Contacts of the helix formed by residues 5421 - 5452 (chain c) in PDB entry 2AXT
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 SER5421 (chain c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5303c GLY* 3.6 14.4 - - - -
5304c PRO 4.7 0.2 + - - -
5398c HIS 5.0 0.4 - - - -
5399c ALA 5.0 0.4 - - - -
5400c PRO* 3.9 31.1 - - - +
5419c PHE* 3.7 19.4 - - - -
5420c VAL* 1.3 76.1 - - - +
5422c PRO* 1.3 79.5 - - - +
5423c ARG* 3.3 18.2 + - - +
5424c SER* 2.8 18.1 + - - -
5425c TRP* 3.1 11.8 + - - -
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Residues in contact with PRO5422 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5082c TYR* 3.7 33.2 - - + +
5085c GLY* 5.6 2.2 - - - -
5086c LEU 3.9 23.6 - - - +
5087c ILE* 4.4 8.3 - - + -
5301c PHE 4.7 0.4 - - - +
5302c TYR* 4.0 23.1 - - + -
5303c GLY 3.6 13.2 - - - +
5420c VAL 3.5 4.5 - - - +
5421c SER* 1.3 91.0 - - - +
5423c ARG* 1.3 55.4 + - - +
5424c SER 3.0 0.3 + - - -
5425c TRP* 3.2 10.0 + - + +
5426c LEU* 2.7 41.1 + - + +
5494c CLA 5.4 0.4 - - + -
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Residues in contact with ARG5423 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5290c VAL* 2.9 43.5 + - + +
5291c TRP* 3.4 25.7 + - + -
5293c ASN 3.1 22.2 + - - -
5294c ASN* 4.1 1.2 - - - +
5297c TYR* 2.8 36.6 + - - +
5299c SER* 3.7 14.5 - - - +
5302c TYR* 4.0 16.2 - - + +
5303c GLY 2.9 21.3 + - - -
5304c PRO 3.5 21.1 - - - +
5305c THR* 3.7 19.8 + - - +
5306c GLY 5.2 0.2 - - - +
5400c PRO* 5.1 2.2 - - + -
5421c SER* 3.4 10.8 - - - +
5422c PRO* 1.3 80.4 - - - +
5424c SER* 1.3 59.7 + - - +
5427c ALA* 3.2 25.9 + - - +
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Residues in contact with SER5424 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5295a PHE* 3.0 23.2 + - - +
5296a ASN 4.4 5.3 + - - -
5297a LEU* 5.1 3.8 - - - -
5291c TRP* 3.8 6.0 - - - -
5400c PRO* 3.5 26.9 + - - +
5420c VAL* 3.9 16.9 - - - +
5421c SER 2.8 11.9 + - - -
5423c ARG* 1.3 77.8 - - - +
5425c TRP* 1.3 67.7 + - - -
5426c LEU 3.0 0.7 + - - -
5427c ALA* 3.2 2.9 + - - +
5428c THR* 2.7 29.1 + - - -
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Residues in contact with TRP5425 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5297a LEU* 3.8 27.4 - - + -
5085c GLY* 5.7 0.2 - - - -
5087c ILE* 5.3 0.4 - - + -
5404c LEU* 3.8 19.3 - - + -
5406c SER* 3.5 13.9 - - - -
5420c VAL* 3.2 40.7 - - + +
5421c SER 3.1 8.6 + - - -
5422c PRO* 3.6 6.3 - - + +
5424c SER* 1.3 76.4 - - - +
5426c LEU* 1.3 66.1 + - + +
5428c THR* 3.7 4.3 - - - +
5429c SER* 3.1 21.1 + - - -
5494c CLA 3.0 91.8 - + + +
5508c DGD 2.9 41.9 + - + -
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Residues in contact with LEU5426 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5087c ILE* 4.5 16.4 - - + -
5091c HIS* 5.0 3.1 - - + -
5290c VAL* 3.4 34.3 - - + -
5297c TYR* 5.0 0.4 - - + -
5302c TYR* 3.9 24.5 - - + -
5422c PRO* 2.7 25.5 + - + +
5425c TRP* 1.3 68.9 - - - +
5427c ALA* 1.3 67.8 + - - +
