Contacts of the helix formed by residues 850 - 872 (chain A) in PDB entry 1QXP
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 ASP 850 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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759A LEU* 5.6 9.4 - - + -
812A GLY 5.6 6.3 - - - -
848A ASN* 4.8 4.6 - - + +
849A MET* 1.4 71.1 - - - +
851A PHE* 1.3 68.2 + - - +
852A ASP* 2.8 12.5 + - + +
853A ASN* 2.8 39.4 + - - +
854A PHE* 2.9 12.4 + - - +
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Residues in contact with PHE 851 (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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749A LEU* 5.5 3.4 - - + -
759A LEU* 4.6 29.7 - - + +
760A LYS* 4.0 26.0 - - + -
764A PHE* 3.3 41.7 - + - -
796A ILE* 5.6 5.4 - - + -
800A GLN* 3.2 50.0 - - + -
812A GLY 5.8 0.2 + - - -
850A ASP* 1.3 73.0 - - - +
852A ASP* 1.4 53.4 + - - +
854A PHE* 2.8 10.3 + + - -
855A ILE* 2.7 62.4 + - + +
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Residues in contact with ASP 852 (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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763A GLY* 3.5 35.6 + - - +
764A PHE* 3.9 22.8 - - + +
768A THR* 4.5 15.8 + - - +
850A ASP* 3.5 11.1 - - + +
851A PHE* 1.4 74.8 - - - +
853A ASN* 1.3 80.7 + - - +
856A SER* 3.5 19.8 + - - -
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Residues in contact with ASN 853 (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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836A SER 5.2 5.7 - - - +
849A MET* 3.0 25.2 - - + +
850A ASP* 2.8 22.1 + - - +
852A ASP* 1.3 105.5 + - - +
854A PHE* 1.3 62.8 + - - -
856A SER* 3.9 4.0 - - - -
857A CYS* 3.0 14.2 + - - +
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Residues in contact with PHE 854 (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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799A TRP* 3.8 17.3 - - + -
800A GLN 4.7 3.8 - - - -
802A ILE* 3.1 45.3 - - + -
822A ALA* 4.1 12.6 - - + -
823A PHE* 3.2 39.9 - + - -
826A ALA* 5.5 2.5 - - + -
849A MET* 3.6 21.1 - - + -
850A ASP 2.9 9.8 + - - +
851A PHE* 2.8 18.9 + + - +
853A ASN* 1.3 74.4 - - - +
855A ILE* 1.3 65.9 - - + +
856A SER 3.1 0.4 - - - -
857A CYS* 2.9 7.8 - - - +
858A LEU* 2.8 38.2 + - + +
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Residues in contact with ILE 855 (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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749A LEU* 5.7 0.7 - - + -
764A PHE* 3.8 24.0 - - + -
772A MET* 4.4 16.4 - - + -
796A ILE* 4.1 24.9 - - + +
799A TRP* 3.9 33.5 - - + +
851A PHE* 2.7 55.1 + - + +
854A PHE* 1.3 83.7 - - + +
856A SER* 1.3 63.7 + - - +
857A CYS 3.2 0.2 - - - -
858A LEU* 3.8 7.5 + - - +
859A VAL* 3.3 19.6 - - + +
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Residues in contact with SER 856 (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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764A PHE* 5.3 0.7 - - - -
768A THR* 4.1 24.0 - - - -
772A MET* 4.9 9.8 - - - +
852A ASP* 3.5 18.1 + - - -
853A ASN* 4.6 3.1 - - - -
854A PHE 3.1 0.8 - - - -
855A ILE* 1.3 82.8 - - - +
857A CYS* 1.3 63.7 + - - +
859A VAL* 3.6 7.8 + - - +
860A ARG* 3.0 31.2 + - - +
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Residues in contact with CYS 857 (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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823A PHE* 3.5 29.2 - - + -
849A MET* 4.0 11.7 - - + -
853A ASN 3.0 14.1 + - - +
854A PHE 2.9 15.2 + - - +
856A SER* 1.3 77.0 - - - +
858A LEU* 1.4 50.6 + - - +
859A VAL 2.7 16.5 + - - -
