Contacts of the helix formed by residues 807 - 827 (chain A) in PDB entry 2RD0
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 LEU 807 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802A LYS* 4.1 27.6 - - + +
805A ASP* 3.3 21.2 + - + +
806A ASP* 1.3 74.7 + - - +
808A ARG* 1.3 65.5 + - - +
809A GLN 3.2 1.6 + - - -
810A ASP* 3.4 20.7 + - - +
811A MET* 2.9 21.5 + - - +
838A CYS* 3.9 27.3 - - - -
839A LEU 5.0 0.9 - - - +
840A SER* 4.2 21.3 + - - +
844A CYS* 4.9 1.8 - - - +
845A VAL 3.9 3.1 - - - +
846A GLY* 3.7 34.5 - - - +
847A LEU 5.3 0.2 - - - +
848A ILE* 4.4 13.2 - - + -
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Residues in contact with ARG 808 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A SER* 5.4 2.2 - - - +
674A GLU* 3.5 31.5 + - - +
676A HIS* 5.8 5.1 + - - -
677A ASN* 5.7 2.8 + - - -
806A ASP* 2.8 34.3 + - - +
807A LEU* 1.3 76.3 - - - +
809A GLN* 1.3 64.8 - - - +
811A MET* 3.2 14.4 - - + +
812A LEU* 3.0 22.0 + - - +
840A SER* 4.1 20.6 - - - +
1005A MET* 5.8 3.0 - - + +
1008A SER* 4.7 3.9 - - - -
1009A GLY* 3.9 18.4 - - - +
1010A MET* 3.7 40.7 - - - +
1011A PRO* 4.9 3.2 - - - +
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Residues in contact with GLN 809 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806A ASP* 3.0 47.9 + - - +
808A ARG* 1.3 72.0 - - - +
810A ASP* 1.3 64.6 + - - +
812A LEU* 2.9 8.1 + - - +
813A THR* 2.9 26.6 + - - +
935A GLY* 3.8 23.3 + - - +
936A HIS* 6.1 1.0 - - - -
937A PHE* 4.1 15.0 - - + -
1010A MET* 3.8 17.3 - - + -
1011A PRO* 6.0 0.2 - - - -
1012A GLU* 3.1 41.0 + - + +
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Residues in contact with ASP 810 (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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802A LYS* 5.4 2.9 + - - -
805A ASP* 6.0 1.4 - - - +
806A ASP 4.9 4.1 - - - +
807A LEU* 3.4 22.9 - - + +
809A GLN* 1.3 76.8 - - - +
811A MET* 1.3 63.1 + - - +
813A THR* 3.1 7.5 + - - +
814A LEU* 2.9 34.5 + - + +
836A TYR* 5.6 1.8 - - - -
838A CYS* 4.4 12.6 - - - -
933A ASP* 4.1 15.5 - - - +
934A PHE* 3.3 20.0 + - - +
935A GLY* 3.2 28.8 + - - -
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Residues in contact with MET 811 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A ILE* 4.4 25.9 - - + +
670A HIS* 3.4 38.4 - - + +
673A SER* 6.0 1.3 - - - +
807A LEU 2.9 14.8 + - - +
808A ARG* 3.2 15.9 - - + +
810A ASP* 1.3 72.9 - - - +
812A LEU* 1.3 62.1 + - - +
814A LEU* 3.5 9.8 + - - +
815A GLN* 3.0 22.2 + - - +
818A ARG* 4.8 1.6 + - - -
838A CYS* 3.4 21.7 - - - +
839A LEU* 4.2 0.7 - - + -
840A SER* 3.5 41.5 - - - +
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Residues in contact with LEU 812 (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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633A ILE* 4.8 3.5 - - + +
634A GLN* 3.7 14.8 - - - +
808A ARG 3.0 10.4 + - - +
809A GLN* 2.9 12.6 + - - +
811A MET* 1.3 72.6 - - - +
813A THR* 1.3 59.4 + - - +
815A GLN* 3.1 25.2 + - - +
816A ILE* 3.0 50.1 + - + +
937A PHE* 3.2 33.9 - - + -
1001A LEU 5.2 1.6 - - - +
1002A PHE* 4.2 4.9 - - + -
1005A MET* 3.9 23.3 - - + -
1010A MET* 3.7 22.0 - - + -
1013A LEU* 4.0 4.5 - - + -
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Residues in contact with THR 813 (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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809A GLN* 2.9 24.6 + - + +
810A ASP* 3.1 9.8 + - - +
812A LEU* 1.3 72.6 - - - +
814A LEU* 1.3 63.6 + - - +
816A ILE* 3.1 9.5 + - - +
817A ILE* 2.9 29.3 + - - +
911A LEU* 4.9 6.5 - - - +
