Contacts of the helix formed by residues 5092 - 5117 (chain b) 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 SER5092 (chain b).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5071b VAL* 3.5 6.3 - - - -
5073b GLY 3.5 14.8 - - - -
5075b TRP* 3.0 38.3 + - - -
5088b PRO* 3.7 14.6 - - - -
5090b PHE 2.6 6.3 + - - -
5091b TRP* 1.3 75.1 - - - +
5093b PHE* 1.3 65.9 + - - +
5094b GLU* 3.1 14.0 + - - -
5095b GLY 2.9 8.3 + - - -
5096b VAL* 2.9 22.2 + - - +
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Residues in contact with PHE5093 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5038b ALA* 5.0 0.7 - - - +
5042b LEU* 3.5 24.7 - - + +
5055b MET* 5.2 0.4 - - + -
5063b LEU* 3.5 33.2 - - + -
5066b MET* 3.8 31.9 - - + +
5067b ALA* 5.2 1.3 - - + -
5071b VAL* 3.4 31.3 - - + +
5072b THR* 3.8 8.3 - - - -
5073b GLY 3.1 35.2 + - - +
5074b SER* 4.4 0.9 - - - -
5078b TRP* 3.9 31.6 - + - -
5080b ILE* 4.3 13.9 - - + -
5092b SER* 1.3 73.5 - - - +
5094b GLU* 1.3 65.5 + - - +
5096b VAL* 3.8 3.6 - - - +
5097b ALA* 3.1 23.6 + - - +
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Residues in contact with GLU5094 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569A LMT 4.2 30.8 - - + +
489C UNK 5.6 3.3 - - + +
5039b LEU* 5.3 1.8 - - + -
5042b LEU* 3.6 29.5 - - + +
5074b SER* 2.7 24.1 + - - -
5075b TRP* 2.6 62.6 + - + +
5076b SER* 4.9 2.5 + - - -
5078b TRP* 5.1 0.3 - - - -
5092b SER* 3.1 8.0 + - - -
5093b PHE* 1.3 78.8 - - - +
5095b GLY* 1.3 58.0 + - - +
5097b ALA* 3.3 4.2 + - - +
5098b LEU* 2.9 27.7 + - - +
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Residues in contact with GLY5095 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5075b TRP* 3.9 6.4 - - - -
5090b PHE* 3.6 39.3 - - - -
5091b TRP* 4.3 1.1 - - - -
5092b SER* 2.9 12.2 + - - -
5094b GLU* 1.3 76.2 - - - +
5096b VAL* 1.3 59.4 + - - +
5098b LEU* 3.0 3.8 + - - +
5099b ALA* 2.8 31.0 + - - +
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Residues in contact with VAL5096 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5066b MET* 3.7 20.6 - - - -
5071b VAL* 3.7 32.8 - - + -
5091b TRP* 4.3 11.1 - - + -
5092b SER 2.9 19.5 + - - +
5093b PHE 3.8 4.3 - - - +
5095b GLY* 1.3 73.9 - - - +
5097b ALA* 1.3 64.8 + - - +
5099b ALA* 3.4 1.4 + - - +
5100b HIS* 3.1 41.1 + - + +
5515b CLA 3.7 25.8 - - + -
5516b CLA 3.8 15.0 - - + +
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Residues in contact with ALA5097 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5035b GLY* 3.8 13.7 - - - +
5038b ALA* 3.5 29.1 - - + +
5039b LEU* 3.6 24.9 - - + -
5042b LEU* 5.0 0.4 - - + -
5093b PHE 3.1 12.6 + - - +
5094b GLU 3.6 4.0 - - - +
5096b VAL* 1.3 81.3 - - - +
5098b LEU* 1.3 65.1 + - - +
5100b HIS* 3.5 2.8 + - - +
5101b ILE* 3.1 25.7 + - - +
5515b CLA 5.8 0.2 - - - -
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Residues in contact with LEU5098 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 6.1 0.2 - - + -
569A LMT 3.3 49.6 - - + +
