Contacts of the helix formed by residues 4924 - 4955 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4919D PHE* 3.4 28.9 + - + +
4920D PHE* 3.2 24.2 - - + +
4921D PHE 3.9 0.6 + - - -
4923D ILE* 1.3 84.1 - - + +
4925D ILE* 1.3 72.3 + - + +
4928D ALA* 3.3 21.1 + - - +
4927F LEU* 5.3 7.9 - - + +
4930F ILE* 4.3 20.9 - - + -
4931F GLN* 3.6 39.4 - - + +
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Residues in contact with ILE4925 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4920D PHE 3.4 17.0 - - - +
4921D PHE* 3.0 24.1 + - + +
4924D VAL* 1.3 86.1 - - + +
4926D LEU* 1.3 67.9 + - - +
4928D ALA* 3.4 9.7 + - - +
4929D ILE* 3.2 27.7 + - + +
4824F ILE* 5.4 9.2 - - + -
4828F VAL* 4.3 19.3 - - + -
4930F ILE* 5.0 5.6 - - + +
4931F GLN* 6.0 0.4 - - - -
4934F ILE* 3.8 46.2 - - + +
----------------------------------------------------------
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Residues in contact with LEU4926 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4838D THR* 4.6 2.6 + - - +
4842D LEU* 4.6 22.9 - - + -
4845D VAL* 5.8 2.5 - - + -
4921D PHE 2.9 6.4 + - - +
4922D VAL* 3.3 30.9 + - + +
4925D ILE* 1.3 78.1 - - - +
4927D LEU* 1.3 63.5 + - - +
4929D ILE* 3.1 18.9 + - - +
4930D ILE* 3.4 16.7 + - - +
----------------------------------------------------------
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Residues in contact with LEU4927 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4919B PHE* 4.7 20.6 - - + -
4920B PHE* 6.0 1.3 - - + -
4924B VAL* 5.9 7.6 - - + -
4842D LEU* 4.7 11.2 - - + -
4889D VAL* 4.4 24.7 - - + +
4892D GLY* 6.0 3.8 - - - -
4922D VAL 3.4 21.1 + - - +
4923D ILE* 3.2 30.4 + - + +
4925D ILE 3.5 0.2 - - - -
4926D LEU* 1.3 80.6 - - - +
4928D ALA* 1.3 55.7 + - - +
4930D ILE* 3.2 11.7 + - + +
4931D GLN* 3.0 44.7 + - + +
----------------------------------------------------------
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Residues in contact with ALA4928 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4923D ILE 4.5 0.2 + - - -
4924D VAL 3.3 21.2 + - - +
4925D ILE* 3.4 6.7 + - - +
4926D LEU 3.2 1.2 - - - -
4927D LEU* 1.3 75.7 - - - +
4929D ILE* 1.3 57.2 + - + +
4931D GLN* 4.0 7.4 - - - +
4932D GLY* 2.7 34.7 + - - -
4931F GLN* 5.6 9.6 - - + +
4934F ILE* 6.3 0.2 - - + -
4935F ILE* 3.7 29.9 - - + +
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Residues in contact with ILE4929 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4838D THR* 4.1 26.0 - - + +
4925D ILE* 3.2 25.8 - - + +
4926D LEU* 3.1 9.3 + - - +
4928D ALA* 1.3 80.8 - - + +
4930D ILE* 1.3 63.4 + - - +
4933D LEU* 3.3 41.2 + - + +
4824F ILE* 3.8 33.4 - - + -
4934F ILE* 5.5 6.1 - - + -
4935F ILE* 5.3 8.3 - - + -
4938F PHE* 4.9 20.9 - - + -
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Residues in contact with ILE4930 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4920B PHE* 6.1 5.6 - - + +
4924B VAL* 4.3 18.8 - - + -
4925B ILE* 5.0 6.7 - - + +
4835D LEU* 5.6 7.2 - - + -
4838D THR* 3.3 36.6 - - + +
4839D VAL* 4.3 18.4 - - + +
4842D LEU* 4.8 14.8 - - + -
4926D LEU 3.5 13.7 - - - +
4927D LEU* 3.2 15.2 + - + +
4929D ILE* 1.3 79.6 - - - +
4931D GLN* 1.3 61.4 + - - +
4933D LEU* 4.8 0.6 - - - +
4934D ILE* 3.3 25.5 + - + +
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Residues in contact with GLN4931 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4924B VAL* 3.6 37.3 - - + +
4925B ILE* 6.0 0.9 - - - -
4928B ALA* 5.6 6.9 - - + +
4927D LEU* 3.0 27.0 + - + +
