Contacts of the helix formed by residues 5109 - 5134 (chain c) in PDB entry 3A0B
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 PHE5109 (chain c).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5107c ASP* 2.6 30.7 + - + +
5108c THR* 1.3 73.0 - - - +
5110c PRO* 1.3 70.2 - - + +
5111c PHE* 2.6 7.2 + - - -
5112c PHE* 2.7 28.4 + + - +
5113c VAL* 3.0 29.5 + - + +
6027c CLA 5.4 11.0 - - + -
5012k PRO* 5.9 2.7 - - + -
5058z ASN* 5.2 12.6 - - - -
5059z PHE* 6.2 4.9 - + - -
6053z BCR 6.0 3.6 - - + -
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Residues in contact with PRO5110 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5097c TRP* 3.1 49.9 - - + -
5098c GLY* 3.6 16.2 - - - +
5106c VAL* 5.7 0.4 - - + -
5107c ASP* 3.0 35.0 - - - +
5109c PHE* 1.3 87.2 - - + +
5111c PHE* 1.3 63.2 + - + +
5113c VAL* 3.0 28.1 - - + +
5114c VAL* 3.5 3.3 - - - +
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Residues in contact with PHE5111 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5068c THR* 3.9 12.6 - - + +
5072c LEU* 4.6 17.3 - - + -
5075c PHE* 6.2 2.0 - + - -
5081c MET* 5.5 3.8 - - + -
5089c ILE* 3.3 42.4 - - + -
5092c ILE* 3.2 32.5 - - + +
5093c ALA* 5.2 4.9 - - + -
5097c TRP 3.3 14.4 - - - -
5098c GLY* 3.4 25.4 - - - -
5105c VAL* 3.4 29.4 - - + -
5107c ASP 3.7 5.8 - - - -
5108c THR* 4.2 4.5 - - - -
5109c PHE 2.6 8.0 + - - -
5110c PRO* 1.3 78.6 - - + +
5112c PHE* 1.3 58.4 + - - +
5113c VAL 2.9 9.8 + - - -
5114c VAL* 3.1 15.6 + - - +
5115c GLY 3.2 8.5 + - - -
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Residues in contact with PHE5112 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5068c THR* 5.3 0.7 - - - -
5069c LEU* 3.2 31.6 - - + -
5072c LEU* 4.4 15.1 - - + +
5108c THR 4.4 11.4 + - - +
5109c PHE* 2.7 25.6 + + - +
5111c PHE* 1.3 75.9 - - - +
5113c VAL* 1.3 56.3 + - - +
5115c GLY 3.9 2.0 - - - +
5116c VAL* 2.9 39.5 + - + +
5011k LEU* 4.8 12.6 - - + -
5012k PRO* 4.0 17.9 - - + -
5015k TYR* 3.1 49.6 - + - -
6052k BCR 4.8 5.4 - - + -
5058z ASN* 4.5 3.8 - - - -
6053z BCR 4.2 12.8 - - + -
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Residues in contact with VAL5113 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5097c TRP* 3.1 34.3 - - + -
5109c PHE* 3.0 41.3 + - + +
5110c PRO* 3.0 16.4 - - + +
5111c PHE 2.9 1.4 + - - -
5112c PHE* 1.3 73.1 - - - +
5114c VAL* 1.3 72.9 + - + +
5116c VAL* 3.5 3.8 - - - +
5117c VAL* 2.6 43.7 + - + +
6027c CLA 4.6 24.2 - - + -
6053z BCR 4.8 6.1 - - + -
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Residues in contact with VAL5114 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5068c THR* 4.5 3.8 - - + +
5092c ILE* 5.0 18.8 - - + -
5097c TRP* 3.9 13.0 - - + -
5110c PRO 3.5 9.9 - - - +
5111c PHE* 3.1 5.5 + - - +
5113c VAL* 1.3 97.2 - - + +
5115c GLY* 1.3 60.3 + - - +
5117c VAL* 4.0 4.8 - - - -
5118c HIS* 2.7 56.7 + - + +
6027c CLA 3.9 41.7 - - + +
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Residues in contact with GLY5115 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5065c GLY* 3.0 24.1 - - - -