486C UNK 4.7 15.7 - - + -
488C UNK 5.0 0.2 - - + -
5039b LEU* 5.5 0.4 - - - +
5075b TRP* 4.4 3.1 - - + -
5090b PHE* 3.6 29.4 - - + -
5094b GLU 2.9 15.1 + - - +
5095b GLY 3.0 8.9 + - - +
5097b ALA* 1.3 74.2 - - - +
5099b ALA* 1.3 69.8 - - - +
5101b ILE* 2.7 24.7 + - + +
5102b VAL* 3.0 28.0 + - + +
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Residues in contact with ALA5099 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5090b PHE* 4.9 3.3 - - + -
5091b TRP* 3.7 13.9 - - + -
5095b GLY 2.8 16.9 + - - +
5096b VAL 3.6 5.6 - - - +
5098b LEU* 1.3 74.1 - - - +
5100b HIS* 1.3 58.8 + - - +
5102b VAL* 3.1 9.7 + - - +
5103b LEU* 2.9 27.2 + - - +
5516b CLA 3.6 44.2 - - + +
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Residues in contact with HIS5100 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5031b ALA* 4.0 14.5 - - + +
5034b ALA* 3.3 26.0 - - + +
5035b GLY* 3.8 16.4 - - - +
5096b VAL* 3.1 34.8 + - + +
5097b ALA 3.6 7.6 - - - +
5098b LEU 2.9 1.0 + - - -
5099b ALA* 1.3 79.1 - - - +
5101b ILE* 1.3 62.3 + - - +
5103b LEU* 3.0 8.6 + - + +
5104b SER* 2.9 26.2 + - - -
5515b CLA 2.5 60.7 + + + -
5516b CLA 3.5 21.3 - - + +
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Residues in contact with ILE5101 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217T LMT 4.9 10.5 - - + -
5032b GLY* 4.2 9.0 - - - +
5035b GLY* 4.3 1.8 - - - -
5036b SER* 4.1 28.3 - - - +
5039b LEU* 4.5 16.8 - - + -
5097b ALA 3.1 16.2 + - - +
5098b LEU* 2.7 19.7 + - + +
5100b HIS* 1.3 71.6 - - - +
5102b VAL* 1.3 60.1 + - + +
5104b SER* 3.1 17.0 + - - -
5105b GLY 3.4 4.7 + - - -
5528b BCR 3.7 53.2 - - + +
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Residues in contact with VAL5102 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486C UNK 5.5 9.6 - - + -
5098b LEU* 3.0 33.4 + - + +
5099b ALA* 3.3 7.4 - - - +
5101b ILE* 1.3 77.4 - - + +
5103b LEU* 1.3 62.2 + - - +
5105b GLY* 2.7 17.7 + - - -
5106b LEU* 3.0 22.3 + - + +
5516b CLA 3.8 19.5 - - + -
5528b BCR 3.4 24.5 - - + +
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Residues in contact with LEU5103 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5031b ALA* 4.7 5.8 - - + -
5099b ALA 2.9 12.7 + - - +
5100b HIS* 3.5 8.5 - - + +
5102b VAL* 1.3 76.5 - - - +
5104b SER* 1.3 58.4 + - - +
5105b GLY 2.9 0.2 + - - -
5106b LEU* 3.1 3.2 + - - +
5107b LEU* 2.8 43.5 + - + +
5515b CLA 3.8 41.1 - - + -
5516b CLA 3.4 37.6 - - + +
5525b CLA 4.7 11.7 - - + -
5529b BCR 3.8 32.3 - - + -
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Residues in contact with SER5104 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5213L SQD 3.2 19.8 - - - +
5028b ALA* 2.9 36.3 - - - +
5031b ALA* 3.6 7.6 - - - +
5032b GLY* 3.4 22.5 - - - -
5100b HIS 2.9 8.9 + - - -
5101b ILE* 3.1 14.9 + - - -
5103b LEU* 1.3 76.4 - - - +
5105b GLY* 1.3 59.9 + - - +
5107b LEU* 4.3 0.2 - - - -
5108b PHE* 3.3 14.0 + - - +
5528b BCR 3.8 11.1 - - - +