4928D ALA* 4.0 6.3 - - - +
4930D ILE* 1.3 76.4 - - - +
4932D GLY* 1.3 64.2 + - - +
4934D ILE* 3.4 2.9 + - - +
4935D ILE* 3.1 35.4 + - + +
----------------------------------------------------------
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Residues in contact with GLY4932 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4928D ALA 2.7 22.9 + - - -
4929D ILE* 4.7 0.4 - - - -
4931D GLN* 1.3 74.6 - - - +
4933D LEU* 1.3 59.9 + - - +
4935D ILE* 3.4 11.1 - - - +
4936D ASP* 3.0 33.2 + - - +
4935F ILE* 6.4 2.9 - - - -
----------------------------------------------------------
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Residues in contact with LEU4933 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4830D HIS 5.6 0.3 - - - +
4831D ASN* 5.6 12.7 - - + +
4834D GLN* 4.9 25.1 - - + +
4835D LEU* 6.2 3.4 - - + +
4838D THR* 5.9 2.9 - - + -
4929D ILE* 3.3 39.4 + - + +
4930D ILE 4.8 1.1 - - - +
4932D GLY* 1.3 78.1 - - - +
4934D ILE* 1.3 66.4 + - + +
4936D ASP* 4.2 6.4 - - + +
4937D ALA* 3.3 21.8 + - - +
4938F PHE* 3.5 38.6 - - + -
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Residues in contact with ILE4934 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4925B ILE* 3.8 42.6 - - + -
4928B ALA* 6.3 0.2 - - + -
4929B ILE* 5.5 6.5 - - + +
4827D SER* 3.1 44.9 + - - +
4828D VAL* 4.2 12.1 - - + +
4830D HIS 5.5 1.8 - - - +
4835D LEU* 4.1 28.3 - - + -
4930D ILE* 3.3 22.0 + - + +
4931D GLN* 3.4 3.9 + - - +
4932D GLY 3.2 0.6 - - - -
4933D LEU* 1.3 81.3 - - + +
4935D ILE* 1.3 69.9 + - + +
4937D ALA* 3.2 2.2 + - - -
4938D PHE* 3.2 10.1 + - + +
----------------------------------------------------------
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Residues in contact with ILE4935 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4928B ALA* 3.7 34.5 - - + +
4929B ILE* 5.3 6.3 - - + -
4932B GLY* 6.4 3.1 - - - -
4931D GLN* 3.1 22.2 + - + +
4932D GLY* 3.4 12.8 - - - +
4934D ILE* 1.3 80.9 - - + +
4936D ASP* 1.3 61.5 + - + +
4938D PHE* 3.5 8.9 + - - +
4939D GLY* 3.1 22.5 + - - -
----------------------------------------------------------
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Residues in contact with ASP4936 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4932D GLY 3.0 20.2 + - - +
4933D LEU* 4.2 7.6 - - + +
4935D ILE* 1.3 77.8 - - + +
4937D ALA* 1.3 60.0 + - - +
4939D GLY* 3.7 1.5 - - - +
4940D GLU* 2.8 33.0 + - - +
----------------------------------------------------------
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Residues in contact with ALA4937 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4827D SER* 3.5 28.3 - - - +
4830D HIS* 4.1 28.6 - - + +
4831D ASN* 5.1 3.8 - - + -
4933D LEU 3.3 16.7 + - - +
4934D ILE 3.2 2.0 + - - +
4936D ASP* 1.3 79.1 - - - +
4938D PHE* 1.3 57.9 + - - +
4940D GLU* 4.0 4.5 - - - +
4941D LEU* 3.0 31.5 + - - +
----------------------------------------------------------
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Residues in contact with PHE4938 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4834B GLN* 6.1 4.0 - - + -
4929B ILE* 4.9 13.7 - - + -
4933B LEU* 3.5 42.2 - - + -
4823D THR* 3.1 39.0 - - + -
4824D ILE* 4.6 17.7 - - + -
4827D SER* 3.6 10.7 + - - +
4934D ILE* 3.2 10.7 + - + +
4935D ILE* 3.8 10.5 - - - +
4936D ASP 3.3 0.2 - - - -
4937D ALA* 1.3 78.8 - - - +
4939D GLY* 1.3 62.3 + - - +
4941D LEU* 3.4 3.3 + - - +
4942D ARG* 2.8 45.1 + - + +
----------------------------------------------------------
