Contacts of the helix formed by residues 5236 - 5258 (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 THR5236 (chain b).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5135b LEU* 6.4 0.2 - - + -
5229b LEU* 3.6 18.0 + - - +
5230b ARG 3.7 13.9 - - - +
5231b MET* 4.3 6.1 - - - -
5233b ASN 2.9 16.1 + - - +
5234b ILE 2.7 2.8 + - - -
5235b GLU* 1.3 75.9 - - - +
5237b VAL* 1.3 76.1 + - + +
5238b LEU 3.3 0.4 - - - -
5239b SER* 3.9 6.6 + - - -
5240b SER* 3.4 20.1 + - - -
5473b THR* 3.5 18.0 - - - +
5518b CLA 3.3 26.2 - - - +
5520b CLA 4.5 14.5 - - + +
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Residues in contact with VAL5237 (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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5135b LEU* 3.7 24.2 - - + -
5234b ILE* 2.8 13.3 + - - +
5236b THR* 1.3 82.5 - - + +
5238b LEU* 1.3 64.1 + - - +
5240b SER* 2.6 20.9 + - - -
5241b SER* 2.9 19.3 + - - +
5520b CLA 3.4 68.0 - - + +
5522b CLA 3.5 19.3 - - + +
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Residues in contact with LEU5238 (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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5234b ILE 3.5 0.8 + - - -
5235b GLU* 4.3 13.0 - - + +
5236b THR 3.3 0.4 - - - -
5237b VAL* 1.3 80.3 - - - +
5239b SER* 1.3 56.3 + - - +
5241b SER* 3.9 1.6 - - - -
5242b ILE* 3.0 39.8 + - + +
5469b HIS* 3.5 44.2 - - + +
5521b CLA 3.6 37.5 - - + -
5522b CLA 3.4 59.4 - - + +
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Residues in contact with SER5239 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5235b GLU 3.5 8.6 + - - -
5236b THR* 3.9 7.0 + - - -
5237b VAL 3.3 0.4 - - - -
5238b LEU* 1.3 74.8 - - - +
5240b SER* 1.3 65.3 + - - +
5242b ILE* 4.1 4.2 - - - +
5243b ALA* 3.3 9.5 + - - +
5466b HIS* 2.8 29.5 + - - +
5469b HIS* 2.9 16.5 + - - +
5470b GLY* 2.7 41.6 + - - -
5473b THR* 3.8 0.2 + - - -
5518b CLA 3.4 13.7 - - - -
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Residues in contact with SER5240 (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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5236b THR 3.5 11.4 + - - -
5237b VAL* 2.6 29.3 + - - +
5239b SER* 1.3 78.2 - - - +
5241b SER* 1.3 63.6 + - - +
5243b ALA* 3.3 8.1 + - - +
5244b ALA* 3.3 18.4 + - - +
5518b CLA 4.3 14.8 + - - -
5520b CLA 3.4 54.4 + - - +
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Residues in contact with SER5241 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5237b VAL* 2.9 19.1 + - - +
5238b LEU 3.9 1.8 - - - -
5240b SER* 1.3 74.0 + - - +
5242b ILE* 1.3 51.0 + - - +
5243b ALA 2.9 4.5 - - - -
5244b ALA* 2.7 12.1 + - - +
5245b VAL* 2.6 37.3 + - - +
5520b CLA 3.7 29.9 - - - +
5522b CLA 3.0 40.5 + - - -
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Residues in contact with ILE5242 (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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5238b LEU* 3.0 24.7 + - + +
5239b SER 4.1 2.7 - - - +
5241b SER* 1.3 75.5 - - - +
5243b ALA* 1.3 56.5 + - - +
5245b VAL* 3.9 8.9 - - - +
5246b PHE* 3.2 26.5 + - - +
5462b PHE* 3.0 33.8 - - + +
5465b GLY 3.9 4.3 - - - +
5466b HIS* 3.2 18.2 - - + +
5469b HIS* 4.1 17.0 - - + -
5521b CLA 3.5 59.5 - - + -
5522b CLA 4.8 1.1 + - - +
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Residues in contact with ALA5243 (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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5239b SER 3.3 17.4 + - - +
5240b SER 3.4 7.0 - - - +
5241b SER 2.9 1.0 - - - -
5242b ILE* 1.3 78.3 - - - +
5244b ALA* 1.3 62.5 + - - +
5246b PHE* 3.5 12.6 - - - -
5247b PHE 3.2 10.9 + - - -
5466b HIS* 3.5 22.2 - - + +
5518b CLA 3.1 45.7 - - + +
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Residues in contact with ALA5244 (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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5240b SER 3.3 8.6 + - - +
