Contacts of the helix formed by residues 5109 - 5137 (chain a) 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 GLY5109 (chain a).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5058a VAL* 3.1 24.0 - - - +
5083a VAL 4.4 2.7 - - - -
5085a SER* 3.4 24.0 - - - -
5106a LEU 3.0 11.8 + - - -
5108a ASN* 1.3 80.3 - - - +
5110a GLY* 1.3 66.1 + - - +
5111a PRO* 3.2 6.5 - - - -
5112a TYR* 3.1 14.1 + - - +
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Residues in contact with GLY5110 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5085a SER* 5.3 1.3 - - - -
5094a TYR* 3.9 13.8 - - - +
5105a TRP* 2.6 52.3 + - - -
5108a ASN 3.5 1.8 - - - -
5109a GLY* 1.3 70.4 - - - +
5111a PRO* 1.3 64.1 - - - +
5112a TYR 3.1 1.2 + - - -
5113a GLN* 3.3 14.7 + - - +
5114a LEU 3.4 8.3 + - - -
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Residues in contact with PRO5111 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5047a CYS* 4.6 6.3 - - - -
5051a ALA* 4.5 19.3 - - + -
5055a ALA* 6.0 1.3 - - + -
5058a VAL* 5.7 2.5 - - + -
5082a VAL* 4.5 7.4 - - + -
5083a VAL 5.8 0.2 - - - +
5105a TRP* 3.4 39.9 - - + +
5106a LEU* 3.8 19.7 - - + +
5109a GLY* 3.2 7.2 - - - -
5110a GLY* 1.3 87.4 - - - +
5112a TYR* 1.3 62.3 + - - +
5114a LEU* 3.4 2.0 + - + +
5115a ILE* 2.9 31.1 + - + +
5566a BCR 4.5 6.7 - - + -
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Residues in contact with TYR5112 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5082a VAL* 4.2 9.3 - - + +
5083a VAL 3.4 19.0 + - - +
5084a PRO* 3.5 25.6 - - + -
5085a SER* 3.6 7.9 - - - +
5109a GLY 3.1 9.5 + - - +
5110a GLY 3.1 0.2 + - - -
5111a PRO* 1.3 78.0 - - - +
5113a GLN* 1.3 67.2 + - - +
5115a ILE* 2.9 6.1 + - - +
5116a ILE* 2.8 52.0 + - + +
5158a PHE* 3.8 14.1 + - - -
5162a PRO* 5.9 0.3 - - - +
5168a PHE* 4.0 23.6 - + + -
5171a GLY* 2.9 14.3 + - - -
5172a MET 2.8 28.1 + - - -
5173a PRO* 4.1 2.0 - - + -
5174a LEU* 3.8 27.8 - - + -
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Residues in contact with GLN5113 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5085a SER* 3.9 23.9 + - - +
5089a ILE* 4.5 2.2 - - - +
5092a HIS 3.1 17.0 + - - -
5093a PHE 3.8 0.3 - - - -
5094a TYR* 2.7 42.1 + - + +
5109a GLY 4.1 0.4 + - - -
5110a GLY* 3.3 8.7 + - - +
5112a TYR* 1.3 78.7 - - + +
5114a LEU* 1.3 65.3 + - - +
5116a ILE* 4.0 9.0 - - - -
5117a PHE* 3.0 51.7 + - + -
5168a PHE* 3.0 37.6 - - + -
5563a CLA 4.1 5.4 - - - +
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Residues in contact with LEU5114 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5043a ALA 5.5 2.7 - - - +
5044a ALA* 6.0 0.2 - - - -
5047a CYS* 3.2 37.2 - - + -
5096a ILE* 5.0 0.9 - - + -
5105a TRP* 4.0 10.3 - - + -
5110a GLY 3.4 9.3 + - - +
5111a PRO 3.6 5.4 - - - +
5112a TYR 3.2 0.4 - - - -
5113a GLN* 1.3 78.2 - - - +
5115a ILE* 1.3 63.3 + - - +
5118a HIS* 3.0 46.7 + - + +