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Residues in contact with GLY4939 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4935D ILE 3.1 15.6 + - - -
4936D ASP* 3.8 2.0 - - - -
4938D PHE* 1.3 82.6 - - - +
4940D GLU* 1.3 56.7 + - - +
4942D ARG* 3.9 3.8 - - - +
4943D ASP* 2.9 30.1 + - - +
----------------------------------------------------------
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Residues in contact with GLU4940 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4830D HIS* 6.1 3.6 - - + +
4936D ASP 2.8 22.6 + - - +
4937D ALA* 4.1 4.7 - - - +
4939D GLY* 1.3 74.1 - - - +
4941D LEU* 1.3 57.3 + - - +
4943D ASP* 3.4 6.1 + - - +
4944D GLN* 2.8 29.0 + - - +
----------------------------------------------------------
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Residues in contact with LEU4941 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4823D THR* 5.3 16.2 - - + +
4826D SER* 4.2 26.7 - - - +
4827D SER* 5.1 6.7 - - - +
4830D HIS* 5.3 19.7 - - + +
4937D ALA 3.0 19.7 + - - +
4938D PHE* 4.0 4.0 - - - +
4940D GLU* 1.3 74.1 - - - +
4942D ARG* 1.3 61.4 + - - +
4944D GLN* 3.2 11.9 + - + +
4945D GLN* 2.8 49.6 + - + +
----------------------------------------------------------
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Residues in contact with ARG4942 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4823D THR* 6.5 1.6 - - + -
4938D PHE* 2.8 36.4 + - + +
4939D GLY* 3.9 5.8 - - - +
4941D LEU* 1.3 77.9 - - - +
4943D ASP* 1.3 55.8 + - - +
4945D GLN* 3.4 6.4 + - - +
4946D GLU* 2.9 28.9 + - - +
----------------------------------------------------------
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Residues in contact with ASP4943 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4939D GLY 2.9 18.8 + - - +
4940D GLU* 3.8 6.1 - - - +
4942D ARG* 1.3 73.8 - - - +
4944D GLN* 1.3 55.4 + - - +
4946D GLU* 3.6 6.7 - - - +
4947D GLN* 2.7 36.1 + - - +
----------------------------------------------------------
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Residues in contact with GLN4944 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4940D GLU 2.8 18.5 + - - +
4941D LEU* 3.5 17.7 - - + +
4943D ASP* 1.3 77.7 - - - +
4945D GLN* 1.3 62.6 + - + +
4947D GLN* 3.7 6.7 - - - +
4948D VAL* 3.1 26.2 + - - +
----------------------------------------------------------
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Residues in contact with GLN4945 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4214D PHE* 4.9 11.0 - - - +
4823D THR* 6.2 4.3 - - + -
4941D LEU* 2.8 36.0 + - + +
4942D ARG* 3.9 6.7 - - - +
4944D GLN* 1.3 76.4 - - + +
4946D GLU* 1.3 60.1 + - - +
4948D VAL* 3.3 14.3 - - - +
4949D ARG* 3.3 23.0 + - - +
----------------------------------------------------------
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Residues in contact with GLU4946 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4942D ARG 2.9 19.2 + - - +
4943D ASP* 3.8 7.2 - - - +
4944D GLN 3.2 0.2 - - - -
4945D GLN* 1.3 75.0 - - - +
4947D GLN* 1.3 59.9 + - - +
4949D ARG* 3.8 5.6 - - - +
4950D GLU* 3.0 28.4 + - - +
----------------------------------------------------------
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Residues in contact with GLN4947 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4943D ASP 2.7 20.3 + - - +
4944D GLN* 3.3 8.0 + - - +
4946D GLU* 1.3 72.0 - - - +
4948D VAL* 1.3 55.1 + - - +
4950D GLU* 3.1 6.9 + - - +
