Contacts of the helix formed by residues 5194 - 5219 (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 ASN5194 (chain b).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5184b GLU* 3.6 23.0 + - - +
5188b ASP* 2.8 34.9 + - - +
5189b GLY* 4.8 0.7 - - - -
5191b ASN* 2.9 18.4 + - + +
5192b PRO 3.5 0.7 - - - +
5193b TYR* 1.3 77.8 - - - +
5195b PRO* 1.3 55.8 - - - +
5196b GLY* 2.6 37.6 + - - -
5197b GLY* 2.7 31.9 + - - +
5198b VAL* 3.7 3.8 + - - +
5261b ALA* 4.3 2.2 - - - -
5512b CLA 5.7 0.5 - - - +
5064h ALA* 5.6 8.2 - - + +
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Residues in contact with PRO5195 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5166b MET* 4.1 10.3 - - + -
5167b TRP 5.5 0.2 - - - +
5168b VAL* 4.1 24.5 - - + -
5181b VAL* 3.7 27.1 - - + -
5193b TYR 3.1 11.9 - - - +
5194b ASN* 1.3 84.6 - - - +
5196b GLY* 1.3 53.8 + - - +
5197b GLY 2.7 0.9 + - - -
5198b VAL* 2.5 43.4 + - + +
5199b VAL* 3.2 6.2 + - - +
5261b ALA* 3.8 15.9 - - + +
5064h ALA* 6.0 2.2 - - + -
5065h LEU* 6.3 2.9 - - + -
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Residues in contact with GLY5196 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5181b VAL* 3.5 8.0 - - - +
5182b ALA 3.3 23.1 - - - -
5184b GLU* 3.2 22.3 + - - -
5194b ASN* 2.6 17.9 + - - -
5195b PRO* 1.3 73.6 - - - +
5197b GLY* 1.3 54.7 + - - -
5199b VAL* 3.3 2.3 + - - +
5200b ALA* 3.0 23.9 + - - +
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Residues in contact with GLY5197 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5189b GLY* 3.2 30.9 - - - -
5194b ASN* 2.7 15.5 + - - -
5196b GLY* 1.3 76.9 - - - +
5198b VAL* 1.3 64.1 + - - +
5199b VAL 3.1 0.4 - - - -
5201b HIS* 3.0 26.7 + - - +
5512b CLA 3.6 15.9 - - - +
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Residues in contact with VAL5198 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5158b LEU* 3.6 12.5 - - + +
5166b MET* 4.2 12.1 - - + -
5192b PRO 5.6 2.5 - - - +
5194b ASN 4.4 2.5 - - - +
5195b PRO* 2.5 29.5 + - + +
5197b GLY* 1.3 72.8 - - - +
5199b VAL* 1.3 56.3 + - - +
5201b HIS* 4.1 1.3 - - - +
5202b HIS* 2.7 42.6 + - + -
5261b ALA* 4.7 8.7 - - + -
5262b THR* 4.2 14.1 - - - +
5512b CLA 4.4 13.0 - - + -
5513b CLA 3.8 37.0 - - + +
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Residues in contact with VAL5199 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5154b GLY* 3.6 23.7 - - - +
5158b LEU* 4.0 20.0 - - + -
5159b THR* 3.9 6.1 - - - +
5166b MET* 4.8 1.6 - - - -
5181b VAL* 3.3 43.7 - - + +
5182b ALA 4.4 0.2 - - - +
5183b PRO* 3.6 28.0 - - + -
5195b PRO 3.5 4.9 - - - +
5196b GLY* 3.6 4.9 - - - +
5197b GLY 3.1 0.6 - - - -
5198b VAL* 1.3 75.2 - - - +
5200b ALA* 1.3 66.8 + - - +
5201b HIS 3.0 2.6 + - - -
5202b HIS* 3.2 5.0 + - - +
5203b ILE* 3.1 22.2 + - + +
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Residues in contact with ALA5200 (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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5183b PRO* 4.0 5.5 - - + +
5184b GLU 3.4 35.7 - - - +
5185b TRP* 3.7 22.9 - - + -
5196b GLY 3.0 12.1 + - - +
5199b VAL* 1.3 77.0 - - - +
5201b HIS* 1.3 57.6 + - - +
5203b ILE* 3.3 1.0 + - - +
5204b ALA* 2.9 32.2 + - - +
5512b CLA 3.6 14.6 - - + -
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Residues in contact with HIS5201 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5197b GLY 3.0 19.5 + - - +
5198b VAL* 4.1 4.0 - - - +
5200b ALA* 1.3 76.2 - - - +
5202b HIS* 1.3 97.7 + + - +
5203b ILE 3.0 0.5 + - - -
5204b ALA 3.1 0.5 + - - -
5205b ALA* 2.8 45.0 + - + +
5512b CLA 2.1 84.5 + + + -
5513b CLA 3.1 43.0 - + + -
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Residues in contact with HIS5202 (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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5150b CYS* 3.2 37.9 - - - +
5151b PHE* 3.5 5.9 - - - -
5153b PHE* 3.8 23.6 - + - -
5154b GLY* 3.9 15.0 - - - -