5068c THR* 3.1 32.8 - - - +
5069c LEU* 3.3 15.7 - - - +
5111c PHE 3.2 9.3 + - - -
5112c PHE 3.7 0.6 + - - -
5113c VAL 3.2 0.2 - - - -
5114c VAL* 1.3 77.9 - - - +
5116c VAL* 1.3 59.7 + - - +
5118c HIS* 3.4 0.5 - - - +
5119c LEU 3.3 7.3 + - - -
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Residues in contact with VAL5116 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5069c LEU* 3.2 12.9 - - + +
5112c PHE* 2.9 34.5 + - + +
5113c VAL 3.5 5.4 - - - +
5115c GLY* 1.3 68.7 - - - +
5117c VAL* 1.3 63.0 + - - +
5118c HIS 2.8 11.1 + - - -
5119c LEU* 3.0 11.1 + - - +
5120c ILE* 3.0 23.1 + - + +
6052k BCR 3.5 29.2 - - + -
6053z BCR 3.4 45.1 - - + -
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Residues in contact with VAL5117 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5113c VAL* 2.6 29.9 + - + +
5114c VAL* 4.0 4.5 - - - +
5116c VAL* 1.3 79.8 - - + +
5118c HIS* 1.3 57.3 + - - +
5120c ILE* 4.1 6.3 - - - +
5121c SER* 3.0 24.3 + - - -
6027c CLA 3.4 60.4 - - + +
6053z BCR 4.3 42.0 - - + +
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Residues in contact with HIS5118 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5061c VAL* 3.4 17.8 - - - +
5064c ALA* 3.5 20.1 - - + +
5065c GLY* 3.2 25.6 - - - +
5068c THR* 5.4 1.1 - - - -
5088c LEU* 6.5 0.2 - - + -
5114c VAL* 2.7 41.7 + - + +
5116c VAL 2.8 0.8 - - - -
5117c VAL* 1.3 77.0 - - - +
5119c LEU* 1.3 54.7 + - - +
5120c ILE 3.2 1.8 - - - -
5121c SER* 3.2 5.1 - - - -
5122c SER* 2.4 34.9 + - - -
6027c CLA 2.6 74.0 + + + -
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Residues in contact with LEU5119 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5062c PHE* 3.3 33.7 - - + +
5065c GLY 3.5 3.4 - - - -
5066c ALA* 2.8 49.1 - - + +
5069c LEU* 4.3 7.9 - - + -
5115c GLY 3.3 6.0 + - - +
5116c VAL* 3.0 8.6 + - - +
5118c HIS* 1.3 78.7 - - - +
5120c ILE* 1.3 59.3 + - - +
5122c SER* 3.5 1.3 - - - -
5123c ALA* 3.0 23.4 + - - +
5025k LEU* 4.0 7.4 - - + -
6051k BCR 4.1 1.6 - - + -
6052k BCR 3.6 49.3 - - + +
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Residues in contact with ILE5120 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5116c VAL* 3.0 26.3 + - + +
5117c VAL 4.4 3.4 - - - +
5119c LEU* 1.3 75.6 - - - +
5121c SER* 1.3 54.4 + - - +
5122c SER 3.3 0.2 - - - -
5123c ALA* 3.8 5.6 - - - +
5124c VAL* 2.8 32.2 + - + +
6052k BCR 3.7 30.7 - - + -
5047z TRP* 3.4 36.0 - - + -
5051z VAL* 3.7 13.2 - - + -
6053z BCR 3.2 49.3 - - + +
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Residues in contact with SER5121 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5061c VAL* 3.1 21.0 - - - +
5117c VAL 3.0 23.8 + - - -
5118c HIS* 3.2 11.9 + - - -
5120c ILE* 1.3 73.1 - - - +
5122c SER* 1.3 56.9 + - - -
5124c VAL* 2.3 33.4 - - - +
5125c LEU* 2.9 19.9 + - - +
6027c CLA 4.7 12.9 + - - +
6036c CLA 5.9 2.8 - - - +
6053z BCR 5.3 8.5 - - - +
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Residues in contact with SER5122 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5058c GLY 4.1 1.0 + - - -