4951D ASP* 2.5 50.6 + - + +
4954D THR* 4.7 9.5 - - - +
----------------------------------------------------------
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Residues in contact with VAL4948 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4213D ILE* 4.2 13.0 - - + +
4214D PHE* 4.4 14.4 - - + -
4217D VAL* 3.7 30.7 - - + -
4944D GLN 3.1 19.5 + - - +
4945D GLN* 3.3 22.7 - - - +
4947D GLN* 1.3 76.9 - - - +
4949D ARG* 1.3 67.4 + - - +
4951D ASP* 3.2 20.3 + - + +
4952D MET* 3.5 8.7 + - - +
----------------------------------------------------------
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Residues in contact with ARG4949 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4945D GLN 3.3 15.8 + - - +
4946D GLU* 3.8 7.0 - - - +
4947D GLN 3.2 0.4 - - - -
4948D VAL* 1.3 85.0 - - + +
4950D GLU* 1.3 59.1 + - - +
4952D MET* 3.7 15.1 + - - +
4953D GLU* 4.8 1.0 + - - +
----------------------------------------------------------
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Residues in contact with GLU4950 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4946D GLU 3.0 18.7 + - - +
4947D GLN* 3.8 9.0 - - - +
4949D ARG* 1.3 72.1 - - - +
4951D ASP* 1.3 63.3 + - - +
4952D MET 3.2 2.2 - - - -
4953D GLU* 3.3 17.1 + - - +
4954D THR* 3.3 15.8 + - + +
----------------------------------------------------------
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Residues in contact with ASP4951 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4217D VAL* 6.4 0.4 - - + -
4947D GLN* 2.5 30.7 + - + +
4948D VAL* 3.2 17.0 + - + +
4950D GLU* 1.3 73.8 - - - +
4952D MET* 1.3 51.3 + - - +
4953D GLU 3.1 0.2 - - - -
4954D THR* 3.7 11.9 - - + -
4955D LYS* 2.7 46.8 + - + +
----------------------------------------------------------
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Residues in contact with MET4952 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4948D VAL 3.5 7.4 + - - +
4949D ARG* 3.8 12.3 - - - +
4950D GLU 3.2 1.0 - - - -
4951D ASP* 1.3 77.1 - - - +
4953D GLU* 1.3 57.8 + - - +
4955D LYS 3.6 10.7 - - - +
4956D CYS* 5.4 1.4 - - - +
4963D SER 5.7 0.5 - - - +
----------------------------------------------------------
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Residues in contact with GLU4953 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4949D ARG 4.8 0.4 + - - +
4950D GLU* 3.3 11.0 + - - +
4951D ASP 3.1 0.4 - - - -
4952D MET* 1.3 79.8 - - - +
4954D THR* 1.3 59.3 + - - +
4955D LYS 3.5 1.1 - - - -
4963D SER* 3.5 18.0 + - - +
4964D ASP* 5.2 2.8 - - - +
----------------------------------------------------------
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Residues in contact with THR4954 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4947D GLN* 4.7 9.6 - - - +
4950D GLU* 3.3 19.1 - - + +
4951D ASP* 3.7 11.7 - - + -
4953D GLU* 1.3 76.2 - - - +
4955D LYS* 1.3 63.7 + - + +
4963D SER* 3.2 28.4 + - - -
----------------------------------------------------------
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Residues in contact with LYS4955 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4951D ASP* 2.7 27.4 + - + +
4952D MET* 3.6 14.7 - - - +
4953D GLU 3.5 1.8 + - - -
4954D THR* 1.3 82.4 - - + +
4956D CYS* 1.3 65.8 + - - +
4962D GLY* 3.9 3.6 - - - -
4963D SER* 3.9 10.5 - - - +
----------------------------------------------------------
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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