860A ARG* 3.1 7.6 + - - +
861A LEU* 2.9 28.7 + - - +
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Residues in contact with LEU 858 (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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799A TRP* 2.3 76.9 - - + +
823A PHE* 5.7 5.4 - - + -
826A ALA* 5.6 2.0 - - + -
828A PHE* 4.4 8.3 - - + -
854A PHE* 2.8 24.9 + - + +
855A ILE 3.8 2.1 - - - +
856A SER 3.3 0.8 - - - -
857A CYS* 1.4 76.3 - - + +
859A VAL* 1.3 51.5 + - - +
861A LEU* 4.0 10.1 - - - +
862A ASP* 3.4 8.5 - - - +
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Residues in contact with VAL 859 (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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772A MET* 4.1 29.8 - - + -
775A VAL* 4.3 15.9 - - + +
776A MET* 5.1 6.2 - - + +
792A LEU* 3.5 27.6 - - + -
799A TRP* 3.2 27.6 - - + -
855A ILE* 3.3 18.2 - - + +
856A SER* 3.8 7.0 - - - +
857A CYS 2.8 0.6 - - - -
858A LEU* 1.3 77.5 - - - +
860A ARG* 1.3 69.0 - - + +
861A LEU 3.3 1.3 - - - -
862A ASP* 3.9 2.1 - - - +
863A ALA* 3.0 24.6 + - - +
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Residues in contact with ARG 860 (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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700A SER 4.3 17.6 + - - +
701A VAL* 4.3 14.3 - - - +
771A SER* 3.6 22.2 + - - +
772A MET* 6.0 2.5 - - + -
775A VAL* 4.7 9.6 - - + +
856A SER* 3.0 25.8 - - - +
857A CYS* 4.1 5.2 - - - +
859A VAL* 1.3 85.0 - - + +
861A LEU* 1.4 64.6 + - - +
863A ALA* 3.9 6.1 - - - +
864A MET* 3.0 25.8 + - - +
893A SER* 3.3 35.3 + - - -
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Residues in contact with LEU 861 (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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697A LEU* 4.9 16.8 - - + +
823A PHE* 3.7 32.3 - - + -
828A PHE* 3.9 14.6 - - + -
830A LEU* 3.8 22.9 - - + -
857A CYS* 2.9 19.2 + - - +
858A LEU* 4.8 3.4 - - - -
860A ARG* 1.4 79.0 - - - +
862A ASP* 1.3 67.2 + - - +
864A MET* 3.2 2.5 + - + +
865A PHE* 3.1 50.1 + - + +
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Residues in contact with ASP 862 (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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776A MET* 5.6 2.4 - - - +
791A TYR* 3.4 33.9 + - - -
795A ASN* 4.0 10.0 - - - +
799A TRP* 4.0 5.8 - - + -
828A PHE* 3.6 23.2 - - + -
858A LEU 3.4 20.0 + - - +
859A VAL* 3.8 3.3 + - - +
861A LEU* 1.3 81.5 - - - +
863A ALA* 1.3 65.1 + - - +
865A PHE* 3.3 3.5 + - - +
866A ARG* 3.1 22.7 + - - +
869A ARG* 4.6 8.1 + - - -
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Residues in contact with ALA 863 (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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2A ALA* 5.0 9.8 - - - +
775A VAL* 3.3 34.3 - - + +
776A MET* 5.8 2.6 - - - -
859A VAL 3.0 21.3 + - - +
860A ARG* 3.9 7.0 - - - +
862A ASP* 1.3 77.5 - - - +
864A MET* 1.2 66.4 + - + +
866A ARG* 3.5 5.0 + - - +
867A ALA* 3.1 21.5 + - - +
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Residues in contact with MET 864 (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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696A TRP* 2.9 36.7 + - + +
697A LEU* 4.8 7.6 - - + -
700A SER* 3.6 28.0 - - - +
860A ARG 3.0 20.9 + - - +
861A LEU* 3.2 2.9 + - + +
863A ALA* 1.2 81.0 - - + +
865A PHE* 1.3 57.8 + - - +
867A ALA* 3.6 7.2 - - - -
868A PHE* 3.2 12.1 + - - +
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Residues in contact with PHE 865 (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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693A LEU* 6.0 3.1 - - + -
