Contacts of the helix formed by residues 817 - 839 (chain D) in PDB entry 3V53
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 GLU 817 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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777C LYS* 4.0 17.8 - - + +
815D LEU 3.1 0.2 + - - -
816D ASP* 1.3 77.4 - - + +
818D GLU* 1.3 60.3 + - - +
819D ALA 3.2 6.6 + - - -
820D GLU* 3.7 14.8 + - - +
821D VAL* 4.3 7.4 + - - +
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Residues in contact with GLU 818 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782D TYR* 3.7 32.5 + - + +
815D LEU* 3.0 15.2 + - + +
817D GLU* 1.3 77.1 - - - +
819D ALA* 1.3 58.4 + - - +
820D GLU 3.4 0.4 - - - -
821D VAL* 3.7 10.8 + - + +
822D PHE* 3.0 27.2 + - - +
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Residues in contact with ALA 819 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808D LEU* 4.7 4.7 - - + +
811D VAL* 3.8 7.9 - - + -
812D ALA* 3.4 32.8 - - + +
815D LEU* 3.7 18.7 + - + +
816D ASP 3.4 15.2 + - - +
817D GLU 3.2 1.0 - - - -
818D GLU* 1.3 76.7 - - - +
820D GLU* 1.3 60.6 + - - +
822D PHE* 3.2 6.5 + - - +
823D ILE* 2.9 33.8 + - - +
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Residues in contact with GLU 820 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749D LYS* 3.8 29.9 + - + +
808D LEU* 4.2 28.8 - - + +
816D ASP 4.5 1.2 + - - +
817D GLU 3.7 10.1 + - - +
818D GLU 3.4 0.4 - - - -
819D ALA* 1.3 75.8 - - - +
821D VAL* 1.3 65.9 + - + +
823D ILE* 4.1 0.7 - - - +
824D VAL* 3.0 38.1 + - + +
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Residues in contact with VAL 821 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782D TYR* 4.1 6.5 - - - +
817D GLU 4.3 9.1 + - - +
818D GLU* 3.7 11.3 + - + +
820D GLU* 1.3 76.9 - - + +
822D PHE* 1.3 65.3 + - - +
824D VAL* 3.8 4.3 - - - +
825D LYS* 2.9 59.5 + - + +
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Residues in contact with PHE 822 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774D TRP* 3.6 28.2 - + - -
775D ILE* 4.3 15.0 - - + -
778D LYS* 4.1 13.2 - - + -
779D ILE* 4.6 8.5 - - + -
782D TYR* 3.7 30.5 + + + -
794D VAL* 4.2 19.3 - - + -
811D VAL* 4.0 23.6 - - + -
815D LEU* 4.2 3.4 - - + -
818D GLU 3.0 16.3 + - - +
819D ALA* 3.3 8.3 - - - +
821D VAL* 1.3 78.1 - - - +
823D ILE* 1.3 90.6 + - + +
825D LYS* 3.3 5.1 + - - +
826D MET* 3.0 36.5 + - - +
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Residues in contact with ILE 823 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753D PHE* 3.8 24.0 - - + -
804D PRO* 3.9 23.3 - - + +
807D ILE* 3.5 30.3 - - + -
808D LEU* 3.8 28.5 - - + +
811D VAL* 4.8 3.1 - - + -
819D ALA 2.9 22.0 + - - +
820D GLU 4.3 1.1 - - - +
822D PHE* 1.3 95.7 - - + +
824D VAL* 1.3 62.5 + - - +
826D MET* 3.2 15.9 + - + +
827D TRP* 2.9 25.2 + - + +
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Residues in contact with VAL 824 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749D LYS* 4.3 26.7 - - + -
752D LEU* 3.7 23.1 - - + -
753D PHE* 4.3 5.4 - - + -
820D GLU* 3.0 29.7 + - + +
821D VAL* 3.8 4.9 - - - +
823D ILE* 1.3 74.5 - - - +
825D LYS* 1.3 67.1 + - + +
827D TRP* 2.9 15.1 + - - +
828D ARG* 2.9 29.0 + - - +
