Contacts of the helix formed by residues 807 - 829 (chain D) in PDB entry 2X36
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 GLY 807 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806D LEU* 1.3 80.1 - - - +
808D GLU* 1.3 69.9 + - - -
809D VAL* 3.2 4.9 - - - -
810D MET* 3.1 12.0 + - - +
811D LYS* 3.1 8.5 + - - +
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Residues in contact with GLU 808 (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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805C GLN* 3.4 27.9 + - + +
807D GLY* 1.3 70.7 - - - -
809D VAL* 1.3 65.2 - - - +
811D LYS* 2.9 34.3 + - - +
812D GLU* 2.8 22.7 + - - +
815D ARG* 5.1 7.8 + - - -
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Residues in contact with VAL 809 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
805C GLN* 3.6 17.7 + - - +
846C GLU* 5.8 4.0 - - - +
807D GLY* 4.9 2.5 - - - -
808D GLU* 1.3 76.9 - - - +
810D MET* 1.3 57.6 + - - +
812D GLU* 3.5 2.4 + - - +
813D SER* 3.0 26.9 + - - -
850D PRO* 5.0 9.2 - - + +
854D PRO* 3.6 30.7 - - + -
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Residues in contact with MET 810 (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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806D LEU* 3.3 43.9 - - + +
807D GLY 3.1 5.9 + - - +
809D VAL* 1.3 77.4 - - - +
811D LYS* 1.3 60.2 + - - +
813D SER* 3.3 6.2 + - - -
814D ALA* 3.0 30.2 + - + +
844D VAL* 3.5 37.5 - - + -
848D ALA* 5.7 3.6 - - + -
853D GLY* 3.3 42.0 - - - +
854D PRO* 4.2 3.8 - - - -
856D ALA* 4.1 7.4 - - + -
860D ILE* 5.1 4.9 - - + -
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Residues in contact with LYS 811 (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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802D VAL* 5.0 21.3 + - + +
806D LEU* 3.7 26.3 - - + +
807D GLY 3.1 10.4 + - - +
808D GLU* 2.9 42.3 + - - +
810D MET* 1.3 75.6 - - - +
812D GLU* 1.3 64.0 + - + +
814D ALA* 3.5 6.5 + - - +
815D ARG* 3.2 27.9 + - - +
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Residues in contact with GLU 812 (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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802C VAL 4.9 1.0 - - - +
803C THR* 3.3 14.8 - - + -
804C GLY* 2.6 29.9 + - - -
805C GLN* 3.0 50.3 + - - +
806C LEU 4.7 0.2 + - - -
843C HIS* 4.9 0.2 + - - -
846C GLU* 5.6 0.7 - - - +
808D GLU* 2.8 14.2 + - - +
809D VAL 4.3 1.6 - - - +
811D LYS* 1.3 72.5 - - + +
813D SER* 1.3 66.8 + - - +
815D ARG* 3.3 33.6 + - - +
816D ILE* 3.0 35.9 + - + +
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Residues in contact with SER 813 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809D VAL 3.0 18.6 + - - -
810D MET* 3.3 13.0 + - - -
812D GLU* 1.3 77.0 - - - +
814D ALA* 1.3 56.1 + - - +
816D ILE* 3.5 10.9 + - - +
817D ALA* 3.0 28.6 + - - +
854D PRO* 3.4 37.1 + - - +
857D GLY* 4.8 6.9 - - - -
860D ILE* 5.4 3.8 - - - -
882D GLU* 5.7 1.0 - - - +
883D VAL* 5.5 1.7 + - - +
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Residues in contact with ALA 814 (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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800D LEU* 5.0 4.0 - - + +
802D VAL* 4.2 18.4 - - + -
810D MET* 3.0 16.8 + - + +
811D LYS 3.8 4.7 - - - +
813D SER* 1.3 72.3 - - - +
815D ARG* 1.3 60.2 + - - +
816D ILE 3.1 2.0 + - - -
817D ALA* 3.2 4.1 + - - +
818D TYR* 2.8 30.4 + - - +
842D LEU* 4.0 25.8 - - + -
844D VAL* 6.1 0.2 - - + -
860D ILE* 4.6 16.3 - - + +
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Residues in contact with ARG 815 (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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801C GLU* 3.3 31.9 + - - +
