Contacts of the helix formed by residues 5198 - 5221 (chain a) 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 HIS5198 (chain a).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5192a ILE* 2.8 57.9 + - + +
5193a LEU* 4.4 12.0 - - + +
5195a HIS* 3.9 3.1 + - - +
5197a PHE* 1.3 78.6 - - - +
5199a GLN* 1.3 65.2 + - - +
5201a GLY* 3.0 12.6 + - - -
5202a VAL* 3.1 20.2 + - + +
5286a ALA* 4.5 6.9 - - + +
5289a GLY* 5.0 0.8 - - - -
5290a ILE* 5.6 1.3 - - - -
6003a CLA 2.5 84.4 + + + +
6006a CLA 4.1 6.1 + - - -
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Residues in contact with GLN5199 (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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5195a HIS 3.3 15.3 + - - +
5196a PRO* 3.0 30.0 + - + -
5198a HIS* 1.3 79.8 - - - +
5200a LEU* 1.3 87.9 + - - +
5202a VAL* 2.8 7.1 + - - +
5203a ALA* 2.4 33.6 + - - +
6006a CLA 3.8 25.7 - - - +
6057c DGD 2.9 63.7 - - + +
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Residues in contact with LEU5200 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5196a PRO 3.3 21.8 - - - +
5197a PHE* 3.2 4.0 + - + +
5198a HIS 3.2 0.8 - - - -
5199a GLN* 1.3 101.8 + - - +
5201a GLY* 1.3 59.8 + - - +
5203a ALA* 3.2 12.8 - - + +
5204a GLY 3.1 14.2 + - - -
5278a TRP* 6.2 1.1 - - + -
5281a VAL* 5.9 2.7 - - + -
5282a GLY* 2.8 25.6 - - - -
5285a PHE* 3.0 59.0 - - + -
6056c DGD 4.0 15.0 - - + -
6057c DGD 4.5 25.1 - - + -
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Residues in contact with GLY5201 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5197a PHE 3.7 3.4 + - - -
5198a HIS 3.0 6.8 + - - -
5200a LEU* 1.3 74.3 - - - +
5202a VAL* 1.3 56.2 + - - +
5203a ALA 3.0 0.9 - - - -
5204a GLY 3.1 0.3 + - - -
5205a VAL* 2.5 39.8 + - - +
5279a ARG* 3.6 2.9 + - - -
5282a GLY 3.3 16.6 + - - -
5283a VAL* 4.5 0.4 - - - -
5286a ALA* 3.7 7.0 - - - -
6003a CLA 3.5 21.1 - - - -
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Residues in contact with VAL5202 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5198a HIS* 3.1 16.0 + - + +
5199a GLN 2.8 7.4 + - - +
5201a GLY* 1.3 78.6 - - - +
5203a ALA* 1.3 53.4 + - - +
5205a VAL* 3.6 7.2 - - - -
5206a PHE* 2.5 62.9 + - + +
6003a CLA 3.6 32.9 - - + +
6006a CLA 2.8 49.1 - - + +
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Residues in contact with ALA5203 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5199a GLN* 2.4 34.3 + - - +
5200a LEU* 3.2 21.5 - - + +
5202a VAL* 1.3 77.4 - - - +
5204a GLY* 1.3 59.7 + - - +
5207a GLY 3.4 5.5 + - - -
5278a TRP* 3.5 15.4 + - + -
5282a GLY* 5.4 0.4 - - - -
6006a CLA 2.9 34.1 - - - +
6057c DGD 3.8 15.7 - - + -
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Residues in contact with GLY5204 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5200a LEU 3.1 10.2 + - - -
5201a GLY 3.7 0.9 - - - -
5203a ALA* 1.3 79.5 - - - +
5205a VAL* 1.3 54.2 + - - +
5207a GLY 3.3 1.1 - - - -
5208a GLY* 2.4 36.4 + - - -
5278a TRP* 3.7 29.5 - - - -
5279a ARG* 4.0 16.2 - - - +
5282a GLY* 4.9 0.4 - - - -
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Residues in contact with VAL5205 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5201a GLY 2.5 25.0 + - - +
5202a VAL* 3.6 11.4 - - - -
5204a GLY* 1.3 67.5 - - - -
5206a PHE* 1.3 61.8 + - - +
5207a GLY 2.8 9.4 + - - -
5209a ALA* 3.3 14.2 + - - +
5279a ARG* 3.1 21.9 - - - +
6003a CLA 3.7 31.2 - - + -
5204d VAL* 3.2 45.8 - - + +
5205d LEU* 4.0 19.5 - - + -
5208d ALA* 3.7 9.3 - - + +
6004d CLA 5.3 0.9 - - + -
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Residues in contact with PHE5206 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5202a VAL* 2.5 33.9 + - + +
5203a ALA 3.8 2.9 - - - -
