Contacts of the helix formed by residues 5034 - 5062 (chain z) 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 ASP5034 (chain z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5032z ASP* 2.9 3.3 - - - -
5033z TRP* 1.3 80.4 - - - +
5035z ARG* 1.3 65.0 + - - +
5037z LYS* 3.3 17.2 - - - +
5038z GLN* 3.8 5.2 + - - +
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Residues in contact with ARG5035 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5032z ASP* 3.4 20.8 + - + +
5034z ASP* 1.3 77.3 - - - +
5036z SER* 1.3 58.4 + - - +
5038z GLN* 3.0 24.1 + - - +
5039z LEU* 3.2 21.8 + - + +
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Residues in contact with SER5036 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5026z ALA* 4.0 29.2 - - - -
5032z ASP 3.5 11.5 + - - -
5033z TRP* 5.0 4.7 - - - -
5034z ASP 3.5 0.2 - - - -
5035z ARG* 1.3 76.7 - - - +
5037z LYS* 1.3 60.8 + - - +
5039z LEU* 3.2 22.1 - - - +
5040z ILE* 2.6 40.7 + - - +
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Residues in contact with LYS5037 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5033z TRP 3.6 18.0 + - - +
5034z ASP* 3.3 16.9 - - - +
5036z SER* 1.3 77.3 - - - +
5038z GLN* 1.3 63.9 + - - +
5040z ILE* 4.3 5.9 - - - +
5041z PHE* 3.4 17.8 + - - +
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Residues in contact with GLN5038 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5034z ASP 3.8 4.4 + - - +
5035z ARG* 3.0 12.6 + - - +
5037z LYS* 1.3 76.4 - - - +
5039z LEU* 1.3 66.4 + - + +
5041z PHE* 2.8 20.8 + - - +
5042z LEU* 3.1 10.7 + - - +
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Residues in contact with LEU5039 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5035z ARG* 3.5 13.2 - - + +
5036z SER* 3.2 32.5 - - - +
5038z GLN* 1.3 78.8 - - + +
5040z ILE* 1.3 57.4 + - + +
5042z LEU* 2.8 45.0 + - + +
5043z GLY* 3.0 5.4 + - - -
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Residues in contact with ILE5040 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5127c PHE* 4.1 20.0 - - + -
5019z MET* 4.4 5.4 - - + +
5023z VAL* 4.1 23.3 - - + +
5026z ALA* 3.5 31.9 - - + -
5027z TYR* 4.6 19.7 - - + +
5036z SER* 2.6 28.7 + - - +
5037z LYS* 4.3 4.9 - - - +
5039z LEU* 1.3 73.6 - - + +
5041z PHE* 1.3 58.8 + - - +
5042z LEU 3.2 0.3 + - - -
5043z GLY* 3.2 2.8 + - - +
5044z SER* 2.9 43.4 + - - +
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Residues in contact with PHE5041 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5037z LYS 3.4 12.5 + - - +
5038z GLN* 2.8 17.6 + - - +
5040z ILE* 1.3 76.9 - - - +
5042z LEU* 1.3 63.2 + - - +
5044z SER* 4.1 6.7 - - - -
5045z GLY* 3.2 24.4 + - - -
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Residues in contact with LEU5042 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5015z LEU* 6.2 0.2 - - + -
5038z GLN 3.1 6.4 + - - +
5039z LEU* 2.8 27.0 + - + +
5041z PHE* 1.3 78.3 - - - +
5043z GLY* 1.3 67.0 + - - +
5044z SER 3.3 0.3 + - - -
5046z LEU* 2.8 53.6 + - + +
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Residues in contact with GLY5043 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5015z LEU* 4.1 11.3 - - - +
5019z MET* 3.3 29.6 - - - -
5039z LEU 3.0 7.6 + - - -
5040z ILE 3.2 1.3 + - - -
5042z LEU* 1.3 83.0 - - - +
5044z SER* 1.3 53.0 + - - +
5046z LEU* 4.3 1.1 - - - -
5047z TRP* 2.6 39.2 + - - +
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Residues in contact with SER5044 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5127c PHE* 4.0 24.3 - - - -