5428c THR 2.8 1.2 + - - -
5429c SER* 2.8 22.0 + - - -
5430c HIS* 3.1 18.9 + - + -
5492c CLA 3.9 46.0 - - + -
5494c CLA 4.2 9.4 - - + -
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Residues in contact with ALA5427 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5295a PHE* 4.1 10.7 - - + -
5287c THR* 3.1 47.5 + - + +
5290c VAL* 3.5 17.8 - - + +
5291c TRP* 4.0 15.5 - - + -
5423c ARG 3.2 17.7 + - - +
5424c SER 3.2 1.9 + - - +
5426c LEU* 1.3 78.0 - - - +
5428c THR* 1.3 60.4 - - - +
5430c HIS* 5.0 0.4 - - - -
5431c PHE* 3.3 6.9 + - - +
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Residues in contact with THR5428 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5292a THR* 3.5 30.5 + - - +
5295a PHE* 4.4 9.6 - - - +
5297a LEU* 3.5 29.6 - - + +
5424c SER 2.7 21.2 + - - -
5425c TRP* 3.7 5.4 - - - +
5426c LEU 2.8 2.6 + - - -
5427c ALA* 1.3 69.8 - - - +
5429c SER* 1.3 70.3 + - - +
5431c PHE* 3.3 11.2 + - - +
5432c VAL* 3.4 14.6 + - - +
5508c DGD 3.3 31.6 - - + -
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Residues in contact with SER5429 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5425c TRP 3.1 10.3 + - - -
5426c LEU 2.8 7.2 + - - -
5428c THR* 1.3 82.7 - - - +
5430c HIS* 1.3 83.6 + - - +
5432c VAL* 3.0 9.7 + - - +
5433c LEU* 3.0 32.6 + - - +
5494c CLA 3.4 30.6 - - - +
5508c DGD 4.0 19.1 - - - -
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Residues in contact with HIS5430 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5283c GLY* 3.8 5.9 - - - +
5286c ALA* 4.9 4.3 - - + -
5287c THR* 3.3 19.1 - - - +
5426c LEU* 3.1 26.4 + - + +
5429c SER* 1.3 103.9 + - - +
5431c PHE* 1.3 60.9 + - - +
5433c LEU* 4.0 7.1 - - + +
5434c ALA* 2.7 32.1 + - - +
5492c CLA 2.5 83.3 + + + +
5494c CLA 3.6 19.1 - - + -
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Residues in contact with PHE5431 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5160a ILE* 3.2 43.1 - - + -
5288a LEU* 4.5 8.7 - - + -
5291a SER* 3.3 36.6 - - - +
5292a THR* 6.0 0.7 - - - +
5295a PHE* 4.6 9.9 - + + -
5284c PHE* 3.1 36.1 - + - -
5287c THR* 3.2 21.0 + - + +
5427c ALA 3.3 13.3 + - - +
5428c THR* 3.3 6.5 + - - +
5429c SER 3.2 1.0 - - - -
5430c HIS* 1.3 77.8 - - - +
5432c VAL* 1.3 59.6 + - + +
5434c ALA* 3.7 2.4 - - - +
5435c PHE* 2.8 36.6 + + + +
5507c DGD 4.5 6.5 - - + -
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Residues in contact with VAL5432 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5197a PHE* 4.6 9.4 - - + -
5285a PHE* 6.1 0.7 - - + -
5288a LEU* 3.8 26.9 - - + -
5292a THR* 4.2 14.8 - - - +
5428c THR 3.4 15.3 - - - +
5429c SER* 3.3 7.0 - - - +
5431c PHE* 1.3 76.3 - - + +
5433c LEU* 1.3 74.9 + - + +
5435c PHE* 3.6 0.9 - - - +
5436c PHE* 3.0 44.6 + - + +
5508c DGD 4.5 17.0 - - + -
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Residues in contact with LEU5433 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5429c SER* 3.0 21.4 + - - +
5430c HIS* 4.0 8.5 - - + +
5432c VAL* 1.3 86.9 - - + +