5158b LEU* 4.1 0.6 - - - +
5198b VAL* 2.7 32.1 + - + -
5199b VAL 3.2 4.0 + - - +
5201b HIS* 1.3 88.6 - + - +
5203b ILE* 1.3 60.2 + - - +
5206b GLY* 3.4 12.2 + - - -
5513b CLA 2.1 78.6 + + + -
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Residues in contact with ILE5203 (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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5151b PHE* 3.7 19.1 - - + -
5154b GLY 4.0 0.2 - - - -
5155b ALA* 3.8 34.8 - - + +
5159b THR* 4.8 1.1 - - - +
5183b PRO* 3.6 30.3 - - + -
5185b TRP* 3.2 26.0 - - + -
5199b VAL* 3.1 18.2 + - + +
5200b ALA 3.6 7.0 - - - +
5201b HIS 3.0 1.0 - - - -
5202b HIS* 1.3 77.2 - - - +
5204b ALA* 1.3 65.6 + - - +
5207b ILE* 3.3 29.0 + - + +
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Residues in contact with ALA5204 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5185b TRP* 4.5 6.7 - - + -
5200b ALA 2.9 17.9 + - - +
5203b ILE* 1.3 74.3 - - - +
5205b ALA* 1.3 52.4 + - - +
5206b GLY 2.9 3.4 - - - -
5207b ILE* 2.8 12.1 + - - +
5208b VAL* 2.8 36.0 + - + +
5511b CLA 4.5 13.7 - - + +
5512b CLA 3.6 39.0 - - + -
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Residues in contact with ALA5205 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5150b CYS* 4.4 4.7 - - - -
5201b HIS* 2.8 40.6 + - + +
5204b ALA* 1.3 73.8 - - - +
5206b GLY* 1.3 55.0 + - - +
5208b VAL* 3.9 0.4 - - - -
5209b GLY* 3.0 19.0 + - - -
5512b CLA 3.6 38.1 - - + +
5513b CLA 5.0 0.7 - - + -
5515b CLA 3.1 23.5 - - + +
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Residues in contact with GLY5206 (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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5147b GLY 3.5 18.8 - - - +
5150b CYS* 3.9 8.7 - - - -
5151b PHE* 3.9 5.2 - - - -
5202b HIS 3.4 21.3 + - - -
5203b ILE 4.0 0.9 - - - -
5204b ALA 2.8 1.6 + - - -
5205b ALA* 1.3 76.3 - - - +
5207b ILE* 1.3 58.5 + - - +
5209b GLY* 3.0 2.8 + - - -
5210b ILE* 2.8 32.8 + - - +
5515b CLA 4.3 0.4 - - - -
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Residues in contact with ILE5207 (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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5151b PHE* 3.8 24.4 - - + -
5203b ILE* 3.3 21.7 + - + +
5204b ALA* 2.8 9.5 + - - +
5206b GLY* 1.3 71.9 - - - +
5208b VAL* 1.3 62.5 + - + +
5209b GLY 2.8 4.3 - - - -
5210b ILE* 2.8 29.4 + - + +
5211b ILE* 2.9 32.9 + - + +
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Residues in contact with VAL5208 (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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5204b ALA* 2.8 17.7 + - + +
5207b ILE* 1.3 77.7 - - + +
5209b GLY* 1.3 59.2 + - - +
5211b ILE* 4.2 10.2 - - + +
5212b ALA* 3.4 22.0 + - - +
5511b CLA 4.9 4.7 - - - +
5512b CLA 3.3 52.0 - - + -
5519b CLA 3.8 22.7 - - + +
5107h BCR 4.4 7.4 - - + -
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Residues in contact with GLY5209 (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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5143b LEU* 3.4 21.3 - - - +
5147b GLY* 4.2 5.6 - - - -
5205b ALA 3.0 16.2 + - - -
5206b GLY 3.3 5.6 - - - -
5207b ILE 2.8 1.2 - - - -
5208b VAL* 1.3 79.0 - - - +
5210b ILE* 1.3 62.1 + - - +
5212b ALA* 4.1 1.5 - - - +
5213b GLY* 3.3 15.8 + - - -
5515b CLA 4.0 20.0 - - - -
5519b CLA 5.7 0.9 - - - -
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Residues in contact with ILE5210 (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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5144b PHE* 3.7 31.6 - - + +
5147b GLY 4.5 1.6 - - - +
5148b LEU* 3.7 41.7 - - + +
5151b PHE* 4.5 15.0 - - + -
5206b GLY 2.8 17.6 + - - +
5207b ILE* 2.8 14.3 + - + +
5209b GLY* 1.3 74.7 - - - +
5211b ILE* 1.3 72.0 + - + +
5213b GLY* 3.2 9.4 + - - -
5214b LEU* 3.3 19.3 + - + +
