Contacts of the helix formed by residues 6486 - 6507 (chain F) in PDB entry 2H7C
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 SER6486 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6451F TYR* 4.0 5.2 + - - -
6454F SER* 5.7 0.4 - - - -
6484F GLY 3.6 3.2 + - - -
6485F ALA* 1.3 76.6 - - - +
6487F GLU* 1.3 64.1 + - - +
6488F GLU* 3.6 10.2 + - - +
6489F GLU* 3.1 26.2 + - - +
6490F ILE* 3.0 22.6 + - - +
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Residues in contact with GLU6487 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6486F SER* 1.3 74.3 - - - +
6488F GLU* 1.3 63.5 + - - +
6490F ILE* 3.4 22.5 + - - +
6491F ARG* 3.0 59.5 + - - +
6494F LYS* 5.8 1.7 + - - -
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Residues in contact with GLU6488 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6451F TYR* 3.1 29.4 + - + +
6486F SER* 3.6 8.3 + - - +
6487F GLU* 1.3 81.3 - - - +
6489F GLU* 1.3 56.5 + - - +
6491F ARG* 3.5 8.5 + - - +
6492F LEU* 3.0 27.0 + - + +
6531F ALA* 3.7 31.1 - - + +
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Residues in contact with GLU6489 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6451F TYR* 3.8 21.3 - - + +
6453F PRO* 3.1 18.9 - - - +
6454F SER* 2.7 48.6 + - - -
6455F PHE* 3.5 14.0 - - + -
6473F PHE* 5.4 0.3 - - - +
6474F SER* 5.3 3.4 + - - +
6479F PRO* 3.9 11.1 - - + +
6485F ALA* 3.6 11.9 - - + -
6486F SER* 3.1 23.2 + - - +
6488F GLU* 1.3 75.4 - - - +
6490F ILE* 1.3 65.1 + - - +
6492F LEU* 3.3 7.4 + - + +
6493F SER* 3.1 22.2 + - - -
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Residues in contact with ILE6490 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6479F PRO* 4.0 17.7 - - + +
6480F PHE* 3.7 26.6 - - + -
6485F ALA* 4.0 24.0 - - + +
6486F SER 3.0 19.7 + - - +
6487F GLU* 3.4 28.5 + - - +
6489F GLU* 1.3 75.6 - - - +
6491F ARG* 1.3 64.9 + - + +
6493F SER* 3.2 5.7 + - - -
6494F LYS* 3.1 34.7 + - - +
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Residues in contact with ARG6491 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6487F GLU* 3.0 48.6 + - - +
6488F GLU* 3.8 7.4 - - - +
6490F ILE* 1.3 78.2 - - + +
6492F LEU* 1.3 64.5 + - - +
6494F LYS* 3.4 13.5 + - + +
6495F MET* 3.1 23.0 + - - +
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Residues in contact with LEU6492 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6449F PHE* 4.0 8.7 - - + -
6451F TYR* 3.6 46.4 - - + -
6474F SER* 3.6 18.8 - - - +
6488F GLU* 3.0 17.4 + - + +
6489F GLU* 3.3 6.7 + - + +
6491F ARG* 1.3 75.2 - - - +
6493F SER* 1.3 63.2 + - - +
6495F MET* 3.2 25.1 + - + +
6496F VAL* 2.9 29.8 + - + +
6529F ILE* 3.9 13.7 - - + -
6530F GLY 3.6 23.6 - - - +
6531F ALA* 6.2 1.1 - - - -
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Residues in contact with SER6493 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6474F SER* 3.0 31.7 + - - +
6477F GLY* 3.3 21.0 - - - -
6479F PRO* 3.8 17.9 - - - +
6480F PHE* 3.7 5.1 - - - -
6489F GLU 3.1 12.1 + - - -
6490F ILE 3.5 8.1 - - - -
6492F LEU* 1.3 77.1 - - - +
6494F LYS* 1.3 63.5 + - - +
6496F VAL* 3.2 1.2 + - - -
6497F MET* 2.9 31.3 + - - +
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Residues in contact with LYS6494 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6160F HIS* 4.8 10.8 - - + +