5434c ALA* 1.3 65.9 + - - +
5436c PHE* 3.3 3.8 + - - +
5437c PHE* 3.0 26.2 + - + +
5492c CLA 3.4 70.0 - - + +
5494c CLA 4.8 9.0 - - + -
5500c CLA 4.4 32.1 - - + -
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Residues in contact with ALA5434 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5280c SER* 2.6 36.8 + - - +
5283c GLY* 3.4 29.2 - - - +
5284c PHE* 3.8 15.0 - - + +
5430c HIS 2.7 25.3 + - - +
5431c PHE 3.7 3.1 - - - +
5433c LEU* 1.3 74.4 - - - +
5435c PHE* 1.3 60.6 + - - +
5437c PHE 3.4 0.2 + - - -
5438c LEU 3.4 0.9 + - - -
5492c CLA 3.8 13.8 - - - +
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Residues in contact with PHE5435 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5148a SER* 4.1 2.0 - - - -
5152a ALA* 3.6 25.8 - - + -
5284a TRP* 3.6 40.6 - + + -
5287a ALA* 5.8 0.7 - - + -
5288a LEU* 3.8 26.7 - - + -
5284c PHE* 3.8 11.8 - + + -
5431c PHE* 2.8 29.5 + + + +
5432c VAL 3.6 2.0 - - - +
5433c LEU 3.1 0.6 + - - -
5434c ALA* 1.3 68.4 - - - +
5436c PHE* 1.3 75.4 + + - +
5437c PHE 2.9 1.6 - - - -
5438c LEU* 2.5 38.1 + - + +
5439c VAL* 3.1 28.4 + - + -
5507c DGD 4.0 31.4 - - + -
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Residues in contact with PHE5436 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5281a VAL* 6.2 0.9 - - + -
5284a TRP* 4.1 33.0 - + + -
5285a PHE* 4.5 13.5 - + - -
5288a LEU* 3.5 26.9 - - + -
5567a LHG 3.4 35.7 - - + -
5432c VAL* 3.0 33.0 + - + +
5433c LEU 3.9 1.3 - - - +
5435c PHE* 1.3 87.0 - + - +
5437c PHE* 1.3 50.4 + - - +
5439c VAL* 3.1 11.1 + - + +
5440c GLY 2.6 31.0 + - - -
5498c CLA 3.3 20.8 - - + +
5500c CLA 3.5 31.0 - - + -
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Residues in contact with PHE5437 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5276c LEU* 3.9 15.0 - - + +
5279c LEU* 3.8 27.8 - - + -
5280c SER* 3.4 19.2 - - - -
5433c LEU* 3.0 16.7 + - + +
5434c ALA 3.4 4.3 - - - +
5435c PHE 2.7 4.9 + - - -
5436c PHE* 1.3 73.0 - - + +
5438c LEU* 1.3 54.0 + - - +
5440c GLY* 3.0 0.9 + - - -
5441c HIS* 2.6 34.1 + - - +
5492c CLA 3.4 31.9 - - + -
5498c CLA 3.1 42.8 - - + -
5500c CLA 3.6 53.4 - + + -
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Residues in contact with LEU5438 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5127a MET* 5.2 1.3 - - + -
5277c GLY* 6.0 0.9 - - - -
5280c SER* 3.2 23.3 + - - +
5284c PHE* 5.0 5.2 - - + -
5434c ALA 4.2 0.4 - - - +
5435c PHE* 2.5 22.3 + - + +
5437c PHE* 1.3 68.7 - - - +
5439c VAL* 1.3 66.8 + - + +
5441c HIS* 3.0 9.7 + - + +
5442c LEU* 3.0 32.6 + - + +
5495c CLA 3.7 43.3 - - + -
5507c DGD 3.4 45.8 - - + -
5201i MGE 5.3 5.6 - - + -
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Residues in contact with VAL5439 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5145a VAL* 4.4 9.7 - - + +
5148a SER* 4.0 8.1 - - - +
5284a TRP* 3.6 41.5 - - + +
5435c PHE* 3.1 40.3 + - + +
5436c PHE* 3.1 14.5 + - + +
5438c LEU* 1.3 78.9 - - + +
5440c GLY* 1.3 65.8 + - - +
5442c LEU* 3.0 12.7 + - - +