5241b SER 2.7 13.3 + - - +
5243b ALA* 1.3 73.5 - - - +
5245b VAL* 1.3 55.5 + - - +
5246b PHE 3.1 0.2 - - - -
5247b PHE* 2.8 9.4 + - - +
5248b ALA* 2.7 35.6 + - - +
5513b CLA 4.0 32.8 - - + +
5515b CLA 5.9 0.4 - - + -
5520b CLA 4.5 24.7 - - + +
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Residues in contact with VAL5245 (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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5241b SER 2.6 20.7 + - - +
5242b ILE* 4.1 4.9 - - - +
5244b ALA* 1.3 73.8 - - - +
5246b PHE* 1.3 58.5 + - - +
5248b ALA* 3.7 6.4 - - - +
5249b ALA* 3.0 24.8 + - - +
5462b PHE* 3.8 23.6 - - + -
5514b CLA 3.5 28.2 - - + +
5520b CLA 4.7 5.2 - - + +
5521b CLA 6.4 0.2 - - + -
5522b CLA 3.5 53.2 - - + +
5523b CLA 4.3 7.9 - - + -
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Residues in contact with PHE5246 (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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5242b ILE 3.2 24.3 + - - +
5243b ALA* 3.5 17.9 - - - -
5244b ALA 3.1 0.6 - - - -
5245b VAL* 1.3 76.2 - - - +
5247b PHE* 1.3 64.1 + - - +
5249b ALA* 3.5 8.0 - - - +
5250b PHE* 3.1 46.3 + + - -
5459b ALA* 3.7 19.1 - - - +
5462b PHE* 3.8 12.6 - - + -
5463b PHE* 3.8 39.5 - + - -
5466b HIS* 4.1 11.4 - + + -
5512b CLA 4.9 5.8 - - + -
5514b CLA 4.6 1.1 - - - -
5518b CLA 3.7 40.8 - + + -
5208h DGD 4.9 4.5 - - + -
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Residues in contact with PHE5247 (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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5243b ALA 3.2 11.6 + - - +
5244b ALA* 2.8 9.8 + - - +
5246b PHE* 1.3 84.5 - - - +
5248b ALA* 1.3 66.1 + - - +
5250b PHE* 3.3 4.4 + - - +
5251b VAL* 3.0 33.1 + - + +
5512b CLA 3.5 71.6 - - + -
5513b CLA 3.7 72.5 - - + -
5518b CLA 4.1 12.6 - - + -
5042h LEU* 4.7 15.5 - - + -
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Residues in contact with ALA5248 (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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5244b ALA 2.7 18.7 + - - +
5245b VAL* 3.7 3.4 - - - +
5247b PHE* 1.3 72.8 - - - +
5249b ALA* 1.3 64.0 + - - +
5251b VAL* 2.9 14.2 + - - +
5252b VAL* 3.0 15.1 + - - +
5513b CLA 4.0 34.7 - - + +
5514b CLA 3.4 21.3 - - + -
5522b CLA 3.9 14.8 - - + -
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Residues in contact with ALA5249 (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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5245b VAL 3.0 15.8 + - - +
5246b PHE 3.5 6.7 - - - +
5248b ALA* 1.3 77.8 - - - +
5250b PHE* 1.3 56.0 + - - +
5251b VAL 2.7 11.8 + - - -
5252b VAL* 2.8 30.1 + - + +
5253b ALA* 2.9 9.6 + - - +
5455b HIS* 4.1 6.9 - - + +
5459b ALA* 3.8 10.5 - - + -
5514b CLA 3.5 32.9 - - + +
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Residues in contact with PHE5250 (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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5246b PHE* 3.1 37.0 + + - +
5247b PHE* 3.3 5.4 + - - +
5249b ALA* 1.3 77.9 - - - +
5251b VAL* 1.3 59.5 + - - +
5253b ALA* 4.0 5.4 - - + +
5254b GLY 3.4 13.5 + - - -
5456b ALA* 4.1 11.2 - - + -
5459b ALA* 3.6 31.8 - - + +
5460b LEU* 3.8 27.8 - - + -
5463b PHE* 5.6 0.4 - - + -
5512b CLA 3.6 59.0 - - + -
5159d ILE* 3.8 13.5 - - + -
5208h DGD 3.4 35.9 - - + +
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Residues in contact with VAL5251 (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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5247b PHE* 3.0 40.4 - - + +
5248b ALA 3.3 6.7 - - - +
5249b ALA 2.7 5.3 + - - -
5250b PHE* 1.3 76.0 - - - +
5252b VAL* 1.3 58.5 + - - +
5253b ALA 3.2 1.6 - - - -
5254b GLY* 3.5 0.5 + - - -
5255b THR* 3.1 27.4 + - + +
5512b CLA 3.9 58.8 - - + +
5513b CLA 4.1 18.2 - - + -