802C VAL 3.9 16.3 + - - -
803C THR* 3.2 27.8 - - + +
841C HIS* 3.9 3.1 + - - +
800D LEU* 6.0 0.7 - - - -
808D GLU* 5.1 7.1 + - - -
811D LYS* 3.2 14.8 + - - +
812D GLU* 3.6 33.0 + - - +
814D ALA* 1.3 77.6 - - - +
816D ILE* 1.3 57.6 + - - +
818D TYR* 3.7 17.3 - - + +
819D THR* 3.1 29.6 + - - -
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Residues in contact with ILE 816 (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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803C THR* 3.4 25.4 - - - +
841C HIS* 4.2 5.8 - - + -
843C HIS* 3.7 30.1 - - + +
812D GLU* 3.0 31.4 + - + +
813D SER* 3.6 7.6 - - - +
815D ARG* 1.3 77.5 - - - +
817D ALA* 1.3 61.7 + - - +
819D THR 3.4 0.7 + - - -
820D PHE* 3.1 25.8 + - - +
883D VAL 3.7 22.4 - - - +
884D SER* 4.0 1.3 - - - +
885D LEU* 3.9 34.3 - - + +
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Residues in contact with ALA 817 (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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813D SER 3.0 17.4 + - - +
814D ALA 3.8 2.7 - - - +
816D ILE* 1.3 77.7 - - - +
818D TYR* 1.3 57.0 + - - +
820D PHE* 4.4 3.4 - - - -
821D ALA* 2.9 29.5 + - - +
857D GLY* 3.5 26.7 - - - +
860D ILE* 4.3 10.1 - - + -
861D VAL* 3.6 17.1 - - + +
864D LEU* 4.1 3.4 - - - +
883D VAL* 3.7 13.0 - - + -
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Residues in contact with TYR 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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801C GLU* 6.0 2.0 - - - -
798D GLY 3.6 0.3 - - - -
799D SER* 3.3 24.8 + - - -
800D LEU* 3.6 39.3 - - + -
814D ALA 2.8 20.8 + - - +
815D ARG* 3.7 15.5 - - + +
817D ALA* 1.3 70.2 - - - +
819D THR* 1.3 69.0 + - - +
820D PHE 3.2 0.2 + - - -
821D ALA* 3.3 1.6 + - + +
822D ARG* 2.7 74.7 + - + +
835D LEU* 3.8 14.7 + - + -
838D SER 4.5 1.0 + - - -
840D ILE* 5.1 8.1 - - + +
864D LEU* 3.7 28.0 - - + +
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Residues in contact with THR 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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783C SER* 4.1 6.5 - - - +
784C LEU 3.8 10.0 - - - +
785C ARG* 3.4 32.2 + - + +
801C GLU* 3.8 2.6 + - - -
841C HIS* 2.9 39.5 - - + -
815D ARG 3.1 13.1 + - - -
816D ILE 3.4 4.7 + - - -
818D TYR* 1.3 79.8 - - - +
820D PHE* 1.3 58.4 + - - +
822D ARG* 3.0 11.4 + - - +
823D ALA* 2.9 23.6 + - - +
885D LEU* 4.0 9.6 - - + -
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Residues in contact with PHE 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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816D ILE 3.1 15.8 + - - +
817D ALA* 3.8 3.8 - - - +
819D THR* 1.3 73.5 - - - +
821D ALA* 1.3 60.5 + - - +
823D ALA* 3.1 9.1 + - + +
824D PHE* 2.7 66.8 + + + +
861D VAL* 3.8 20.2 - - + -
883D VAL* 4.2 3.6 - - + -
884D SER 4.2 5.8 - - - +
885D LEU 3.4 26.5 - - - +
886D THR* 3.9 6.7 - - - -
887D GLY* 3.5 28.5 - - - -
938D HIS* 4.4 6.1 - - - -
939D TYR* 3.4 38.1 - + + -
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Residues in contact with ALA 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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817D ALA 2.9 20.1 + - - +
818D TYR 3.7 3.6 - - - +
820D PHE* 1.3 75.6 - - - +
822D ARG* 1.3 66.5 + - - +
824D PHE* 4.4 1.8 - - - -
825D LEU* 2.9 27.4 + - - +
835D LEU* 3.7 18.6 - - + -
861D VAL* 4.1 14.1 - - + -
864D LEU* 3.8 17.7 - - + -
865D LEU* 3.9 14.9 - - + +