6161F GLU* 4.6 1.9 - - - +
6480F PHE* 3.4 38.1 - - + -
6487F GLU* 5.8 1.6 + - - -
6490F ILE* 3.1 19.1 + - + +
6491F ARG* 3.7 15.8 - - + +
6492F LEU 3.3 0.2 - - - -
6493F SER* 1.3 77.4 - - - +
6495F MET* 1.3 62.2 + - - +
6497F MET* 3.6 11.8 + - + +
6498F LYS* 3.1 31.3 + - - +
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Residues in contact with MET6495 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6491F ARG 3.1 13.3 + - - +
6492F LEU* 3.5 17.7 - - + +
6494F LYS* 1.3 74.7 - - - +
6496F VAL* 1.3 64.8 + - + +
6498F LYS* 3.4 2.8 + - - +
6499F PHE* 2.9 48.3 + - + +
6514F LEU* 3.8 20.9 - - + +
6515F PRO* 4.0 23.3 - - + -
6529F ILE* 3.8 23.3 - - + -
6533F THR* 3.1 32.8 - - + +
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Residues in contact with VAL6496 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6449F PHE* 4.7 3.8 - - + -
6471F GLU* 6.1 0.7 - - + -
6474F SER* 3.9 18.2 - - - +
6475F VAL* 3.6 37.9 - - + +
6492F LEU* 2.9 25.3 + - + +
6493F SER 3.7 2.7 - - - +
6495F MET* 1.3 75.5 - - + +
6497F MET* 1.3 66.9 + - - +
6499F PHE* 3.1 7.2 + - - -
6500F TRP* 2.9 41.0 + - + +
6529F ILE* 4.1 28.0 - - + -
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Residues in contact with MET6497 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6156F ALA 4.2 0.9 - - - +
6157F LEU* 3.9 38.1 - - + +
6160F HIS* 3.9 22.4 - - + +
6161F GLU* 3.4 10.3 - - + +
6474F SER 3.5 5.6 - - - +
6475F VAL* 3.4 19.1 - - - +
6477F GLY* 3.7 18.8 - - - -
6480F PHE* 3.6 34.3 - - + -
6493F SER* 2.9 25.4 + - - +
6494F LYS* 4.0 8.3 - - - +
6496F VAL* 1.3 73.1 - - - +
6498F LYS* 1.3 57.1 + - - +
6500F TRP* 3.4 4.9 + - - +
6501F ALA* 2.8 32.2 + - - +
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Residues in contact with LYS6498 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6160F HIS 5.0 1.2 + - - -
6161F GLU* 3.0 34.1 + - - +
6494F LYS* 3.1 22.0 + - - +
6495F MET* 3.7 4.0 - - - +
6496F VAL 3.2 0.2 - - - -
6497F MET* 1.3 73.8 - - - +
6499F PHE* 1.3 61.5 + - - +
6502F ASN* 2.9 45.7 + - - +
6505F ARG* 4.7 0.4 - - - +
6512F GLU 4.7 8.7 - - - +
6513F GLY 6.0 0.2 - - - -
6514F LEU* 3.8 32.1 - - + -
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Residues in contact with PHE6499 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6347F MET* 5.0 0.2 - - - -
6495F MET* 2.9 47.9 + - + -
6496F VAL* 3.1 8.7 + - - +
6498F LYS* 1.3 77.2 - - - +
6500F TRP* 1.3 74.8 + - + +
6503F PHE* 3.0 23.9 + - - +
6509F PRO* 3.2 31.5 - - + +
6510F ASN* 4.6 2.5 - - - -
6514F LEU* 3.7 21.1 - - + -
6515F PRO* 3.3 31.6 - - + -
6517F TRP* 3.8 31.0 - + + -
6527F LEU* 3.5 26.2 - - + -
6529F ILE* 5.1 3.8 - - + -
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Residues in contact with TRP6500 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6136F MET* 3.7 13.5 - - + +
6157F LEU* 5.5 3.4 - - + -
6218F PHE* 4.0 11.4 - + - -
6244F ILE* 3.7 19.2 - - + +
6246F GLU* 3.0 25.7 + - + -
6347F MET* 3.8 21.1 - - + -
6447F TYR* 3.5 41.3 - + - -
6449F PHE* 6.5 0.4 - + - -
6471F GLU* 5.4 1.6 - - + -
6475F VAL* 3.7 35.3 - - + +
6496F VAL* 2.9 37.2 + - + +
6497F MET* 3.7 6.7 - - - +
6499F PHE* 1.3 84.1 - - + +
