VAL* 3.2 17.4 + - + +
4950F GLU* 1.3 74.3 - - - +
4952F MET* 1.3 50.1 + - - +
4953F GLU 3.1 0.2 - - - -
4954F THR* 3.7 11.7 - - + -
4955F LYS* 2.7 46.9 + - + +
----------------------------------------------------------
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Residues in contact with MET4952 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4948F VAL 3.5 7.2 + - - +
4949F ARG* 3.8 13.0 - - - +
4950F GLU 3.2 1.0 - - - -
4951F ASP* 1.3 77.6 - - - +
4953F GLU* 1.3 57.1 + - - +
4955F LYS 3.6 11.2 - - - +
4956F CYS* 5.4 1.6 - - - +
4963F SER 5.7 0.3 - - - +
----------------------------------------------------------
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Residues in contact with GLU4953 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4949F ARG 4.8 0.6 + - - +
4950F GLU* 3.3 11.2 + - - +
4951F ASP 3.1 0.4 - - - -
4952F MET* 1.3 80.0 - - - +
4954F THR* 1.3 58.2 + - - +
4955F LYS 3.5 1.1 - - - -
4963F SER* 3.5 18.7 + - - +
4964F ASP* 5.2 2.8 - - - +
----------------------------------------------------------
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Residues in contact with THR4954 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4947F GLN* 4.7 9.4 - - - +
4950F GLU* 3.3 19.5 - - + +
4951F ASP* 3.7 12.3 - - + -
4953F GLU* 1.3 75.0 - - - +
4955F LYS* 1.3 61.8 + - + +
4963F SER* 3.2 27.9 + - - -
----------------------------------------------------------
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Residues in contact with LYS4955 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4951F ASP* 2.7 27.1 + - + +
4952F MET* 3.6 14.6 - - - +
4953F GLU 3.5 1.8 - - - -
4954F THR* 1.3 83.5 - - + +
4956F CYS* 1.3 65.3 + - - +
4962F GLY* 3.9 3.6 - - - -
4963F SER* 3.9 10.9 - - - +
----------------------------------------------------------
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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