5019z MET* 3.7 7.7 - - - +
5040z ILE* 2.9 26.4 + - - +
5041z PHE* 4.0 8.7 - - - -
5043z GLY* 1.3 72.1 - - - +
5045z GLY* 1.3 69.1 + - - +
5047z TRP* 3.5 4.6 - - - +
5048z ILE* 3.1 27.3 + - - +
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Residues in contact with GLY5045 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5041z PHE* 3.2 17.3 + - - -
5042z LEU 3.9 0.9 - - - -
5044z SER* 1.3 80.7 - - - +
5046z LEU* 1.3 63.8 + - - +
5048z ILE* 3.1 10.3 + - - +
5049z ALA* 3.0 22.0 + - - +
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Residues in contact with LEU5046 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5015z LEU* 3.4 30.5 - - + -
5042z LEU* 2.8 47.9 + - + +
5043z GLY 3.7 0.9 - - - +
5045z GLY* 1.3 71.1 - - - +
5047z TRP* 1.3 62.1 + - - +
5049z ALA* 3.2 11.4 + - + +
5050z LEU* 2.8 34.5 + - + +
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Residues in contact with TRP5047 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5120c ILE* 3.6 27.4 - - + -
5123c ALA* 3.5 33.4 - - + -
5124c VAL* 5.3 7.4 - - + -
5504c BCR 4.3 16.7 - - + +
5012z LEU* 3.3 17.1 - - + +
5015z LEU* 3.7 17.5 - - + -
5016z SER* 2.5 41.8 + - - -
5019z MET* 4.6 9.0 - - + -
5043z GLY 2.6 23.8 + - - +
5044z SER* 3.5 6.3 - - - +
5046z LEU* 1.3 72.9 - - - +
5048z ILE* 1.3 76.8 + - + +
5050z LEU* 2.9 8.3 + - - +
5051z VAL* 2.9 50.4 + - + +
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Residues in contact with ILE5048 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5044z SER* 3.2 18.8 - - - +
5045z GLY* 3.1 9.8 + - - +
5047z TRP* 1.3 89.2 - - + +
5049z ALA* 1.3 68.8 + - - +
5051z VAL* 3.3 5.3 + - - +
5052z LEU* 2.9 40.9 + - + +
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Residues in contact with ALA5049 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5045z GLY 3.0 9.8 + - - +
5046z LEU* 3.5 14.8 - - + +
5048z ILE* 1.3 78.0 - - - +
5050z LEU* 1.3 52.8 + - - +
5052z LEU* 2.8 13.9 + - - +
5053z VAL* 2.6 44.6 + - + +
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Residues in contact with LEU5050 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5008z ALA* 3.7 28.3 - - + +
5011z ALA* 4.0 13.0 - - + -
5012z LEU* 3.6 30.5 - - + +
5015z LEU* 3.4 31.9 - - + -
5046z LEU* 2.8 26.6 + - + +
5047z TRP* 3.0 9.4 - - - +
5049z ALA* 1.3 71.1 - - - +
5051z VAL* 1.3 65.2 + - - +
5053z VAL* 2.9 13.5 + - + +
5054z VAL* 2.8 28.4 + - - +
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Residues in contact with VAL5051 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5120c ILE* 4.0 29.4 - - + -
5505c BCR 4.0 23.5 - - + +
5012z LEU* 3.8 27.3 - - + +
5047z TRP* 2.9 52.4 + - + +
5048z ILE* 3.4 8.1 - - + +
5050z LEU* 1.3 71.1 - - - +
5052z LEU* 1.3 68.2 + - + +
5054z VAL* 3.0 4.8 + - - +
5055z GLY* 2.8 21.8 + - - -
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Residues in contact with LEU5052 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5505c BCR 4.5 22.4 - - + -
5048z ILE* 2.9 35.6 + - + +
5049z ALA* 2.8 12.6 + - - +
5051z VAL* 1.3 74.4 - - + +
5053z VAL* 1.3 63.7 + - + +
5055z GLY* 3.5 2.4 + - - +
5056z VAL* 3.4 25.3 + - - +
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Residues in contact with VAL5053 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5004z LEU* 6.0 2.5 - - + -
5008z ALA* 4.8 8.3 - - + -
5049z ALA* 2.6 34.1 + - + +
5050z LEU* 3.2 13.9 - - + +
5052z LEU* 1.3 73.0 - - + +
5054z VAL* 1.3 58.3 - - + +
5056z VAL* 3.2 7.3 + - - +
5057z LEU* 2.9 46.0 + - + +