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Residues in contact with LYS 825 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774D TRP* 3.7 16.8 - - + -
778D LYS* 4.4 23.6 - - + +
781D GLU* 5.7 2.8 + - - -
782D TYR* 4.8 4.9 + - - +
821D VAL* 2.9 46.9 + - + +
822D PHE* 3.8 2.2 - - - +
824D VAL* 1.3 72.8 - - + +
826D MET* 1.3 56.5 - - - +
828D ARG* 3.1 18.2 + - - +
829D LEU* 2.9 27.5 + - - +
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Residues in contact with MET 826 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771D ILE* 5.1 2.7 - - + -
774D TRP* 3.4 27.9 - - + -
775D ILE* 4.2 14.1 - - + -
794D VAL* 3.9 23.3 - - + -
798D VAL* 4.0 16.4 - - + -
807D ILE* 4.4 3.4 - - + -
822D PHE* 3.0 22.2 + - + +
823D ILE* 3.5 27.6 - - + +
825D LYS* 1.3 76.0 - - - +
827D TRP* 1.3 90.1 + - + +
829D LEU* 3.3 9.4 + - + +
830D LEU* 2.9 32.2 + - + +
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Residues in contact with TRP 827 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752D LEU* 3.4 43.0 + - + -
753D PHE* 4.1 8.8 + + + -
755D TYR* 5.0 6.0 + - + +
757D LEU* 4.7 9.3 - - + +
759D TRP* 3.8 30.3 - + - -
798D VAL* 5.1 0.9 - - + -
802D SER 3.5 19.3 - - - -
804D PRO* 3.3 49.2 - - + +
807D ILE* 4.3 7.0 - - + -
823D ILE* 2.9 11.7 + - + +
824D VAL* 2.9 9.4 + - - +
826D MET* 1.3 104.4 - - + +
828D ARG* 1.3 66.2 + - - +
830D LEU* 3.4 16.3 + - + +
831D ILE* 3.1 39.4 + - + +
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Residues in contact with ARG 828 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742D ILE* 5.3 14.3 - - - +
745D ILE* 4.2 44.4 - - + +
746D PRO 5.3 1.6 + - - -
747D THR* 5.4 6.5 + - - +
752D LEU* 4.4 9.2 - - + +
824D VAL* 2.9 34.2 + - + +
825D LYS* 3.4 16.4 - - - +
827D TRP* 1.3 74.8 - - - +
829D LEU* 1.3 57.5 + - - +
831D ILE* 3.3 3.8 + - - +
832D TYR* 2.9 31.2 + - - +
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Residues in contact with LEU 829 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770D ARG* 3.6 33.4 - - + +
771D ILE* 4.4 24.9 - - + -
774D TRP* 3.7 47.6 - - + +
825D LYS 2.9 13.2 + - - +
826D MET* 3.4 10.8 - - + +
828D ARG* 1.3 75.6 - - - +
830D LEU* 1.3 62.5 + - + +
832D TYR* 3.3 5.0 + - + +
833D GLU* 3.0 52.3 + - + +
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Residues in contact with LEU 830 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757D LEU* 3.8 16.3 - - + +
759D TRP* 3.9 20.4 - - + -
762D VAL* 4.3 13.5 - - + -
766D LEU* 5.1 2.0 - - + +
771D ILE* 3.6 36.8 - - + -
798D VAL* 4.1 20.9 - - + -
826D MET* 2.9 22.1 + - + +
827D TRP* 3.4 37.4 + - + +
829D LEU* 1.3 76.5 - - + +
831D ILE* 1.3 57.8 + - - +
833D GLU* 4.5 1.7 - - - +
834D THR* 2.8 34.1 + - - +
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Residues in contact with ILE 831 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741D LEU 5.3 0.4 - - - +
744D LYS* 4.6 3.4 - - + +
745D ILE* 4.0 23.3 - - + +
746D PRO* 4.0 6.3 - - + -
752D LEU* 3.4 33.2 - - + -
755D TYR* 3.7 50.9 - - + +
757D LEU* 3.7 19.7 - - + -
827D TRP* 3.1 19.2 + - + +
828D ARG 3.7 2.9 - - - +
830D LEU* 1.3 73.5 - - - +
832D TYR* 1.3 64.4 + - - +
834D THR* 3.9 0.2 - - - -
835D GLU* 3.0 35.4 + - + +
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Residues in contact with TYR 832 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734D LYS* 2.7 52.1 + - + -