697A LEU* 3.8 33.7 - - + -
828A PHE* 3.9 24.2 - + + -
829A HIS 6.2 0.4 - - - -
830A LEU* 4.9 10.1 - - + -
861A LEU* 3.1 46.6 + - + +
862A ASP* 3.4 6.1 - - - +
864A MET* 1.3 75.8 - - - +
866A ARG* 1.3 60.8 + - - +
867A ALA 3.1 0.7 - - - -
868A PHE* 3.1 22.5 + - + +
869A ARG* 3.2 29.2 + - + +
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Residues in contact with ARG 866 (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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2A ALA* 5.3 15.9 - - + +
6A MET* 5.9 3.4 - - - -
791A TYR* 5.8 1.8 - - - +
862A ASP* 3.1 16.5 + - - +
863A ALA* 4.1 5.4 - - - +
865A PHE* 1.3 70.4 - - - +
867A ALA* 1.3 57.6 + - - +
869A ARG* 3.0 32.8 + - - +
870A SER* 2.7 41.6 + - - +
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Residues in contact with ALA 867 (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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2A ALA 5.6 2.2 + - - +
5A ALA* 3.8 27.4 - - + -
696A TRP* 4.3 17.5 - - + +
863A ALA 3.1 17.7 + - - +
864A MET* 3.7 10.3 - - - +
865A PHE 3.1 0.2 - - - -
866A ARG* 1.3 76.3 - - - +
868A PHE* 1.2 70.0 + - - +
870A SER* 4.0 0.9 - - - -
871A LEU* 3.4 28.1 + - + +
889A LEU* 4.7 6.1 - - + -
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Residues in contact with PHE 868 (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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692A ASP* 3.5 5.4 - - - -
693A LEU* 3.0 50.0 - - + -
696A TRP* 3.4 32.5 - + + +
697A LEU* 6.1 1.3 - - + -
864A MET 3.2 9.2 + - - +
865A PHE* 3.1 15.5 + + + +
867A ALA* 1.2 84.7 - - - +
869A ARG* 1.3 74.8 + - + +
872A ASP* 2.9 32.4 + - + +
877A GLY* 3.7 20.6 - - - -
879A ILE* 3.8 31.4 - - + +
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Residues in contact with ARG 869 (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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791A TYR* 5.3 4.0 + - - -
862A ASP* 4.6 8.5 + - - -
865A PHE* 3.2 33.1 + - + +
866A ARG* 3.0 37.7 + - - +
868A PHE* 1.3 80.3 - - + +
870A SER* 1.4 56.8 + - - +
871A LEU 2.6 14.6 + - - -
872A ASP* 2.6 29.0 + - - +
873A LYS* 3.2 2.8 + - - -
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Residues in contact with SER 870 (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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2A ALA 4.6 2.1 + - - -
5A ALA* 4.3 10.0 - - - +
6A MET* 3.8 35.2 + - - -
9A ALA* 4.3 15.0 - - - +
866A ARG 2.7 23.9 + - - -
867A ALA* 4.0 5.3 - - - -
869A ARG* 1.4 76.8 - - - +
871A LEU* 1.3 75.7 + - - +
873A LYS* 3.7 15.2 - - - +
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Residues in contact with LEU 871 (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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5A ALA* 3.9 32.3 - - + +
8A LEU* 4.5 14.8 - - + -
9A ALA* 4.5 9.9 - - + +
12A ARG* 3.7 30.2 + - - +
696A TRP* 6.1 0.4 - - + -
867A ALA* 3.4 20.3 + - + +
869A ARG 2.6 5.1 + - - -
870A SER* 1.3 85.8 - - - +
872A ASP* 1.3 57.0 + - - +
873A LYS* 3.1 8.2 + - - +
879A ILE* 3.6 35.4 - - + -
881A VAL* 5.7 3.1 - - + -
889A LEU* 4.6 16.8 - - + -
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Residues in contact with ASP 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868A PHE* 2.9 18.5 + - + +
869A ARG* 2.6 17.3 + - - +
871A LEU* 1.3 69.3 - - - +
873A LYS* 1.4 61.5 - - - +
874A ASN 3.4 0.9 - - - -
875A GLY* 3.3 21.3 + - - -
876A THR* 3.1 36.4 + - - +
877A GLY* 3.4 13.9 + - - -
878A GLN 3.8 5.9 - - - +
879A ILE* 3.3 22.7 - - + +
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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