5443c TRP* 3.0 22.6 + - + +
5498c CLA 4.0 15.0 - - + -
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Residues in contact with GLY5440 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5276c LEU* 4.0 6.7 - - - -
5436c PHE 2.6 15.0 + - - -
5437c PHE 3.3 4.3 - - - -
5439c VAL* 1.3 73.3 - - - +
5441c HIS* 1.3 62.2 + - - +
5443c TRP* 3.1 6.6 + - - +
5444c HIS* 3.1 25.6 + - - -
5498c CLA 3.4 36.1 - - - -
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Residues in contact with HIS5441 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5273c SER* 3.6 15.1 + - - -
5274c TYR* 4.8 0.7 - - - -
5276c LEU* 4.0 11.3 - - - +
5277c GLY* 3.4 37.5 - - - +
5437c PHE 2.6 15.8 + - - +
5438c LEU* 3.0 15.2 + - + +
5440c GLY* 1.3 74.2 - - - +
5442c LEU* 1.3 63.7 + - - +
5444c HIS* 3.3 0.7 + - - +
5445c ALA* 2.7 49.7 + - + +
5495c CLA 2.4 74.7 + + + -
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Residues in contact with LEU5442 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5127a MET* 3.6 31.4 - - + -
5142a TRP* 4.8 1.2 + - - -
5144a CYS* 4.6 11.7 - - - +
5145a VAL* 3.7 22.4 - - + -
5148a SER* 4.8 6.5 - - - -
5438c LEU* 3.0 20.9 + - + +
5439c VAL* 3.0 12.4 + - - +
5441c HIS* 1.3 83.8 + - - +
5443c TRP* 1.3 56.4 + - - +
5445c ALA* 4.5 2.0 - - - -
5446c GLY* 2.7 34.3 + - - -
5495c CLA 3.4 55.4 - - + +
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Residues in contact with TRP5443 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5142a TRP* 2.9 92.4 + + + +
5145a VAL* 4.0 15.1 - - + +
5567a LHG 3.5 46.6 + - + -
5439c VAL* 3.0 14.4 + - + +
5440c GLY* 3.2 13.0 - - - +
5442c LEU* 1.3 76.3 - - - +
5444c HIS* 1.3 80.8 + + - +
5447c ARG* 3.2 14.7 + - - +
5498c CLA 3.3 66.0 + + + -
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Residues in contact with HIS5444 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5269c GLU* 2.8 32.1 + - + +
5272c LEU* 3.4 12.4 - - + +
5273c SER* 4.1 13.2 - - - -
5276c LEU* 3.3 28.7 - - + -
5440c GLY 3.1 10.6 + - - +
5441c HIS 4.1 0.9 - - - +
5443c TRP* 1.3 87.1 - + - +
5445c ALA* 1.3 62.8 + - - +
5446c GLY 2.9 1.6 - - - -
5447c ARG 2.9 0.7 + - - -
5448c ALA* 2.7 34.5 + - - +
5498c CLA 2.3 72.2 + + + -
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Residues in contact with ALA5445 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5273c SER* 3.4 17.7 - - - -
5441c HIS* 2.7 42.2 + - + +
5442c LEU* 4.1 2.7 - - - +
5444c HIS* 1.3 73.5 - - - +
5446c GLY* 1.3 57.4 + - - +
5448c ALA* 5.0 2.0 - - - -
5449c ARG* 2.9 29.1 + - - +
5495c CLA 3.3 34.4 - - + +
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Residues in contact with GLY5446 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5131a TRP* 4.4 18.2 + - - -
5141a PRO* 3.7 27.2 - - - +
5442c LEU 2.7 18.5 + - - -
5443c TRP 4.2 0.4 - - - -
5445c ALA* 1.3 78.1 - - - +
5447c ARG* 1.3 61.8 + - - +
5449c ARG* 3.8 2.3 + - - +
5450c ALA* 3.6 17.0 + - - +
5495c CLA 4.6 2.9 - - - +