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Residues in contact with GLY5105 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5213L SQD 5.1 0.2 - - - -
5104T BCR 5.6 0.2 - - - -
5101b ILE 3.4 1.6 + - - -
5102b VAL 2.7 12.3 + - - -
5104b SER* 1.3 80.8 + - - +
5106b LEU* 1.3 62.6 + - - -
5108b PHE* 3.1 13.5 + - - +
5109b LEU* 3.1 17.5 + - - +
5528b BCR 3.9 40.9 - - - +
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Residues in contact with LEU5106 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5102b VAL* 3.0 16.7 + - + +
5103b LEU 3.7 4.5 - - - +
5105b GLY* 1.3 73.2 - - - +
5107b LEU* 1.3 66.4 + - - +
5109b LEU* 2.9 17.0 + - + +
5110b ALA* 2.8 25.9 + - - +
5516b CLA 4.2 32.5 - - + -
5528b BCR 4.7 6.9 - - + +
5529b BCR 3.6 58.5 - - + +
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Residues in contact with LEU5107 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5024b LEU* 3.2 32.4 - - + +
5027b THR* 3.3 35.2 - - + +
5028b ALA* 3.6 26.7 - - + +
5103b LEU* 2.8 41.2 + - + +
5104b SER* 4.6 0.2 - - - -
5106b LEU* 1.3 75.9 - - - +
5108b PHE* 1.3 57.3 + - - +
5110b ALA* 3.8 4.7 - - - +
5111b ALA* 2.9 30.1 + - - +
5515b CLA 4.6 4.0 - - + -
5525b CLA 4.7 9.4 - - + -
5526b CLA 4.1 16.2 - - + -
5529b BCR 4.6 4.7 - - + +
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Residues in contact with PHE5108 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5213L SQD 3.7 37.2 - - + -
15T ALA* 6.4 0.4 - - + -
18T PHE* 3.8 42.2 - + - -
19T PHE* 4.7 9.9 - + - -
5104T BCR 4.3 26.2 - - + -
5025b MET* 3.5 33.0 - - + -
5028b ALA* 3.9 5.1 - - - +
5104b SER 3.3 14.8 + - - +
5105b GLY* 3.1 11.7 + - - +
5106b LEU 3.0 0.6 - - - -
5107b LEU* 1.3 77.5 - - - +
5109b LEU* 1.3 75.0 + - + +
5111b ALA* 3.1 19.4 + - - +
5112b CYS* 3.3 14.4 + - - -
5527b BCR 4.5 4.5 - - + -
5528b BCR 4.9 0.4 - - + -
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Residues in contact with LEU5109 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5212A SQD 5.1 10.3 - - + +
18T PHE* 4.5 12.1 - - + -
5104T BCR 3.7 27.1 - - + -
5105b GLY 3.1 13.7 + - - +
5106b LEU* 2.9 14.9 + - + +
5108b PHE* 1.3 81.8 - - + +
5110b ALA* 1.3 58.0 + - - +
5112b CYS* 2.7 28.6 + - - +
5113b TRP 3.2 9.4 + - - -
5528b BCR 4.0 23.3 - - + -
5529b BCR 3.9 34.1 - - + +
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Residues in contact with ALA5110 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5024b LEU* 3.4 11.8 - - + +
5106b LEU 2.8 17.5 + - - +
5107b LEU 3.8 4.5 - - - +
5109b LEU* 1.3 73.6 - - - +
5111b ALA* 1.3 61.5 + - - +
5112b CYS 3.1 0.9 + - - -
5113b TRP* 3.3 5.9 + - - +
5114b HIS* 3.1 22.1 + - - +
5526b CLA 3.6 43.7 - - + -
5529b BCR 3.8 17.5 - - + +
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Residues in contact with ALA5111 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5021b ALA* 3.8 16.6 - - - +
5024b LEU* 3.3 27.8 - - + +
5025b MET* 4.1 19.3 - - + +
5107b LEU 2.9 19.3 + - - +
5108b PHE* 3.2 11.0 - - - +
5109b LEU 3.0 0.4 - - - -