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Residues in contact with ARG 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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785C ARG* 3.3 51.0 + - - +
801C GLU* 5.7 0.2 + - - -
797D ASP* 2.6 33.2 + - - -
798D GLY 3.5 10.3 + - - +
818D TYR* 2.7 69.0 + - + +
819D THR* 3.1 15.2 + - - +
821D ALA* 1.3 71.1 - - - +
823D ALA* 1.3 55.8 + - - +
825D LEU* 3.5 1.4 + - - +
826D MET* 3.0 36.2 + - - +
835D LEU* 3.2 39.3 + - + +
836D VAL* 3.7 12.5 + - + +
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Residues in contact with ALA 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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783C SER* 3.4 25.8 - - - +
784C LEU* 3.7 7.2 + - + +
819D THR 2.9 9.2 + - - +
820D PHE* 3.1 14.8 + - + +
822D ARG* 1.3 74.0 - - - +
824D PHE* 1.3 66.9 + - - +
826D MET* 3.5 15.6 + - + +
827D GLN* 3.0 23.2 + - - +
885D LEU 5.6 0.2 - - - +
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Residues in contact with PHE 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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820D PHE* 2.7 52.1 + + + +
821D ALA* 3.9 6.7 - - - +
823D ALA* 1.3 72.8 - - - +
825D LEU* 1.3 55.6 + - + +
827D GLN* 3.0 8.4 + - + +
828D HIS* 2.6 54.8 + + + +
865D LEU* 4.1 17.7 - - + -
938D HIS* 5.4 2.2 - + - -
939D TYR* 4.5 2.0 - + - -
940D ARG* 4.0 36.1 - - + -
943D PHE* 3.7 44.4 - + + -
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Residues in contact with LEU 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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821D ALA 2.9 18.7 + - - +
822D ARG 4.0 2.0 - - - +
824D PHE* 1.3 81.3 - - + +
826D MET* 1.3 55.7 + - - +
828D HIS* 4.3 14.8 - - + +
829D ALA* 2.9 51.2 + - + +
832D ASN* 4.3 21.3 - - + +
835D LEU* 2.6 43.1 - - + -
865D LEU* 3.9 14.8 - - + -
868D ALA* 3.5 10.8 - - + -
869D MET* 4.4 17.3 - - + -
943D PHE* 6.1 0.9 - - + -
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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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784C LEU* 4.0 33.7 - - + +
785C ARG 4.6 0.9 - - - -
786C ARG* 3.5 9.0 - - - +
787C PRO* 3.3 46.9 - - + -
822D ARG 3.0 15.6 + - - +
823D ALA* 3.6 24.5 - - + +
825D LEU* 1.3 77.3 - - - +
827D GLN* 1.3 67.4 + - - +
829D ALA 4.6 2.5 - - - -
830D PRO* 3.7 24.5 - - - +
836D VAL* 4.5 12.1 - - + -
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Residues in contact with GLN 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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823D ALA 3.0 12.6 + - - +
824D PHE* 3.0 10.0 + - + +
826D MET* 1.3 83.4 + - - +
828D HIS* 1.3 62.8 + - - +
830D PRO* 3.6 9.2 - - - +
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Residues in contact with HIS 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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824D PHE* 2.6 37.6 + + + +
825D LEU* 4.3 12.0 - - - +
827D GLN* 1.3 74.4 - - - +
829D ALA* 1.3 68.5 + - + +
830D PRO* 3.3 6.5 - - - +
869D MET* 4.4 12.0 - - - -
940D ARG* 5.8 5.6 - - - -
943D PHE* 3.5 39.6 - + - -
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Residues in contact with ALA 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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825D LEU* 2.9 30.7 + - + +
826D MET* 4.6 0.3 - - - -
828D HIS* 1.3 87.0 - - + +
830D PRO* 1.4 66.9 - - - +
831D ALA 3.2 2.9 - - - -
832D ASN* 3.0 30.4 + - + +
869D MET* 6.4 0.7 - - + -
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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
------------------------------------------------------------
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