5205a VAL* 1.3 79.4 - - - +
5207a GLY* 1.3 56.0 + - - +
5209a ALA* 4.6 2.2 - - - -
5210a LEU* 4.2 7.0 - - - +
6003a CLA 3.3 39.9 - - + -
6006a CLA 2.8 69.5 - + + +
6039a PHO 3.2 29.2 - - + +
5204d VAL* 4.1 11.9 - - + -
6004d CLA 3.2 47.3 - + + -
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Residues in contact with GLY5207 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5203a ALA 3.4 3.8 + - - -
5204a GLY 3.0 6.3 + - - -
5205a VAL 2.8 3.4 - - - -
5206a PHE* 1.3 80.5 - - - +
5208a GLY* 1.3 64.1 + - - -
5209a ALA 2.6 5.9 + - - -
5210a LEU* 2.9 2.1 + - - -
5211a PHE* 2.6 25.4 + - - +
5278a TRP* 3.5 25.6 - - - -
6006a CLA 4.0 7.4 - - - -
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Residues in contact with GLY5208 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5204a GLY 2.4 24.7 + - - -
5207a GLY* 1.3 65.3 - - - -
5209a ALA* 1.3 50.3 + - - +
5211a PHE* 4.1 0.4 - - - -
5212a CYS* 2.5 38.7 + - - +
5278a TRP* 4.0 6.3 - - - -
5279a ARG* 5.1 4.5 - - - -
5207d GLY 4.0 4.5 - - - -
5208d ALA* 4.0 9.9 - - - -
5211d CYS* 3.2 27.7 - - - +
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Residues in contact with ALA5209 (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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5205a VAL 3.3 20.0 + - - +
5207a GLY 2.6 4.9 + - - +
5208a GLY* 1.3 70.0 - - - +
5210a LEU* 1.3 56.7 + - - +
5211a PHE 2.6 15.2 + - - -
5212a CYS* 3.0 11.1 + - - +
5213a ALA* 3.1 12.5 + - - +
6039a PHO 3.5 30.7 - - + +
5204d VAL* 4.0 22.7 - - + +
5207d GLY 4.8 3.4 - - - -
5208d ALA* 4.4 1.2 - - - +
5275d PRO* 4.2 9.3 - - + +
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Residues in contact with LEU5210 (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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5206a PHE 4.2 0.4 + - - +
5207a GLY* 2.9 7.1 + - - +
5209a ALA* 1.3 76.6 - - - +
5211a PHE* 1.3 70.0 + - + +
5213a ALA* 3.3 14.7 - - - +
5214a MET* 3.2 29.0 - - + +
6006a CLA 3.2 44.4 - - + -
6039a PHO 3.0 84.0 - - + +
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Residues in contact with PHE5211 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5207a GLY 2.6 16.6 + - - +
5209a ALA 2.6 3.6 + - - -
5210a LEU* 1.3 102.5 - - + +
5212a CYS* 1.3 61.9 + - - +
5213a ALA 2.8 5.2 - - - -
5214a MET* 2.8 16.8 + - - +
5215a HIS* 3.2 12.6 + - - +
5274a PHE* 3.5 38.4 - + - -
5275a LEU* 5.3 6.9 - - + +
5278a TRP* 3.5 32.8 - + + -
6006a CLA 4.1 14.8 - - + -
6039a PHO 6.4 0.2 - - - -
6043a PQ9 4.3 37.6 - - + +
5211d CYS* 3.5 17.2 - - - -
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Residues in contact with CYS5212 (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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5208a GLY 2.5 23.3 + - - +
5209a ALA 3.0 0.2 + - - -
5211a PHE* 1.3 73.3 - - - +
5213a ALA* 1.3 60.7 + - - +
5215a HIS* 4.8 1.5 - - - +
5216a GLY 3.1 16.8 + - - -
5207d GLY 3.4 10.1 - - - +
5210d LEU* 3.7 18.6 - - - -
5211d CYS* 3.6 8.5 - - + -
5271d MET* 2.9 66.2 - - - +
5275d PRO* 3.9 15.0 - - + -
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Residues in contact with ALA5213 (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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5209a ALA 3.1 10.2 + - - +
5210a LEU 3.3 15.9 - - - +
5211a PHE 2.8 0.4 - - - -
5212a CYS* 1.3 80.3 - - - +
5214a MET* 1.3 56.3 + - - +
5217a SER* 2.8 27.6 + - - -
6039a PHO 3.9 29.6 - - + -
5145d ALA* 4.4 0.9 - - - +
5271d MET 4.0 6.9 + - - -
5272d LEU* 3.8 7.2 - - - +
5275d PRO* 4.5 1.9 - - + +
5276d VAL* 4.1 20.2 - - + -
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Residues in contact with MET5214 (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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5210a LEU* 3.2 35.7 - - + +