913A ILE* 4.2 12.4 - - + +
934A PHE* 3.6 35.1 - - + +
935A GLY 5.7 0.9 - - - +
937A PHE* 4.1 22.0 - - + +
1002A PHE* 6.5 0.7 - - - -
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Residues in contact with LEU 814 (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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810A ASP* 2.9 25.8 + - + +
811A MET* 3.8 3.1 - - - +
813A THR* 1.3 76.2 + - - +
815A GLN* 1.3 63.9 + - - +
817A ILE* 3.3 9.1 + - + +
818A ARG* 3.1 38.4 + - - +
834A LEU 4.8 0.2 - - - +
835A PRO* 3.6 9.3 - - + +
836A TYR* 3.6 49.6 - - + +
838A CYS* 3.2 35.9 - - + -
934A PHE* 3.5 27.6 - - + -
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Residues in contact with GLN 815 (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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630A GLN* 2.6 31.2 + - + +
631A TYR* 3.9 3.0 - - - +
633A ILE* 3.3 25.0 - - + +
634A GLN* 2.9 41.8 + - - +
811A MET 3.0 15.3 + - - +
812A LEU* 3.1 15.5 + - - +
814A LEU* 1.3 76.4 - - - +
816A ILE* 1.3 57.8 + - - +
818A ARG* 3.3 19.3 + - - +
819A ILE* 3.1 46.1 + - + +
1001A LEU* 5.1 1.1 - - - +
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Residues in contact with ILE 816 (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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812A LEU* 3.0 34.7 + - + +
813A THR* 3.1 8.7 + - - +
815A GLN* 1.3 75.1 - - + +
817A ILE* 1.3 60.1 + - - +
819A ILE* 3.2 8.4 + - + +
820A MET* 2.9 35.2 + - + +
911A LEU* 3.9 27.8 - - + -
998A PHE* 3.7 27.4 - - + -
1001A LEU* 4.9 12.1 - - + -
1002A PHE* 3.3 39.9 - - + -
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Residues in contact with ILE 817 (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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813A THR* 2.9 20.9 + - - +
814A LEU* 3.4 9.6 - - + +
816A ILE* 1.3 72.2 - - - +
818A ARG* 1.3 67.1 + - - +
820A MET* 3.2 8.7 + - - +
821A GLU* 2.9 22.0 + - - +
833A MET* 3.5 41.4 - - + +
835A PRO* 3.8 17.3 - - + -
904A TYR* 4.2 13.5 - - + +
907A ALA* 4.5 10.5 - - + -
911A LEU* 5.1 5.8 - - + -
913A ILE* 5.4 4.0 - - + -
934A PHE* 3.4 39.5 - - + -
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Residues in contact with ARG 818 (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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630A GLN* 5.8 7.4 - - + -
811A MET 4.8 1.2 + - - -
814A LEU* 3.1 43.8 + - - +
815A GLN* 3.3 17.7 - - - +
817A ILE* 1.3 76.1 - - - +
819A ILE* 1.3 65.9 + - + +
821A GLU* 3.2 10.2 + - + +
822A ASN* 2.9 34.4 + - - +
835A PRO* 3.7 37.5 + - + +
836A TYR 4.6 6.3 + - - -
837A GLY* 5.3 3.8 - - - -
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Residues in contact with ILE 819 (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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630A GLN* 3.2 39.9 - - + +
631A TYR* 4.3 13.9 - - + +
815A GLN* 3.1 51.2 + - + +
816A ILE* 3.2 7.5 + - - +
818A ARG* 1.3 76.3 - - + +
820A MET* 1.3 62.5 + - - +
822A ASN* 3.0 12.7 + - - +
823A ILE* 3.0 25.9 + - + +
997A LEU* 3.7 14.4 - - + -
998A PHE* 3.4 30.7 - - + -
1001A LEU* 4.4 9.6 - - + -
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Residues in contact with MET 820 (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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816A ILE* 2.9 35.6 + - + +
817A ILE* 3.5 8.3 - - - +
819A ILE* 1.3 74.8 - - - +
821A GLU* 1.3 64.0 + - - +
822A ASN 2.9 1.7 + - - -
823A ILE* 2.9 16.2 + - - +
824A TRP* 2.9 29.0 + - + -
833A MET* 5.7 0.4 - - + -
907A ALA* 3.7 29.8 - - + -
910A ILE* 4.0 23.6 - - + -