5061c VAL* 3.6 6.7 - - - +
5062c PHE* 2.7 54.8 + - - +
5118c HIS 2.4 26.3 + - - -
5119c LEU* 3.5 9.4 - - - -
5121c SER* 1.3 72.5 - - - +
5123c ALA* 1.3 59.7 + - - +
5125c LEU* 3.2 6.3 + - - +
5126c GLY 2.9 24.3 + - - -
6052k BCR 3.4 12.1 - - - +
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Residues in contact with ALA5123 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5119c LEU 3.0 15.6 + - - +
5120c ILE 3.9 3.1 - - - +
5121c SER 3.2 0.4 - - - -
5122c SER* 1.3 75.4 - - - +
5124c VAL* 1.3 57.7 + - - +
5126c GLY* 3.2 1.7 + - - -
5127c PHE* 2.9 29.2 + - - +
6035c CLA 5.0 3.9 - - + +
6052k BCR 3.5 22.9 - - + +
5047z TRP* 3.3 42.6 - - + -
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Residues in contact with VAL5124 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5120c ILE* 2.8 19.9 + - + +
5121c SER* 2.3 41.5 - - - +
5123c ALA* 1.3 74.2 - - - +
5125c LEU* 1.3 63.1 + - + +
5127c PHE* 3.2 16.5 + - + +
6037c CLA 3.5 29.2 - - + +
5047z TRP* 5.9 2.2 - - + -
6053z BCR 4.1 38.6 - - + -
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Residues in contact with LEU5125 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5054c VAL* 3.8 13.6 - - - +
5055c ALA* 4.6 0.9 - - - +
5057c ALA 4.0 4.0 - - - +
5058c GLY* 2.4 46.9 - - - +
5061c VAL* 2.3 58.8 - - + -
5121c SER* 2.9 18.5 + - - +
5122c SER* 3.2 4.5 + - - +
5124c VAL* 1.3 79.4 - - + +
5126c GLY* 1.3 61.8 + - - +
5127c PHE 3.5 0.2 + - - -
5128c GLY 3.9 0.3 + - - -
5129c GLY* 3.5 16.1 + - - -
6027c CLA 5.1 2.9 - - - +
6036c CLA 4.7 20.0 - - + +
6037c CLA 5.4 10.0 - - + +
6052k BCR 3.9 3.6 - - - +
----------------------------------------------------------
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Residues in contact with GLY5126 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5122c SER 2.9 10.1 + - - -
5123c ALA 3.2 4.2 + - - -
5125c LEU* 1.3 78.9 - - - +
5127c PHE* 1.3 61.0 + - - +
5128c GLY 3.3 0.9 + - - -
5129c GLY 3.6 1.9 + - - -
5130c VAL* 3.2 27.4 + - - +
6035c CLA 4.1 8.3 - - - +
6052k BCR 3.3 35.6 - - - +
----------------------------------------------------------
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Residues in contact with PHE5127 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5123c ALA 2.9 16.0 + - - +
5124c VAL* 3.2 14.3 + - + +
5126c GLY* 1.3 77.7 - - - +
5128c GLY* 1.3 59.2 + - - +
5130c VAL* 5.2 1.0 - - - +
5131c TYR* 4.5 7.8 + - - +
6035c CLA 4.6 22.9 - - + +
6037c CLA 4.8 28.0 - - + -
5019z MET* 4.3 10.8 - - + -
5023z VAL* 4.7 13.9 - - + +
5027z TYR* 4.6 9.2 + - - -
5040z ILE* 5.1 7.9 - - + -
5041z PHE* 6.0 1.8 - + - -
5044z SER* 3.0 36.3 - - - -
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Residues in contact with GLY5128 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5054c VAL* 5.0 1.3 - - - -
5124c VAL 3.7 1.8 + - - -
5127c PHE* 1.3 79.6 - - - +
5129c GLY* 1.3 60.9 + - - +
5130c VAL 3.6 0.4 - - - -
5131c TYR* 3.1 26.0 - - - +
5132c HIS* 3.4 18.8 + - - -
6037c CLA 3.0 36.1 - - - +
