Contacts of the helix formed by residues 4924 - 4955 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4919B PHE* 3.4 28.6 + - + +
4920B PHE* 3.2 24.4 + - + +
4921B PHE 3.9 0.6 + - - -
4923B ILE* 1.3 85.2 - - + +
4925B ILE* 1.3 70.8 + - + +
4928B ALA* 3.3 22.3 + - - +
4927D LEU* 5.9 7.9 - - + -
4930D ILE* 4.3 21.5 - - + -
4931D GLN* 3.6 38.4 - - + +
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Residues in contact with ILE4925 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4920B PHE 3.4 17.0 - - - +
4921B PHE* 3.0 24.4 + - + +
4924B VAL* 1.3 85.0 - - + +
4926B LEU* 1.3 67.9 + - - +
4928B ALA* 3.4 9.1 + - - +
4929B ILE* 3.2 28.4 + - + +
4824D ILE* 5.4 8.7 - - + -
4828D VAL* 4.3 20.4 - - + -
4930D ILE* 5.0 5.6 - - + +
4931D GLN* 6.0 0.4 - - - -
4934D ILE* 3.8 46.2 - - + +
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Residues in contact with LEU4926 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4838B THR* 4.6 2.4 + - - +
4842B LEU* 4.6 22.2 - - + -
4845B VAL* 5.8 2.2 - - + -
4921B PHE 2.9 6.4 + - - +
4922B VAL* 3.3 30.7 - - + +
4924B VAL 3.6 0.2 - - - -
4925B ILE* 1.3 77.9 - - - +
4927B LEU* 1.3 64.7 + - - +
4929B ILE* 3.1 18.3 + - - +
4930B ILE* 3.4 16.1 + - - +
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Residues in contact with LEU4927 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4842B LEU* 4.7 11.9 - - + -
4889B VAL* 4.4 23.8 - - + +
4892B GLY* 6.0 3.8 - - - -
4922B VAL 3.4 21.3 + - - +
4923B ILE* 3.2 32.2 + - + +
4925B ILE 3.5 0.4 - - - -
4926B LEU* 1.3 79.6 - - - +
4928B ALA* 1.3 56.1 + - - +
4930B ILE* 3.2 11.5 + - + +
4931B GLN* 3.0 43.7 + - + +
4919H PHE* 4.7 19.7 - - + -
4920H PHE* 6.0 2.2 - - + -
4924H VAL* 5.9 7.9 - - + -
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Residues in contact with ALA4928 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4924B VAL 3.3 21.0 + - - +
4925B ILE* 3.4 6.2 + - - +
4926B LEU 3.2 1.0 - - - -
4927B LEU* 1.3 77.0 - - - +
4929B ILE* 1.3 58.4 + - + +
4931B GLN* 4.0 6.9 - - - +
4932B GLY* 2.7 34.0 + - - -
4931D GLN* 5.6 9.6 - - + +
4934D ILE* 6.3 0.4 - - + -
4935D ILE* 3.7 29.7 - - + +
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Residues in contact with ILE4929 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4838B THR* 4.1 26.2 - - + +
4925B ILE* 3.2 25.1 - - + +
4926B LEU* 3.1 9.1 + - - +
4928B ALA* 1.3 80.6 - - + +
4930B ILE* 1.3 63.3 + - - +
4933B LEU* 3.3 42.1 + - + +
4824D ILE* 3.8 33.7 - - + -
4934D ILE* 5.5 6.1 - - + -
4935D ILE* 5.3 7.6 - - + -
4938D PHE* 4.9 20.9 - - + -
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Residues in contact with ILE4930 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4835B LEU* 5.6 7.9 - - + -
4838B THR* 3.3 36.8 - - + +
4839B VAL* 4.3 17.7 - - + +
4842B LEU* 4.8 14.6 - - + -
4926B LEU 3.5 14.4 - - - +
4927B LEU* 3.2 15.0 + - + +
4929B ILE* 1.3 80.0 - - - +
4931B GLN* 1.3 59.5 + - - +
4933B LEU* 4.7 0.7 - - - +
4934B ILE* 3.3 25.5 + - + +
4920H PHE* 6.1 5.6 - - + +
4924H VAL* 4.3 18.6 - - + -
4925H ILE* 5.0 6.9 - - + +
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Residues in contact with GLN4931 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4927B LEU* 3.0 28.0 + - + +
4928B ALA* 4.0 5.0 - - - +
4930B ILE* 1.3 76.4 - - - +
4932B GLY* 1.3 65.0 + - - +
4934B ILE* 3.4 2.7 + - - +
4935B ILE* 3.1 35.8 + - + +
4924H VAL* 3.6 37.3 - - + +