5110b ALA* 1.3 76.8 - - - +
5112b CYS* 1.3 60.2 + - - +
5114b HIS 4.2 0.4 - - - -
5115b TRP* 3.6 18.4 + - - +
5527b BCR 3.9 5.7 - - + +
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Residues in contact with CYS5112 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18T PHE* 3.9 27.8 - - - -
23T PHE* 4.6 4.5 - - + -
5025b MET* 5.6 0.2 - - - -
5108b PHE* 3.3 19.9 + - - -
5109b LEU* 2.7 16.3 + - - +
5111b ALA* 1.3 71.4 - - - +
5113b TRP* 1.3 57.2 + - - +
5115b TRP* 2.7 26.9 + - - +
5116b VAL* 3.0 16.6 + - - +
5527b BCR 3.9 26.9 - - + -
5529b BCR 3.6 23.8 - - + -
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Residues in contact with TRP5113 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5212A SQD 2.9 42.1 + - - -
5109b LEU 3.2 3.2 + - - -
5110b ALA* 3.7 7.6 - - - +
5112b CYS* 1.3 78.1 - - - +
5114b HIS* 1.3 94.8 + + - +
5116b VAL* 3.3 0.3 + - - -
5117b TYR* 3.0 55.7 + + + +
5120b LEU* 4.0 22.9 - - + -
5526b CLA 3.4 69.3 - + + +
5529b BCR 4.0 32.5 - - + +
5003h ARG* 5.8 3.6 - - - -
5005h THR* 5.4 4.0 - - + -
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Residues in contact with HIS5114 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5017b GLY* 3.5 28.8 + - - +
5020b ILE* 3.9 12.3 - - + +
5021b ALA* 4.0 8.3 - - + -
5024b LEU* 3.6 28.9 - - + -
5110b ALA 3.1 13.4 + - - +
5113b TRP* 1.3 97.8 - + - +
5115b TRP* 1.3 59.6 + - - +
5117b TYR 3.7 11.4 + - - +
5118b TRP* 3.9 2.3 - - - -
5120b LEU* 4.4 9.1 - - + +
5123b PHE* 5.4 4.5 - + - -
5526b CLA 2.9 74.1 + + + -
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Residues in contact with TRP5115 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5213L SQD 4.1 30.5 + - - -
23T PHE* 5.5 1.8 - + - -
5018b ARG* 2.6 97.4 + - + +
5021b ALA* 3.6 16.4 - - + -
5022b ALA 5.1 0.4 - - - -
5111b ALA 3.6 12.4 + - - +
5112b CYS 2.7 17.9 + - - +
5114b HIS* 1.3 71.9 - - - +
5116b VAL* 1.3 72.4 + - + +
5118b TRP* 3.6 2.9 - - - +
5524b CLA 3.6 37.5 - + + -
5527b BCR 3.6 41.5 - - + -
5007l ARG* 3.6 22.2 - - - -
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Residues in contact with VAL5116 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5213L SQD 5.6 1.7 + - - -
23T PHE* 5.2 7.6 - - + -
5018b ARG* 5.4 1.1 - - - +
5112b CYS 3.0 9.8 + - - +
5113b TRP 3.9 4.0 - - - +
5115b TRP* 1.3 82.4 - - + +
5117b TYR* 1.3 76.6 + - + +
5118b TRP* 3.1 21.8 + - - -
5529b BCR 3.5 38.1 - - + -
5001l MET* 3.3 39.7 - - + +
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Residues in contact with TYR5117 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5212A SQD 3.1 29.4 + - - -
5113b TRP* 3.0 62.4 + + + +
5114b HIS* 3.7 13.1 + - - +
5116b VAL* 1.3 87.3 - - + +
5118b TRP* 1.3 58.8 + - - +
5119b ASP 3.5 2.7 - - - +
5120b LEU* 3.5 26.4 - - + +
5123b PHE* 5.4 0.3 - - - -
5529b BCR 3.6 14.8 - - + +
5003h ARG* 4.3 38.1 - - - +
5001l MET* 4.5 15.5 - - + -
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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