5563a CLA 3.1 56.6 + - + +
5566a BCR 3.8 30.1 - - + -
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Residues in contact with ILE5115 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5044a ALA* 3.8 11.6 - - + +
5047a CYS* 3.7 22.7 - - + +
5048a PHE* 3.1 43.1 - - + +
5051a ALA* 4.4 2.7 - - + -
5082a VAL* 4.3 16.4 - - + -
5111a PRO 2.9 20.0 + - - +
5112a TYR 2.9 5.9 + - - +
5114a LEU* 1.3 77.3 - - - +
5116a ILE* 1.3 56.8 + - - +
5119a PHE* 3.0 24.4 + - - +
5174a LEU* 3.4 23.1 - - + -
5561a PHO 3.6 24.7 - - + -
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Residues in contact with ILE5116 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5112a TYR* 2.8 62.8 + - + +
5113a GLN* 3.6 11.2 - - - +
5115a ILE* 1.3 70.3 - - + +
5117a PHE* 1.3 93.2 + - + +
5118a HIS 3.0 1.6 - - - -
5119a PHE* 4.2 4.3 - - - +
5120a LEU* 2.8 31.6 + - + +
5158a PHE* 3.4 48.0 - - + +
5159a LEU* 5.9 0.2 - - + -
5168a PHE* 4.1 7.6 - - + -
5174a LEU* 4.3 13.5 - - + -
5561a PHO 5.3 0.4 - - + -
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Residues in contact with PHE5117 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5093a PHE* 3.9 27.4 - + - -
5113a GLN* 3.0 36.8 + - + +
5114a LEU 4.5 0.9 - - - +
5116a ILE* 1.3 96.0 - - + +
5118a HIS* 1.3 58.4 + - - +
5120a LEU* 3.6 5.9 + - + +
5121a LEU* 3.1 27.5 + - - +
5159a LEU* 5.1 5.6 - - + -
5168a PHE* 3.6 32.1 - + - -
5563a CLA 3.6 29.5 - - + +
5218c PHE* 3.6 25.8 - + - -
5201i MGE 3.8 34.8 - - + +
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Residues in contact with HIS5118 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5040a THR* 2.6 57.0 - - + +
5041a LEU 4.7 0.3 + - - -
5043a ALA* 3.6 17.1 - - + +
5044a ALA* 3.7 19.7 - - + -
5114a LEU* 3.0 31.5 + - + +
5116a ILE 3.0 0.6 - - - -
5117a PHE* 1.3 77.3 - - - +
5119a PHE* 1.3 66.1 + - - +
5121a LEU* 4.5 0.4 - - - -
5122a GLY* 3.1 6.8 + - - -
5563a CLA 2.6 81.0 + + + +
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Residues in contact with PHE5119 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5041a LEU* 4.4 7.6 - - + -
5044a ALA* 3.9 5.0 - - - +
5115a ILE 3.0 19.5 + - - +
5116a ILE* 3.2 2.6 + - - +
5118a HIS* 1.3 76.3 - - - +
5120a LEU* 1.3 69.7 + - + +
5123a ALA* 2.8 42.6 + - + +
5154a ALA* 4.0 22.0 - - + -
5158a PHE* 4.3 11.4 - + - -
5558a CLA 3.5 54.1 - - + -
5559a CLA 4.7 1.1 - - + -
5561a PHO 3.6 60.1 - - + -
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Residues in contact with LEU5120 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5116a ILE* 2.8 25.0 + - + +
5117a PHE* 4.0 5.8 - - + +
5119a PHE* 1.3 94.2 - - + +
5121a LEU* 1.3 59.7 + - - +
5123a ALA* 4.1 1.5 - - - -
5124a SER* 2.9 29.5 + - - -
5151a LEU* 5.1 1.6 - - + -
5154a ALA* 3.7 23.6 - - + +
5155a PHE* 3.9 33.5 - - + -
5158a PHE* 4.2 14.6 - - + +
5159a LEU* 3.7 34.8 - - + -
5201i MGE 4.2 13.6 - - + +