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Residues in contact with GLY5129 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5051c GLY* 3.0 25.5 - - - +
5054c VAL* 4.5 5.3 - - - +
5055c ALA* 4.0 20.0 - - - -
5125c LEU 3.5 12.6 + - - -
5126c GLY 3.6 0.8 + - - -
5128c GLY* 1.3 73.2 - - - +
5130c VAL* 1.3 55.9 + - - +
5131c TYR 2.7 13.8 + - - -
5132c HIS 3.1 2.6 + - - -
5133c ALA* 3.0 18.4 + - - +
6052k BCR 4.9 0.7 - - - -
----------------------------------------------------------
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Residues in contact with VAL5130 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5126c GLY* 3.2 21.1 - - - +
5127c PHE 5.3 1.1 - - - +
5129c GLY* 1.3 72.0 - - - +
5131c TYR* 1.3 55.9 + - - +
5133c ALA* 3.5 7.4 - - - -
5134c ILE* 2.8 54.8 + - + +
6035c CLA 3.6 63.0 - - + -
6052k BCR 4.3 11.9 - - + +
5023z VAL* 5.9 2.0 - - + -
5024z PRO* 4.7 14.6 - - + -
5027z TYR* 3.8 7.5 - - + -
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Residues in contact with TYR5131 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5127c PHE 4.5 2.1 + - - +
5128c GLY* 3.1 22.7 + - - +
5129c GLY 2.7 1.0 - - - -
5130c VAL* 1.3 74.1 - - - +
5132c HIS* 1.3 78.5 + + - +
5133c ALA 2.4 15.6 + - - -
5134c ILE 2.7 14.4 + - - -
5135c ARG* 3.2 24.4 + - + -
5136c GLY* 3.0 24.5 + - - -
5137c PRO* 3.5 18.4 - - + +
6037c CLA 3.3 62.2 + + + -
5027z TYR* 3.4 33.8 - + + +
----------------------------------------------------------
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Residues in contact with HIS5132 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5047c GLY* 2.5 29.5 + - - +
5048c LYS* 3.2 12.8 - - - +
5050c LEU* 4.1 15.6 - - + +
5051c GLY* 3.0 35.7 - - - +
5054c VAL* 4.7 5.6 - - + -
5128c GLY 3.6 13.0 - - - -
5129c GLY 3.1 1.4 + - - -
5131c TYR* 1.3 87.5 - + - +
5133c ALA* 1.3 54.4 + - - +
5136c GLY* 3.8 15.7 - - - +
5137c PRO* 5.3 3.9 - - + +
6037c CLA 3.1 75.1 + + + -
----------------------------------------------------------
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Residues in contact with ALA5133 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5048c LYS* 2.6 40.0 - - + +
5051c GLY 4.4 5.6 + - - +
5052c ALA* 5.6 1.3 - - + -
5129c GLY 3.0 17.2 + - - +
5130c VAL* 3.2 12.6 - - - +
5131c TYR 2.4 7.5 + - - -
5132c HIS* 1.3 72.1 - - - +
5134c ILE* 1.3 68.3 + - + +
6035c CLA 4.3 13.5 - - + +
6052k BCR 4.1 15.7 - - + -
----------------------------------------------------------
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Residues in contact with ILE5134 (chain c).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5048c LYS* 4.5 6.0 - - - +
5130c VAL* 2.8 44.2 + - + +
5131c TYR 2.7 11.1 + - - -
5133c ALA* 1.3 91.4 - - + +
5135c ARG* 1.3 56.6 + - - +
5136c GLY 3.6 2.7 - - - -
6035c CLA 3.8 38.4 - - + -
5027y ASN 5.9 1.6 - - - +
5024z PRO* 4.9 3.4 - - + +
5027z TYR* 2.9 48.6 - - + +
5028z ALA* 3.7 11.0 - - + +
----------------------------------------------------------
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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