4925H ILE* 6.0 0.4 - - - -
4928H ALA* 5.6 6.2 - - + +
----------------------------------------------------------
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Residues in contact with GLY4932 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4928B ALA 2.7 22.5 + - - -
4929B ILE* 5.1 0.2 - - - -
4931B GLN* 1.3 73.6 - - - +
4933B LEU* 1.3 60.7 + - - +
4935B ILE* 3.4 11.6 - - - +
4936B ASP* 3.0 33.0 + - - +
4935D ILE* 6.4 2.9 - - - -
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Residues in contact with LEU4933 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4830B HIS 5.6 0.3 - - - +
4831B ASN* 5.6 13.0 - - + +
4834B GLN* 4.9 25.4 - - + +
4835B LEU* 6.4 2.9 - - + +
4838B THR* 5.9 3.1 - - + -
4929B ILE* 3.3 38.1 + - + +
4930B ILE 4.8 1.1 - - - +
4932B GLY* 1.3 78.4 - - - +
4934B ILE* 1.3 65.7 + - + +
4936B ASP* 4.2 6.8 - - + +
4937B ALA* 3.3 20.8 + - - +
4938D PHE* 3.5 38.8 - - + -
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Residues in contact with ILE4934 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4827B SER* 3.1 44.3 + - - +
4828B VAL* 4.2 11.7 - - + +
4830B HIS 5.5 2.0 - - - +
4835B LEU* 4.1 27.1 - - + -
4930B ILE* 3.3 22.2 + - + +
4931B GLN* 3.4 3.9 + - - +
4932B GLY 3.2 0.6 - - - -
4933B LEU* 1.3 80.6 - - + +
4935B ILE* 1.3 69.5 + - + +
4937B ALA* 3.2 2.2 + - - -
4938B PHE* 3.2 9.0 + - - +
4925H ILE* 3.8 42.6 - - + +
4928H ALA* 6.3 0.4 - - + -
4929H ILE* 5.5 6.7 - - + -
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Residues in contact with ILE4935 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4931B GLN* 3.1 22.8 + - + +
4932B GLY* 3.4 12.3 - - - +
4934B ILE* 1.3 81.3 - - + +
4936B ASP* 1.3 59.9 + - + +
4938B PHE* 3.5 9.1 + - - +
4939B GLY* 3.1 22.7 + - - -
4928H ALA* 3.7 35.7 - - + +
4929H ILE* 5.3 6.5 - - + -
4932H GLY* 6.4 2.7 - - - -
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Residues in contact with ASP4936 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4932B GLY 3.0 20.9 + - - +
4933B LEU* 4.2 8.1 - - + +
4934B ILE 3.2 0.2 - - - -
4935B ILE* 1.3 78.2 - - + +
4937B ALA* 1.3 59.3 + - - +
4939B GLY* 3.7 1.1 - - - +
4940B GLU* 2.8 32.9 + - - +
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Residues in contact with ALA4937 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4827B SER* 3.5 28.8 - - - +
4830B HIS* 4.1 28.1 - - + +
4831B ASN* 5.1 4.3 - - + -
4933B LEU 3.3 16.0 + - - +
4934B ILE 3.2 2.3 + - - +
4936B ASP* 1.3 79.8 - - - +
4938B PHE* 1.3 56.3 + - - +
4940B GLU* 4.1 3.9 - - - +
4941B LEU* 3.0 32.1 + - - +
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Residues in contact with PHE4938 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4820B THR 5.5 0.2 - - - -
4823B THR* 3.1 39.3 - - + -
4824B ILE* 4.6 17.3 - - + -
4827B SER* 3.6 11.4 + - - +
4934B ILE 3.2 10.1 + - - +
4935B ILE* 3.8 11.2 - - - +
4936B ASP 3.3 0.2 - - - -
4937B ALA* 1.3 79.0 - - - +
4939B GLY* 1.3 62.2 + - - +
4941B LEU* 3.4 2.9 + - - +
4942B ARG* 2.8 45.6 + - + +
4834H GLN* 6.1 4.3 - - + -
4929H ILE* 4.9 14.4 - - + -
4933H LEU* 3.5 42.2 - - + -
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Residues in contact with GLY4939 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4935B ILE 3.1 15.6 + - - -
4936B ASP* 3.8 2.9 - - - -
4938B PHE* 1.3 83.7 - - - +
4940B GLU* 1.3 56.7 + - - +
4942B ARG* 3.8 4.2 - - - +
4943B ASP* 2.9 30.7 + - - +