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Residues in contact with LEU5121 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5036a ILE* 4.6 8.3 - - + -
5040a THR* 3.7 13.2 - - + +
5117a PHE 3.1 15.5 + - - +
5120a LEU* 1.3 74.9 - - - +
5122a GLY* 1.3 66.3 + - - +
5124a SER* 3.1 13.1 + - - -
5125a CYS* 3.2 18.7 + - - -
5563a CLA 3.7 51.6 - - + -
5495c CLA 4.2 35.2 - - + -
5201i MGE 3.6 35.6 - - + +
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Residues in contact with GLY5122 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5037a MET* 3.6 25.8 - - - +
5040a THR* 3.5 9.5 - - - +
5041a LEU* 4.2 12.1 - - - -
5118a HIS 3.1 12.6 + - - -
5121a LEU* 1.3 79.4 - - - +
5123a ALA* 1.3 57.0 + - - +
5125a CYS* 3.2 1.9 + - - -
5126a TYR* 2.7 31.2 + - - +
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Residues in contact with ALA5123 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5041a LEU* 4.5 4.2 - - - +
5119a PHE* 2.8 47.0 + - + +
5120a LEU* 4.2 2.0 - - - +
5122a GLY* 1.3 71.7 - - - +
5124a SER* 1.3 60.0 + - - +
5126a TYR* 3.4 7.7 - - - +
5127a MET* 3.4 13.0 + - - +
5147a TYR* 3.4 25.1 + - - +
5151a LEU* 3.5 23.4 - - + +
5561a PHO 5.3 2.7 - - - +
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Residues in contact with SER5124 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5120a LEU 2.9 15.8 + - - -
5121a LEU* 3.1 11.8 + - - -
5122a GLY 3.0 0.6 - - - -
5123a ALA* 1.3 74.8 - - - +
5125a CYS* 1.3 57.9 + - - +
5126a TYR 3.0 1.1 - - - -
5127a MET* 2.6 30.4 + - - +
5128a GLY* 2.9 5.5 + - - -
5151a LEU* 3.8 10.8 - - - +
5155a PHE* 3.2 24.8 - - - -
5495c CLA 3.7 31.8 - - - +
5507c DGD 5.4 0.7 - - - +
5201i MGE 4.2 5.2 - - - +
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Residues in contact with CYS5125 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5033a PHE* 3.5 36.0 - - + +
5036a ILE* 3.9 29.4 - - - -
5037a MET* 3.8 10.1 - - + +
5121a LEU* 3.2 14.8 + - - +
5122a GLY 3.7 5.4 - - - +
5124a SER* 1.3 78.8 - - - +
5126a TYR* 1.3 52.1 + - - +
5128a GLY* 3.3 2.2 - - - +
5129a ARG* 2.4 38.4 + - - +
5495c CLA 4.3 24.9 - - - +
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Residues in contact with TYR5126 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5037a MET* 3.3 32.7 - - + -
5122a GLY 2.7 17.8 + - - +
5123a ALA* 3.4 11.2 - - - +
5125a CYS* 1.3 77.1 - - - +
5127a MET* 1.3 56.6 + - - +
5129a ARG* 3.8 9.9 - - - +
5130a GLN* 3.1 57.2 + - + +
5147a TYR* 3.4 21.5 - + - -
5561a PHO 2.6 62.5 + - + +
5256d ILE* 3.5 16.8 + - + -
5257d PHE* 3.2 19.6 - + - -
5361d MGE 5.0 8.5 - - + -
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Residues in contact with MET5127 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5123a ALA 3.4 3.5 + - - +
5124a SER* 2.6 16.8 + - - +
5126a TYR* 1.3 78.0 - - - +
5128a GLY* 1.3 62.8 + - - +
5130a GLN* 3.2 10.5 + - - +