738D ILE* 3.4 23.3 - - + +
741D LEU* 3.6 37.4 - - + +
742D ILE* 3.7 22.9 - - + -
745D ILE* 3.9 21.1 - - + +
828D ARG 2.9 17.7 + - - +
829D LEU* 3.8 5.8 - - + +
831D ILE* 1.3 79.9 - - - +
833D GLU* 1.3 65.7 + - + +
835D GLU* 4.2 2.3 - - - +
836D ALA* 3.2 24.8 + - - +
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Residues in contact with GLU 833 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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734D LYS* 3.2 31.4 + - - +
766D LEU* 4.1 27.9 - - + +
770D ARG* 2.8 45.8 + - + +
771D ILE* 5.7 2.5 - - + -
829D LEU* 3.0 34.5 + - + +
830D LEU* 4.5 2.5 - - - +
832D TYR* 1.3 79.4 - - + +
834D THR* 1.3 63.7 + - - +
836D ALA* 3.4 5.0 + - - +
837D LYS* 3.2 23.6 + - - +
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Residues in contact with THR 834 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757D LEU* 3.5 23.3 - - + -
758D ASP* 3.5 15.8 + - + +
761D ILE* 3.5 37.2 - - - +
762D VAL* 4.2 11.8 - - - +
766D LEU* 4.9 4.6 - - - +
830D LEU 2.8 24.8 + - - +
831D ILE* 3.5 6.5 - - - +
832D TYR 3.3 0.2 - - - -
833D GLU* 1.3 80.1 - - - +
835D GLU* 1.3 74.1 + - + +
838D LYS* 3.4 20.5 + - + +
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Residues in contact with GLU 835 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741D LEU* 3.6 20.2 - - + +
744D LYS* 4.0 25.9 + - + +
755D TYR* 2.6 35.1 + - - +
756D PRO 5.3 1.4 - - - +
758D ASP* 5.3 2.9 + - - +
831D ILE* 3.0 27.4 + - + +
834D THR* 1.3 82.7 - - + +
836D ALA* 1.3 60.5 + - - +
837D LYS 3.3 0.9 - - - -
838D LYS* 3.1 28.8 + - - +
839D ILE* 3.0 32.4 + - - +
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Residues in contact with ALA 836 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733D MET* 3.7 26.1 - - + +
734D LYS* 3.9 25.8 - - + -
741D LEU* 3.8 17.9 - - + +
832D TYR 3.2 19.4 + - - +
833D GLU* 3.4 6.3 + - - +
835D GLU* 1.3 74.7 - - - +
837D LYS* 1.3 65.6 + - - +
839D ILE* 3.6 14.7 + - - +
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Residues in contact with LYS 837 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761D ILE* 3.9 22.4 - - + -
766D LEU* 6.1 3.1 - - + -
833D GLU 3.2 14.1 + - - +
836D ALA* 1.3 78.3 - - - +
838D LYS* 1.3 63.7 + - - +
839D ILE 3.1 12.1 - - - +
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Residues in contact with LYS 838 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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756D PRO 5.9 0.6 + - - -
758D ASP* 3.0 37.5 + - + +
761D ILE* 3.7 20.2 - - + -
834D THR 3.4 12.7 + - - +
835D GLU* 3.1 35.1 + - - +
837D LYS* 1.3 79.5 - - - +
839D ILE* 1.3 58.8 + - + +
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Residues in contact with ILE 839 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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733D MET* 3.4 36.1 - - + +
737D HIS* 4.2 33.9 - - + +
740D SER* 5.6 4.9 - - - -
741D LEU* 4.1 20.0 - - + -
744D LYS* 5.4 11.2 - - - +
835D GLU 3.0 15.6 + - - +
836D ALA* 3.6 8.3 - - - +
837D LYS 3.1 13.2 - - - +
838D LYS* 1.3 80.7 - - - +
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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
------------------------------------------------------------
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