----------------------------------------------------------
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Residues in contact with GLU4940 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4830B HIS* 6.1 3.1 - - - +
4936B ASP 2.8 22.5 + - - +
4937B ALA* 4.1 5.2 - - - +
4939B GLY* 1.3 73.3 - - - +
4941B LEU* 1.3 57.3 + - - +
4943B ASP* 3.4 5.4 + - - +
4944B GLN* 2.8 29.0 + - - +
----------------------------------------------------------
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Residues in contact with LEU4941 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4823B THR* 5.3 15.9 - - + +
4826B SER* 4.2 26.7 - - - +
4827B SER* 5.1 6.5 - - - +
4830B HIS* 5.3 19.3 - - + +
4937B ALA 3.0 19.3 + - - +
4938B PHE* 4.0 3.8 - - - +
4940B GLU* 1.3 74.8 - - - +
4942B ARG* 1.3 62.0 + - - +
4944B GLN* 3.2 12.0 + - + +
4945B GLN* 2.8 49.6 + - + +
----------------------------------------------------------
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Residues in contact with ARG4942 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4823B THR* 6.5 1.3 - - + -
4938B PHE* 2.8 36.8 + - + +
4939B GLY* 3.9 5.4 - - - +
4941B LEU* 1.3 76.9 - - - +
4943B ASP* 1.3 56.4 + - - +
4945B GLN* 3.4 6.3 + - - +
4946B GLU* 2.9 29.2 + - - +
----------------------------------------------------------
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Residues in contact with ASP4943 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4939B GLY 2.9 20.0 + - - +
4940B GLU* 3.8 6.5 - - - +
4942B ARG* 1.3 73.8 - - - +
4944B GLN* 1.3 55.7 + - - +
4946B GLU* 3.6 6.5 - - - +
4947B GLN* 2.7 35.2 + - - +
----------------------------------------------------------
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Residues in contact with GLN4944 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4940B GLU 2.8 19.0 + - - +
4941B LEU* 3.2 18.1 + - + +
4943B ASP* 1.3 78.3 - - - +
4945B GLN* 1.3 62.7 + - + +
4947B GLN* 3.3 6.4 + - - +
4948B VAL* 3.1 25.5 + - - +
----------------------------------------------------------
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Residues in contact with GLN4945 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4214B PHE* 4.9 11.4 - - - +
4823B THR* 6.2 4.0 - - + -
4941B LEU* 2.8 36.5 + - + +
4942B ARG* 3.9 6.5 - - - +
4944B GLN* 1.3 75.8 - - + +
4946B GLU* 1.3 59.5 + - - +
4948B VAL* 3.3 14.5 - - - +
4949B ARG* 3.3 23.0 + - - +
----------------------------------------------------------
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Residues in contact with GLU4946 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4942B ARG 2.9 18.1 + - - +
4943B ASP* 3.8 7.9 - - - +
4944B GLN 3.2 0.2 - - - -
4945B GLN* 1.3 74.8 - - - +
4947B GLN* 1.3 60.0 + - - +
4949B ARG* 3.6 5.6 + - - +
4950B GLU* 3.0 28.6 + - - +
----------------------------------------------------------
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Residues in contact with GLN4947 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4943B ASP 2.7 21.5 + - - +
4944B GLN* 3.3 8.0 + - - +
4946B GLU* 1.3 71.7 - - - +
4948B VAL* 1.3 54.9 + - - +
4950B GLU* 3.1 7.6 + - - +
4951B ASP* 2.5 49.3 + - + +
4954B THR* 4.7 9.7 - - - +
----------------------------------------------------------
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Residues in contact with VAL4948 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4213B ILE* 4.2 12.8 - - + +