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Residues in contact with ARG5447 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5141a PRO* 4.4 6.7 - - + -
5142a TRP* 3.3 17.3 - - + +
5567a LHG 2.5 36.2 + - - -
5033c PHE* 3.7 16.4 - - - -
5269c GLU* 2.7 33.1 + - - +
5443c TRP* 3.2 18.9 + - - +
5444c HIS 2.9 4.9 + - - +
5446c GLY* 1.3 73.5 - - - +
5448c ALA* 1.3 53.9 + - - +
5449c ARG 3.1 1.3 - - - -
5450c ALA* 3.0 6.5 + - - +
5451c ALA* 2.8 42.5 + - - +
5456c GLU* 4.4 24.3 - - + +
5457c LYS* 5.9 0.6 - - - +
5498c CLA 3.5 19.5 - - - -
5229d ALA* 3.5 30.3 - - - +
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Residues in contact with ALA5448 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5265c ILE* 3.8 7.2 - - - +
5267c SER* 4.4 6.2 - - - +
5269c GLU* 3.3 34.1 + - + -
5270c ALA* 3.3 29.4 - - + +
5444c HIS 2.7 15.2 + - - +
5445c ALA* 4.7 1.8 - - - +
5447c ARG* 1.3 75.1 - - - +
5449c ARG* 1.3 57.9 + - - +
5450c ALA 3.1 1.5 + - - -
5451c ALA* 4.1 6.3 - - - +
5452c ALA* 3.3 23.2 + - - +
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Residues in contact with ARG5449 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5131a TRP* 4.0 26.4 - - + +
5135a TYR* 2.7 62.6 + - + -
5136a ARG* 4.1 0.8 - - - +
5263c ALA 4.5 4.2 + - - -
5265c ILE* 3.7 14.1 - - - -
5445c ALA 2.9 22.9 + - - +
5446c GLY* 4.0 5.4 - - - +
5447c ARG 3.1 0.8 - - - -
5448c ALA* 1.3 77.1 - - - +
5450c ALA* 1.3 53.7 + - - +
5452c ALA* 4.3 4.2 - - - +
5453c ALA 4.3 3.6 + - - -
5495c CLA 3.2 54.9 + - + +
5506c BCR 6.2 0.4 - - - +
5023i PHE* 5.6 0.6 - - - -
5027i ASP* 3.1 40.8 + - - +
5028i PRO* 3.2 22.2 - - - +
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Residues in contact with ALA5450 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5135a TYR* 4.5 4.9 - - + -
5139a MET 5.0 0.9 - - - +
5141a PRO* 4.7 13.9 - - + -
5446c GLY 3.6 14.1 + - - +
5447c ARG 3.0 3.9 + - - +
5449c ARG* 1.3 77.6 - - - +
5451c ALA* 1.3 63.0 + - - +
5452c ALA 3.0 1.3 - - - -
5453c ALA 3.9 2.4 - - - +
5454c GLY 2.8 7.9 + - - -
5455c PHE* 2.8 56.2 + - + -
5456c GLU* 3.5 7.8 + - + -
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Residues in contact with ALA5451 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5267c SER* 6.0 1.8 - - - +
5269c GLU* 4.8 1.6 - - - +
5447c ARG* 2.8 24.3 + - - +
5448c ALA* 4.1 10.3 - - - +
5450c ALA* 1.3 77.9 - - - +
5452c ALA* 1.3 59.8 + - - +
5454c GLY* 3.1 14.9 - - - -
5456c GLU* 3.3 34.0 - - + +
5035i LYS* 3.9 11.3 - - - -
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Residues in contact with ALA5452 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5135a TYR* 5.8 1.3 - - - +
5265c ILE* 4.2 23.6 - - + -
5267c SER* 6.0 1.8 - - - -
5448c ALA 3.3 16.3 + - - +
5449c ARG 4.5 3.4 - - - +
5451c ALA* 1.3 79.1 - - - +
5453c ALA* 1.3 58.0 + - - +
5454c GLY 2.5 13.6 + - - -
5034i ARG* 4.1 3.0 - - - +
5035i LYS* 3.3 21.0 + - - +
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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