6501F ALA* 1.3 56.8 + - - +
6503F PHE* 3.2 9.0 + - - +
6504F ALA* 2.9 26.3 + - - +
6517F TRP* 4.0 16.2 - + - -
6529F ILE* 4.2 12.3 - - + -
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Residues in contact with ALA6501 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6136F MET* 4.4 6.7 - - - +
6157F LEU* 5.3 0.7 - - + -
6161F GLU* 3.3 31.4 - - + +
6163F VAL* 4.1 8.3 - - + +
6497F MET 2.8 21.5 + - - +
6498F LYS 4.1 0.2 - - - +
6500F TRP* 1.3 70.6 - - - +
6502F ASN* 1.3 65.6 + - - +
6504F ALA* 3.2 10.6 + - - +
6505F ARG* 3.0 42.2 + - - +
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Residues in contact with ASN6502 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6498F LYS* 2.9 29.6 + - - +
6499F PHE 3.7 0.2 - - - +
6501F ALA* 1.3 75.5 - - - +
6503F PHE* 1.3 58.7 + - - +
6505F ARG* 2.9 29.7 + - - +
6506F ASN* 2.8 35.6 + - - +
6508F ASN 3.1 9.8 - - - +
6509F PRO 3.1 30.2 + - - +
6510F ASN 3.7 10.6 + - - +
6511F GLY* 3.8 6.6 - - - -
6514F LEU* 3.3 19.4 - - - +
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Residues in contact with PHE6503 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6216F THR* 4.7 1.6 - - + -
6242F ARG* 3.6 22.1 - - + +
6243F ALA 3.4 18.2 - - - -
6244F ILE* 3.7 23.3 - - + -
6345F PRO* 3.5 29.8 - - + -
6347F MET* 3.7 28.9 - - + -
6445F TYR* 3.8 18.8 - + - -
6499F PHE 3.0 13.4 + - - +
6500F TRP* 3.4 9.0 - - - +
6501F ALA 3.2 0.2 - - - -
6502F ASN* 1.3 78.2 - - - +
6504F ALA* 1.3 58.6 + - - +
6507F GLY* 2.7 53.4 + - - -
6508F ASN 3.5 9.1 + - - -
6509F PRO* 4.0 13.5 - - + -
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Residues in contact with ALA6504 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6134F PRO* 4.5 13.0 - - + +
6136F MET* 3.9 26.7 - - + -
6163F VAL* 5.1 0.4 - - + -
6214F SER* 3.4 10.0 + - - -
6216F THR* 3.2 23.2 + - - +
6242F ARG* 2.6 27.5 + - - -
6500F TRP 2.9 12.4 + - - +
6501F ALA* 3.3 10.8 - - - +
6502F ASN 3.2 0.2 - - - -
6503F PHE* 1.3 77.6 - - - +
6505F ARG* 1.3 55.3 + - - +
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Residues in contact with ARG6505 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6134F PRO* 4.3 22.3 - - + +
6161F GLU* 2.7 51.7 + - - -
6162F ASN* 4.5 3.4 + - - +
6163F VAL* 4.2 4.6 - - - +
6214F SER* 4.5 4.7 + - - -
6242F ARG* 2.9 13.1 + - - -
6498F LYS* 4.3 1.8 + - - +
6501F ALA* 3.0 25.9 + - - +
6502F ASN* 2.9 30.8 + - - +
6504F ALA* 1.3 77.5 - - - +
6506F ASN* 1.3 77.4 + - - +
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Residues in contact with ASN6506 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6242F ARG* 3.3 11.0 + - - +
6345F PRO* 5.4 0.2 - - - +
6502F ASN* 2.8 29.7 + - - +
6505F ARG* 1.3 93.0 - - - +
6507F GLY* 1.3 60.1 + - - +
6508F ASN* 3.1 18.9 + - + +
6510F ASN 5.0 5.7 + - - -
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Residues in contact with GLY6507 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6242F ARG* 3.5 8.3 - - - +
6345F PRO* 3.6 35.5 - - - +
6443F PRO* 4.6 4.2 - - - +
6445F TYR* 3.6 16.3 + - - -
6503F PHE* 2.7 31.4 + - - -
6506F ASN* 1.3 73.9 - - - +
6508F ASN* 1.3 58.5 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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