5208h DGD 4.3 8.8 - - + +
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Residues in contact with VAL5252 (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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5248b ALA 3.0 10.5 + - - +
5249b ALA* 2.8 34.1 + - - +
5251b VAL* 1.3 74.6 - - - +
5253b ALA* 1.3 65.5 + - - +
5255b THR* 3.3 8.8 + - - +
5256b MET* 3.2 24.8 + - - +
5451b PHE* 3.8 6.9 - - + -
5455b HIS* 4.2 15.7 - - + -
5513b CLA 3.3 26.5 - - + +
5514b CLA 3.3 51.8 - - + +
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Residues in contact with ALA5253 (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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5249b ALA 2.9 14.4 + - - +
5250b PHE* 4.0 7.6 - - + +
5252b VAL* 1.3 80.9 - - - +
5254b GLY* 1.3 63.0 + - - +
5256b MET* 3.4 3.0 + - - -
5257b TRP* 3.1 18.2 + - - +
5451b PHE* 4.7 0.7 - - - -
5452b THR* 3.5 26.9 + - + +
5455b HIS* 4.2 8.5 - - + +
5456b ALA* 4.1 30.5 - - + +
5208h DGD 5.3 5.2 - - + -
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Residues in contact with GLY5254 (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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5250b PHE 3.4 13.7 + - - -
5251b VAL 3.5 3.1 + - - -
5252b VAL 3.3 0.2 - - - -
5253b ALA* 1.3 76.6 - - - +
5255b THR* 1.3 55.8 + - - +
5256b MET 3.0 4.9 - - - -
5257b TRP* 3.2 3.8 + - - -
5258b TYR* 3.0 45.1 + - - -
5208h DGD 4.2 24.4 - - - +
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Residues in contact with THR5255 (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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5251b VAL* 3.1 22.8 + - + +
5252b VAL* 3.3 11.6 + - - +
5254b GLY* 1.3 75.1 - - - +
5256b MET* 1.3 59.1 + - - +
5258b TYR 3.1 5.2 - - - +
5259b GLY 2.8 25.0 - - - +
5260b SER* 3.5 15.9 - - - +
5262b THR* 5.2 6.5 - - - +
5263b THR* 3.1 14.5 + - - -
5512b CLA 4.0 31.2 - - - +
5513b CLA 4.6 4.2 + - - +
5049h TYR* 3.9 19.5 - - + +
5208h DGD 5.5 1.6 - - + -
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Residues in contact with MET5256 (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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5065b PHE* 4.4 4.0 - - + -
5068b ARG* 6.1 1.1 - - - +
5252b VAL 3.2 19.3 + - - +
5253b ALA 3.7 1.1 - - - +
5254b GLY 3.0 0.6 - - - -
5255b THR* 1.3 80.2 + - - +
5257b TRP* 1.3 58.6 + - - +
5262b THR* 5.7 0.9 - - + +
5263b THR* 3.4 27.8 - - - +
5268b PHE* 3.4 40.6 - - + -
5448b ARG* 2.4 53.6 + - - +
5451b PHE* 3.6 33.7 - - + -
5452b THR* 3.1 20.0 - - - +
5514b CLA 5.7 1.3 - - - +
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Residues in contact with TRP5257 (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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5253b ALA 3.1 16.3 + - - +
5254b GLY* 3.9 4.9 - - - +
5256b MET* 1.3 75.6 - - - +
5258b TYR* 1.3 68.2 + + + +
5271b THR* 3.6 11.1 + - - +
5272b ARG* 3.8 24.0 + - + -
5273b TYR* 2.9 38.3 + + - -
5319b PRO* 3.9 30.5 - - + -
5320b ALA* 4.3 2.5 - - - -
5448b ARG* 4.1 9.6 - - + -
5449b GLY* 3.7 24.9 - - - -
5452b THR* 3.5 18.1 + - + -
5162d LEU 4.2 4.7 - - - -
5163d GLY* 2.6 35.9 + - - -
5290d ALA 4.6 0.2 - - - -
5291d LEU* 3.5 45.5 - - + -
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Residues in contact with TYR5258 (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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5193b TYR* 4.9 2.0 - - - +
5254b GLY* 3.0 29.5 + - - +
5255b THR 3.1 8.3 - - - +
5256b MET 3.3 5.4 - - - +
5257b TRP* 1.3 86.4 - + + +
5259b GLY* 1.3 69.6 + - - +
5271b THR* 3.7 5.7 + - - -
5273b TYR* 3.6 31.0 - + - -
5448b ARG* 3.6 6.1 + - - -
5087d HIS* 3.6 15.6 + + - -
5162d LEU* 2.7 50.9 + - - +
5049h TYR* 4.5 9.6 - - + +
5208h DGD 3.5 69.1 + - + +
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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