5131a TRP 3.9 0.2 + - - -
5144a CYS* 3.2 49.1 - - + +
5147a TYR* 3.7 22.2 - - + -
5148a SER* 4.0 15.7 - - - -
5151a LEU* 4.0 21.1 - - + -
5438c LEU* 5.2 0.2 - - + -
5442c LEU* 3.6 21.3 - - + -
5495c CLA 3.4 48.7 - - + -
5507c DGD 4.8 5.4 - - + -
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Residues in contact with GLY5128 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5033a PHE* 3.0 35.1 - - - -
5124a SER 2.9 10.2 + - - -
5125a CYS 3.0 1.7 + - - -
5127a MET* 1.3 75.7 - - - +
5129a ARG* 1.3 65.3 + - - +
5131a TRP* 3.0 23.4 + - - +
5132a GLU 3.2 4.7 + - - -
5495c CLA 3.7 13.6 - - - +
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Residues in contact with ARG5129 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5028a LEU* 4.6 5.7 - - - +
5029a TYR* 2.6 50.6 + - + +
5030a VAL* 4.1 2.8 - - - +
5031a GLY* 4.6 5.2 - - - +
5033a PHE* 3.4 8.6 - - + -
5034a GLY* 4.0 28.2 - - - +
5037a MET* 3.8 29.6 - - - +
5038a ILE* 5.8 2.2 - - - +
5125a CYS 2.4 30.7 + - - +
5126a TYR* 3.8 11.9 - - - +
5128a GLY* 1.3 67.6 - - - +
5130a GLN* 1.3 51.5 + - - +
5131a TRP 2.6 12.6 + - - -
5132a GLU* 3.0 14.0 + - - +
5133a LEU* 3.3 11.4 + - - +
5255d GLN 3.6 4.6 + - - -
5256d ILE* 2.9 57.7 + - + +
5257d PHE 4.1 0.4 - - - +
5361d MGE 4.8 7.9 - - - +
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Residues in contact with GLN5130 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5126a TYR* 3.1 47.0 + - + +
5127a MET 3.4 12.1 - - - +
5128a GLY 3.1 1.4 - - - -
5129a ARG* 1.3 71.2 - - - +
5131a TRP* 1.3 56.6 + - - +
5134a SER* 4.6 2.8 - - - -
5141a PRO 5.2 1.2 - - - +
5143a ILE* 3.8 11.7 + - - +
5144a CYS* 3.5 20.3 + - + +
5147a TYR* 3.4 25.8 - - - +
5561a PHO 3.1 30.2 + - - +
5252d PHE* 3.9 18.7 - - + -
5253d TRP* 3.4 14.5 - - - -
5256d ILE* 3.3 24.2 - - + +
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Residues in contact with TRP5131 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5033a PHE* 4.0 9.6 - + - -
5127a MET 4.4 0.2 - - - +
5128a GLY* 3.2 19.1 - - - +
5129a ARG 2.6 5.7 + - - -
5130a GLN* 1.3 77.2 - - - +
5132a GLU* 1.3 111.3 + - + +
5133a LEU 3.2 0.9 - - - -
5134a SER* 2.7 31.6 + - - -
5135a TYR* 2.9 22.6 + + + +
5141a PRO* 4.6 11.0 - - + -
5144a CYS* 4.3 18.8 - - - -
5446c GLY* 4.4 15.4 + - - -
5449c ARG* 4.0 39.0 - - + +
5495c CLA 3.1 59.5 - + + +
5023i PHE* 4.2 10.8 - + - -
5027i ASP* 4.5 1.6 - - - -
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Residues in contact with GLU5132 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5022a THR* 5.1 0.7 + - - -
5029a TYR* 2.3 32.5 + - + +
5031a GLY* 3.3 2.2 - - - -
5032a TRP* 3.0 40.2 + - - +
5033a PHE* 3.3 17.3 + - - +
5128a GLY 3.2 1.8 + - - +
5129a ARG* 3.0 9.0 + - - +
5131a TRP* 1.3 110.1 - - + +
5133a LEU* 1.3 57.7 + - - +
5135a TYR* 3.1 3.2 + - - +
5136a ARG* 2.8 55.2 + - - +
5023i PHE* 3.9 7.4 - - - -