4214B PHE* 4.4 14.6 - - + -
4217B VAL* 3.7 29.8 - - + -
4944B GLN 3.1 19.3 + - - +
4945B GLN* 3.3 23.8 - - - +
4947B GLN* 1.3 78.0 - - - +
4949B ARG* 1.3 63.8 - - - +
4951B ASP* 3.2 20.4 + - + +
4952B MET* 3.5 8.3 + - - +
----------------------------------------------------------
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Residues in contact with ARG4949 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4945B GLN 3.3 15.4 + - - +
4946B GLU* 3.8 7.2 - - - +
4947B GLN 3.2 0.6 - - - -
4948B VAL* 1.3 84.7 - - + +
4950B GLU* 1.3 60.6 + - - +
4951B ASP 3.6 0.2 + - - -
4952B MET* 3.7 14.7 + - - +
4953B GLU* 4.8 0.9 + - - +
----------------------------------------------------------
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Residues in contact with GLU4950 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4946B GLU 3.0 19.1 + - - +
4947B GLN* 3.8 9.9 - - - +
4949B ARG* 1.3 72.6 - - - +
4951B ASP* 1.3 62.1 + - - +
4952B MET 3.2 2.7 - - - -
4953B GLU* 3.3 16.4 + - - +
4954B THR* 3.3 15.3 + - + +
----------------------------------------------------------
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Residues in contact with ASP4951 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4217B VAL* 6.4 0.4 - - + -
4947B GLN* 2.5 29.4 + - + +
4948B VAL* 3.2 17.6 + - + +
4950B GLU* 1.3 74.5 - - - +
4952B MET* 1.3 50.4 + - - +
4953B GLU 3.1 0.2 - - - -
4954B THR* 3.7 11.0 - - + -
4955B LYS* 2.7 47.5 + - + +
----------------------------------------------------------
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Residues in contact with MET4952 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4948B VAL 3.5 8.0 + - - +
4949B ARG* 3.8 12.8 - - - +
4950B GLU 3.2 1.0 - - - -
4951B ASP* 1.3 77.2 - - - +
4953B GLU* 1.3 56.6 + - - +
4955B LYS 3.6 11.6 - - - +
4956B CYS* 5.4 1.4 - - - +
4963B SER 5.7 0.5 - - - +
----------------------------------------------------------
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Residues in contact with GLU4953 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4949B ARG 4.8 1.1 + - - +
4950B GLU* 3.3 10.3 + - - +
4951B ASP 3.1 0.6 - - - -
4952B MET* 1.3 80.0 - - - +
4954B THR* 1.3 58.6 + - - +
4955B LYS 3.5 1.1 - - - -
4963B SER* 3.5 19.0 + - - +
4964B ASP* 5.2 2.6 - - - +
----------------------------------------------------------
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Residues in contact with THR4954 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4947B GLN* 4.7 10.1 - - - +
4950B GLU* 3.3 19.7 - - + +
4951B ASP* 3.7 11.4 - - + -
4953B GLU* 1.3 75.8 - - - +
4955B LYS* 1.3 63.2 + - + +
4963B SER* 3.2 26.9 + - - -
----------------------------------------------------------
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Residues in contact with LYS4955 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4951B ASP* 2.7 26.9 + - + +
4952B MET* 3.6 15.1 - - - +
4953B GLU 3.5 1.4 - - - -
4954B THR* 1.3 83.0 - - + +
4956B CYS* 1.3 67.2 + - - +
4957B PHE 5.6 0.2 - - - +
4962B GLY* 3.9 4.0 - - - -
4963B SER* 3.9 10.7 - - - +
----------------------------------------------------------
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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
------------------------------------------------------------
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