5211a PHE* 2.8 14.3 + - - +
5213a ALA* 1.3 68.9 - - - +
5215a HIS* 1.3 59.3 + - - +
5216a GLY 2.9 1.3 - - - -
5217a SER* 2.4 30.1 + - - -
5218a LEU* 2.7 25.2 + - + -
5255a PHE* 4.7 4.9 - - - -
6039a PHO 3.1 60.1 - - + +
6043a PQ9 3.3 43.3 - - + +
5142d ASN* 4.6 4.9 - - - -
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Residues in contact with HIS5215 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5211a PHE 3.2 8.0 + - - +
5212a CYS 4.8 0.9 - - - +
5214a MET* 1.3 78.3 - - - +
5216a GLY* 1.3 51.3 + - - +
5219a VAL* 2.3 43.3 + - + +
5246a TYR* 4.3 4.5 - + - -
5271a LEU* 4.6 2.0 - - + -
5272a HIS* 2.3 25.4 - + - -
5275a LEU* 3.1 32.5 - - + -
6002a FE2 2.1 32.9 - - - -
6043a PQ9 3.3 29.4 + - + +
5214d HIS* 3.2 11.6 + + - -
5268d HIS* 2.6 25.4 - + - -
5271d MET* 4.6 7.0 - - + -
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Residues in contact with GLY5216 (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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5212a CYS 3.1 17.4 + - - -
5214a MET 2.7 1.4 + - - -
5215a HIS* 1.3 76.8 - - - +
5217a SER* 1.3 61.5 + - - +
5219a VAL* 2.6 22.0 - - - +
5220a THR* 2.9 11.4 + - - -
5268d HIS* 2.7 26.5 - - - -
5271d MET* 3.9 5.5 - - - +
5272d LEU* 4.2 7.0 - - - -
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Residues in contact with SER5217 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5213a ALA 2.8 23.5 + - - -
5214a MET* 2.4 20.3 + - - -
5216a GLY* 1.3 70.9 - - - +
5218a LEU* 1.3 61.1 + - - +
5220a THR 3.2 0.2 + - - -
5221a SER* 2.8 29.2 + - - -
6039a PHO 5.4 0.4 - - - -
5141d TYR* 2.8 17.6 + - - +
5142d ASN* 2.8 41.0 + - - +
5145d ALA* 4.4 4.7 - - - -
5272d LEU* 4.2 7.4 - - - +
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Residues in contact with LEU5218 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5214a MET* 2.7 24.6 + - + +
5217a SER* 1.3 83.3 + - - +
5219a VAL* 1.3 56.0 + - - +
5221a SER* 3.3 6.5 + - - +
5222a SER* 3.0 31.4 + - - -
5251a ALA* 4.5 8.7 - - + +
5254a TYR* 4.1 33.0 - - + -
5255a PHE* 3.9 26.0 - - + +
5258a LEU* 6.2 0.2 - - + -
6043a PQ9 3.5 57.7 - - + -
5142d ASN* 4.4 9.9 - - + +
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Residues in contact with VAL5219 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5215a HIS* 2.3 36.9 + - + +
5216a GLY 2.6 14.6 - - - +
5218a LEU* 1.3 78.2 - - - +
5220a THR* 1.3 56.7 + - - +
5222a SER 3.1 18.0 - - - +
5246a TYR* 3.7 23.5 - - + +
5251a ALA* 5.9 0.4 - - - -
6043a PQ9 4.7 2.4 - - + +
5265d ARG* 3.1 13.3 + - - +
5268d HIS* 2.4 91.1 - - + +
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Residues in contact with THR5220 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5216a GLY 2.9 15.5 + - - -
5217a SER* 3.9 0.9 - - - -
5219a VAL* 1.3 71.9 - - - +
5221a SER* 1.3 54.4 + - - +
5222a SER 2.9 10.5 + - - -
5223a LEU 3.8 0.5 + - - -
5234a ASN* 5.0 0.7 - - - +
6060b MGE 4.2 4.5 - - - +
5139d ARG* 2.6 32.0 + - - +
5141d TYR* 3.2 36.1 - - + -
5265d ARG* 2.7 34.4 + - - +
5268d HIS* 3.6 6.1 - - - +
5269d PHE* 3.6 33.9 - - + +
5272d LEU* 5.3 1.7 - - - +
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Residues in contact with SER5221 (chain a).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5217a SER 2.8 18.5 + - - -
5218a LEU* 3.3 14.1 + - - -
5220a THR* 1.3 74.8 - - - +
5222a SER* 1.3 56.2 + - - +
5254a TYR* 4.1 11.8 - - - -
5479b ILE* 4.0 0.2 - - - +
5138d VAL* 2.9 27.8 - - - +
5139d ARG* 2.6 49.3 + - - +
5141d TYR* 3.9 10.0 - - - -
5142d ASN 4.7 2.5 - - - -
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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