911A LEU* 4.3 11.9 - - + -
991A ILE* 3.8 47.1 - - + -
998A PHE* 3.8 11.4 - - + -
1022A ILE* 6.1 0.2 - - + -
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Residues in contact with GLU 821 (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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-23A HIS* 5.6 2.3 - - - -
817A ILE 2.9 16.6 + - - +
818A ARG* 3.4 13.0 - - + +
820A MET* 1.3 72.3 - - - +
822A ASN* 1.3 60.8 + - - +
824A TRP* 3.7 13.8 - - - +
825A GLN* 3.2 38.4 + - + +
831A LEU 3.6 1.8 - - - +
832A ARG* 3.3 15.9 - - - +
833A MET* 2.7 50.5 + - + +
835A PRO* 3.8 17.2 - - - +
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Residues in contact with ASN 822 (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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172A GLU* 4.4 18.5 + - - +
271A LYS* 6.1 1.2 - - - +
630A GLN* 3.4 34.8 + - - +
818A ARG* 2.9 20.6 + - - +
819A ILE* 3.0 9.4 + - - +
820A MET 2.9 0.2 + - - -
821A GLU* 1.3 78.0 - - - +
823A ILE* 1.3 69.4 + - + +
824A TRP 3.1 2.1 + - - -
825A GLN* 3.5 5.9 + - - +
826A ASN* 3.3 23.9 + - - +
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Residues in contact with ILE 823 (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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819A ILE* 3.0 45.1 + - + +
820A MET* 2.9 7.2 + - - +
822A ASN* 1.3 75.2 - - + +
824A TRP* 1.3 67.7 + - + +
826A ASN* 4.1 3.3 + - - +
827A GLN* 3.2 29.0 + - - +
990A ALA* 4.2 5.4 - - + +
991A ILE* 3.7 17.9 - - + -
994A HIS* 3.7 47.3 - - + +
997A LEU* 4.4 8.3 - - + -
998A PHE* 3.7 20.2 - - + -
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Residues in contact with TRP 824 (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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820A MET* 2.9 19.3 + - + -
821A GLU* 3.7 23.6 - - - +
823A ILE* 1.3 73.9 - - + +
825A GLN* 1.3 69.5 + - - +
827A GLN* 3.3 5.8 + - - +
828A GLY 3.2 4.2 + - - -
829A LEU* 3.0 47.4 + - + +
831A LEU* 3.6 24.9 - - + +
833A MET* 3.7 31.6 - - + -
903A GLY* 3.8 26.2 - - - -
906A VAL* 4.4 5.8 - - + -
907A ALA* 4.5 9.2 - - + -
987A ALA* 3.3 33.1 + - + +
990A ALA* 4.0 17.3 - - + -
991A ILE* 3.5 29.6 - - + +
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Residues in contact with GLN 825 (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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178A PRO* 3.5 21.3 - - + +
180A HIS* 3.1 34.1 + - + +
181A ILE* 5.0 5.8 - - + -
278A MET* 4.5 10.0 - - + -
821A GLU* 3.2 25.7 + - + +
822A ASN* 3.5 7.4 + - - +
824A TRP* 1.3 75.6 - - - +
826A ASN* 1.3 63.0 + - - +
828A GLY* 3.1 13.9 + - - -
829A LEU 4.9 0.4 - - - +
830A ASP* 3.2 25.1 + - - +
831A LEU 3.3 19.2 + - - +
832A ARG* 4.2 8.5 - - - +
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Residues in contact with ASN 826 (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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174A SER* 4.9 13.0 + - - -
178A PRO* 4.5 12.1 - - - +
822A ASN 3.3 14.4 + - - +
823A ILE* 4.1 2.7 + - - +
824A TRP 3.3 0.6 - - - -
825A GLN* 1.3 74.6 - - - +
827A GLN* 1.3 64.6 + - - +
828A GLY* 2.7 16.7 + - - -
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Residues in contact with GLN 827 (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 ILE* 3.2 21.2 + - + +
824A TRP* 3.3 6.0 + - - +
826A ASN* 1.3 85.8 - - - +
828A GLY* 1.3 54.8 + - - +
829A LEU* 3.1 19.9 + - + +
990A ALA* 3.3 26.5 - - - +
993A GLN* 2.9 29.0 + - - -
994A HIS* 3.0 25.5 + - + +
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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