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Residues in contact with LEU5133 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5024a THR* 5.1 3.8 - - + +
5029a TYR* 3.3 38.6 - - + -
5129a ARG 3.3 8.2 + - - +
5131a TRP 3.2 0.6 - - - -
5132a GLU* 1.3 77.5 - - - +
5134a SER* 1.3 65.5 + - - +
5136a ARG* 3.1 7.0 + - + -
5137a LEU* 2.8 48.6 + - + +
5252d PHE* 3.3 56.1 - - + +
5255d GLN* 4.1 16.4 - - + +
5256d ILE* 4.1 13.2 - - + -
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Residues in contact with SER5134 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5130a GLN 4.6 2.5 - - - -
5131a TRP* 2.7 29.0 + - - -
5133a LEU* 1.3 73.7 - - - +
5135a TYR* 1.3 55.7 + - - +
5137a LEU 3.0 1.7 + - - -
5138a GLY 2.9 9.0 + - - -
5139a MET* 2.8 57.2 + - - +
5140a ARG 3.7 16.1 + - - -
5141a PRO* 3.8 14.5 - - - +
5143a ILE* 6.1 0.7 - - - -
5252d PHE* 3.8 16.0 - - - -
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Residues in contact with TYR5135 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5131a TRP* 2.9 24.6 + + + +
5132a GLU* 3.2 10.3 - - - +
5134a SER* 1.3 76.6 + - - +
5136a ARG* 1.3 79.4 + - - +
5137a LEU 2.9 3.6 - - - -
5138a GLY* 2.7 25.5 + - - +
5139a MET 4.7 1.6 - - - -
5265c ILE* 4.9 1.0 - - - +
5449c ARG* 2.7 60.3 + - + -
5450c ALA* 4.7 2.9 - - + -
5452c ALA* 5.8 0.9 - - - +
5453c ALA* 4.1 18.7 + - + +
5455c PHE* 3.8 20.7 - + - -
5027i ASP 4.1 0.7 - - - -
5028i PRO* 2.8 33.8 + - - +
5030i ARG 3.6 14.8 - - - -
5031i ASN* 4.0 7.4 + - + +
5032i PRO* 3.9 5.7 - - - +
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Residues in contact with ARG5136 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5022a THR* 2.9 41.4 + - - +
5024a THR* 3.5 30.4 + - + +
5029a TYR* 3.7 11.7 - - + +
5032a TRP* 4.5 0.8 - - - -
5131a TRP* 4.6 1.0 - - - -
5132a GLU* 2.8 55.7 + - - +
5133a LEU* 3.5 11.2 - - + +
5135a TYR* 1.3 92.3 - - - +
5137a LEU* 1.3 58.3 + - - +
5138a GLY 3.4 0.9 - - - -
5449c ARG* 4.1 0.8 - - - +
5469c MET* 4.5 2.3 - - - +
5027i ASP* 2.6 47.8 + - - +
5030i ARG* 3.3 26.9 + - - -
5031i ASN* 4.9 3.3 - - - +
5032i PRO* 4.0 11.5 - - - +
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Residues in contact with LEU5137 (chain a).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5024a THR* 3.2 31.4 - - + -
5133a LEU* 2.8 39.7 + - + +
5134a SER 3.5 4.0 - - - +
5135a TYR 2.9 0.4 - - - -
5136a ARG* 1.3 77.5 - - - +
5138a GLY* 1.3 62.3 + - - +
5139a MET* 3.1 22.0 + - + +
5459c ILE* 5.5 2.3 - - - +
5465c PRO* 4.0 14.1 - - - +
5466c VAL* 4.3 14.2 - - + +
5469c MET* 3.6 17.9 - - + -
5248d THR* 4.4 5.0 - - - +
5251d ARG* 3.8 24.2 - - + -
5252d PHE* 3.9 14.4 - - - +
5255d GLN* 4.3 6.1 - - - +
5032i PRO* 4.4 4.7 - - - -
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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) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il