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Residues in contact with ILE5211 (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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5207b ILE* 2.9 35.0 + - + +
5208b VAL* 4.2 8.3 - - + +
5210b ILE* 1.3 83.0 - - + +
5212b ALA* 1.3 67.8 + - - +
5213b GLY 3.0 0.3 + - - -
5214b LEU* 3.1 20.1 + - + +
5215b PHE* 3.2 11.4 + - + +
5519b CLA 4.5 15.5 - - + -
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Residues in contact with ALA5212 (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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5143b LEU* 4.1 11.0 - - + -
5208b VAL 3.4 17.5 + - - +
5209b GLY* 4.1 3.1 - - - +
5210b ILE 3.4 0.2 - - - -
5211b ILE* 1.3 81.7 - - - +
5213b GLY* 1.3 60.5 + - - +
5215b PHE* 3.3 7.9 - - - +
5216b HIS* 3.0 31.5 + - - +
5519b CLA 3.5 43.3 - - + -
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Residues in contact with GLY5213 (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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5140b GLY* 3.3 21.7 - - - +
5143b LEU* 4.0 7.8 - - - +
5144b PHE* 4.0 10.1 - - - -
5209b GLY 3.3 10.1 + - - -
5210b ILE 3.2 7.0 + - - -
5211b ILE 3.1 1.6 - - - -
5212b ALA* 1.3 74.8 - - - +
5214b LEU* 1.3 53.7 + - - +
5216b HIS* 3.1 4.7 + - - -
5217b ILE* 2.8 37.5 + - - +
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Residues in contact with LEU5214 (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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5144b PHE* 3.7 28.4 - - + -
5210b ILE* 3.3 19.8 + - + +
5211b ILE* 3.1 12.5 + - + +
5213b GLY* 1.3 71.8 - - - +
5215b PHE* 1.3 65.9 + - - +
5217b ILE* 2.8 17.5 + - + +
5218b LEU* 2.7 40.9 + - + +
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Residues in contact with PHE5215 (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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5211b ILE* 3.2 7.5 + - + +
5212b ALA* 3.3 16.4 - - - +
5214b LEU* 1.3 77.1 - - - +
5216b HIS* 1.3 70.2 + + - +
5218b LEU* 2.8 9.2 + - - -
5219b VAL* 2.6 72.5 + - + -
5519b CLA 3.5 74.0 - + + -
5027h THR* 3.9 12.3 - - + -
5030h LEU* 4.8 7.6 - - + -
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Residues in contact with HIS5216 (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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5136b PRO* 3.5 19.2 - - + +
5137b LYS* 4.2 4.0 - - - -
5139b PHE* 3.8 21.3 - + - -
5140b GLY* 3.6 24.0 - - - +
5143b LEU* 4.6 1.4 - - + +
5212b ALA 3.0 20.4 + - - +
5213b GLY 3.1 3.7 + - - +
5215b PHE* 1.3 88.7 - + - +
5217b ILE* 1.3 61.8 + - - +
5218b LEU 3.2 0.4 - - - -
5219b VAL 3.8 13.1 - - - +
5519b CLA 2.4 99.6 + + + +
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Residues in contact with ILE5217 (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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5137b LYS* 4.2 23.2 - - + +
5140b GLY* 3.4 26.2 - - - +
5141b ILE* 3.6 21.3 - - + +
5144b PHE* 4.1 17.9 - - + -
5213b GLY 2.8 15.2 + - - +
5214b LEU* 2.8 24.1 + - + +
5216b HIS* 1.3 78.7 - - - +
5218b LEU* 1.3 76.2 + - + +
5014h LEU* 6.5 1.1 - - + -
5017h GLU* 5.7 0.3 - - - +
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Residues in contact with LEU5218 (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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5214b LEU* 2.7 29.6 + - + +
5215b PHE* 2.8 4.2 + - - +
5217b ILE* 1.3 98.9 - - + +
5219b VAL* 1.3 67.8 + - + +
5220b ARG* 3.6 7.3 + - - +
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Residues in contact with VAL5219 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5136b PRO* 6.0 0.5 - - - +
5215b PHE* 2.6 53.1 + - + +
5216b HIS 3.8 11.8 - - - +
5218b LEU* 1.3 74.9 - - + +
5220b ARG* 1.3 76.4 + - - +
5221b PRO* 4.5 0.5 - - - +
5519b CLA 3.7 12.4 - - - +
5022h ALA* 5.7 1.8 - - + -
5027h THR* 3.6 22.0 - - + +
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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