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Residues in contact with VAL5054 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5504c BCR 5.6 1.3 - - + -
5505c BCR 3.8 15.5 - - + -
5015k TYR* 4.7 2.2 - - + +
5005z PHE* 3.4 22.7 - - + -
5008z ALA* 4.1 9.9 - - + +
5009z LEU* 3.5 46.0 - - + +
5012z LEU* 4.3 13.0 - - + -
5050z LEU* 2.8 20.2 + - + +
5051z VAL* 3.7 7.4 - - - +
5053z VAL* 1.3 70.5 - - - +
5055z GLY* 1.3 67.1 + - - +
5057z LEU* 3.8 7.1 - - - +
5058z ASN* 2.9 22.5 + - - +
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Residues in contact with GLY5055 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5505c BCR 3.3 33.6 - - - +
5051z VAL 2.8 15.0 + - - -
5052z LEU* 3.5 3.3 + - - -
5054z VAL* 1.3 79.6 - - - +
5056z VAL* 1.3 60.6 + - - +
5058z ASN* 3.2 15.8 - - - +
5059z PHE* 3.2 18.0 - - - -
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Residues in contact with VAL5056 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5052z LEU 3.4 13.9 + - - +
5053z VAL* 3.2 7.9 + - - +
5055z GLY* 1.3 73.4 - - - +
5057z LEU* 1.3 65.1 + - + +
5059z PHE* 3.1 30.2 + - + +
5060z PHE* 3.5 29.4 + - + -
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Residues in contact with LEU5057 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5001z MET* 3.9 19.7 - - + -
5004z LEU* 3.3 34.3 - - + -
5005z PHE* 3.2 46.4 - - + +
5008z ALA* 3.7 16.6 - - + -
5053z VAL* 2.9 32.2 + - + +
5054z VAL* 3.8 1.6 - - - +
5056z VAL* 1.3 74.2 - - + +
5058z ASN* 1.3 65.1 + - - +
5060z PHE* 3.1 18.2 + - + +
5061z VAL* 3.1 20.6 + - - +
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Residues in contact with ASN5058 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5109c PHE* 4.0 14.1 - - - -
5112c PHE* 3.9 5.1 - - - -
5505c BCR 3.7 19.2 - - + +
5012k PRO* 5.7 0.2 - - - +
5015k TYR* 2.6 42.9 + - - +
5005z PHE* 4.1 9.3 - - - -
5054z VAL 2.9 11.5 + - - +
5055z GLY 3.2 14.4 - - - +
5056z VAL 3.1 0.4 - - - -
5057z LEU* 1.3 76.9 - - - +
5059z PHE* 1.3 78.3 + - - +
5061z VAL* 2.9 18.7 + - - +
5062z VAL* 2.9 24.7 + - - +
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Residues in contact with PHE5059 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5109c PHE* 4.2 18.6 - + - -
5505c BCR 4.3 26.7 - - + -
5055z GLY 3.2 28.3 - - - -
5056z VAL* 3.1 18.5 + - + +
5058z ASN* 1.3 90.3 + - - +
5060z PHE* 1.3 67.5 + - + +
5061z VAL 3.1 0.7 + - - -
5062z VAL 4.1 12.7 - - - +
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Residues in contact with PHE5060 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5001z MET* 3.4 47.3 - - + +
5056z VAL* 3.5 36.3 + - + -
5057z LEU* 3.1 17.9 + - + +
5059z PHE* 1.3 80.5 - - + +
5061z VAL* 1.3 60.4 + - - +
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Residues in contact with VAL5061 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5014k ALA* 3.6 29.6 - - + +
5001z MET* 4.7 8.5 - - + -
5002z THR* 4.4 16.4 - - - +
5005z PHE* 3.8 28.9 - - + -
5057z LEU 3.1 17.3 - - - +
5058z ASN* 2.9 7.2 + - - +
5060z PHE* 1.3 85.4 - - - +
5062z VAL* 1.3 68.3 + - - +
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Residues in contact with VAL5062 (chain z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5109c PHE* 5.5 7.2 - - + -
5012k PRO* 4.8 19.1 - - + -
5014k ALA* 6.3 0.9 - - + -
5015k TYR* 5.7 1.3 - - + -
5058z ASN* 2.9 31.6 + - - +
5059z PHE* 4.1 12.4 - - - +
5061z VAL* 1.3 84.3 - - - +
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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