Contacts of the helix formed by residues 814 - 835 (chain A) in PDB entry 3E0D
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 ASN 814 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A GLY 3.2 4.7 - - - -
426A SER* 3.1 29.0 + - - +
452A ARG* 3.0 33.7 + - - +
744A GLN* 3.6 12.5 + - - +
745A GLU* 2.0 37.8 + - - +
813A PHE* 1.3 84.4 - - + +
815A LYS* 1.3 62.8 + - - +
816A SER* 2.9 22.7 + - - +
817A HIS* 3.4 8.2 + - + +
818A ALA 3.2 15.8 + - - -
1222A DTP 3.8 5.5 + - - +
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Residues in contact with LYS 815 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A PHE* 4.0 12.6 - - - +
447A GLY* 2.9 38.2 - - - +
448A LEU* 3.9 12.6 - - + -
688A GLU* 5.7 3.8 - - - +
691A ILE* 4.4 25.8 - - + -
736A GLU* 3.7 32.6 + - - -
743A TYR* 4.6 24.9 - - + -
745A GLU* 2.4 31.9 + - + +
813A PHE 3.2 1.5 + - - -
814A ASN* 1.3 64.8 - - - +
816A SER* 1.3 54.6 + - - +
818A ALA* 4.2 5.6 - - - -
819A ALA* 2.7 35.3 + - + +
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Residues in contact with SER 816 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A GLY 3.3 8.0 + - - -
426A SER* 3.5 6.8 + - - -
428A ALA* 3.8 8.3 - - - +
429A GLY* 3.7 19.9 - - - -
448A LEU* 3.2 34.6 - - - +
449A LEU 5.5 0.7 - - - -
745A GLU* 3.7 0.4 + - - -
814A ASN* 2.9 25.6 + - - +
815A LYS* 1.3 76.3 - - - +
817A HIS* 1.3 64.5 + - - +
819A ALA* 3.9 0.9 - - - +
820A ALA* 3.0 26.7 + - - +
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Residues in contact with HIS 817 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A ARG* 3.6 8.7 - - + -
425A GLY* 2.8 43.5 + - - +
669A GLN* 5.4 3.4 - - - -
813A PHE* 4.1 18.9 - + + -
814A ASN* 3.4 15.9 + - + +
815A LYS 3.2 0.4 - - - -
816A SER* 1.3 82.5 + - - +
818A ALA* 1.3 62.9 + - - +
820A ALA* 3.6 2.6 + - - +
821A TYR* 3.1 51.3 + + + +
1222A DTP 2.7 39.5 + - + +
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Residues in contact with ALA 818 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A GLN* 4.8 0.7 - - - +
691A ILE* 3.7 14.8 - - + +
694A VAL* 5.5 6.6 - - + +
695A SER* 3.4 26.2 - - - +
813A PHE* 3.6 17.0 - - + -
814A ASN 3.2 5.9 + - - +
815A LYS* 3.1 9.9 + - - +
817A HIS* 1.3 79.4 + - - +
819A ALA* 1.3 53.9 + - - +
821A TYR* 3.4 3.9 + - - +
822A SER* 2.6 38.4 + - - +
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Residues in contact with ALA 819 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A ILE* 3.7 19.9 - - + +
446A PHE* 4.7 9.0 - - + -
448A LEU* 4.3 15.7 - - + -
687A LEU* 5.2 2.1 - - - +
691A ILE* 3.7 30.2 - - + +
815A LYS* 2.7 21.4 + - + +
816A SER 3.9 2.5 - - - +
818A ALA* 1.3 72.5 - - - +
820A ALA* 1.3 64.4 + - - +
822A SER* 3.2 12.4 + - - -
823A LEU* 3.2 8.8 + - - +
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Residues in contact with ALA 820 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A PRO* 3.5 18.0 - - + +
423A GLY* 3.5 35.7 - - - +
428A ALA* 4.7 2.0 - - + -
441A ILE* 3.9 21.9 - - + +
816A SER 3.0 17.3 + - - +
817A HIS* 3.9 3.4 - - - +
819A ALA* 1.3 76.2 - - - +
821A TYR* 1.3 64.5 + - - +
823A LEU* 3.3 16.6 + - - +
824A LEU* 3.8 1.2 + - - +
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Residues in contact with TYR 821 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A PRO* 6.0 0.2 - - + -
423A GLY 3.4 13.2 - - - -
424A ARG* 2.7 56.7 + - + -
467A ASP* 3.0 21.2 + - - -
620A LEU* 4.5 0.5 - - - +
622A LEU* 4.4 7.5 - - + +
668A PHE* 3.4 33.7 - + - -
669A GLN* 3.4 25.8 - - - +
817A HIS* 3.1 40.1 + + + +
818A ALA* 4.0 2.9 - - - +
820A ALA* 1.3 78.5 - - - +
822A SER* 1.3 63.8 + - - +
824A LEU* 2.8 25.7 + - + +
825A SER* 3.3 9.4 + - - -
7C G 4.7 5.6 + + - -
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Residues in contact with SER 822 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669A GLN* 3.7 5.3 + - - -
687A LEU* 4.0 10.3 - - - +
690A ILE* 3.8 16.3 + - - +
691A ILE* 3.3 36.8 + - - -
694A VAL* 4.8 2.4 - - - +
818A ALA* 2.6 25.3 + - - -
819A ALA 3.2 6.9 + - - -
821A TYR* 1.3 75.3 - - - +
823A LEU* 1.3 57.6 + - - +
825A SER* 3.0 13.7 + - - -
826A TYR* 2.9 27.4 + - - +
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Residues in contact with LEU 823 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A PRO* 4.3 20.6 - - + -
440A ASN 4.6 6.1 - - - +
441A ILE* 3.7 27.8 - - + -
446A PHE* 6.3 0.2 - - + -
645A TYR 5.3 1.6 - - - +
650A LEU* 3.9 29.2 - - + -
687A LEU* 4.4 9.6 - - + +
819A ALA 3.2 5.8 + - - +
820A ALA 3.3 10.5 - - - +
821A TYR 3.1 0.2 - - - -
822A SER* 1.3 79.9 - - - +
824A LEU* 1.3 57.1 + - + +
826A TYR* 3.4 9.0 + - + +
827A GLN* 2.9 66.2 + - + +
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Residues in contact with LEU 824 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A GLY* 5.4 0.4 - - - -
422A PRO* 4.2 26.5 - - + -
467A ASP* 5.4 1.6 - - - +
622A LEU* 3.9 27.6 - - + -
624A THR* 4.1 8.4 - - + +
625A LEU* 3.6 27.8 - - + -
628A LEU* 3.9 7.7 - - + +
668A PHE* 3.6 22.9 - - + -
820A ALA 4.5 2.0 - - - +
821A TYR* 2.8 22.8 + - + +
823A LEU* 1.3 70.2 - - - +
825A SER* 1.3 60.6 + - - +
827A GLN* 3.3 21.1 + - - +
828A THR* 2.9 33.7 + - - -
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Residues in contact with SER 825 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A LEU* 6.1 0.7 - - - -
667A VAL* 3.5 11.1 - - - +
668A PHE* 2.9 33.4 + - - -
669A GLN* 3.3 24.4 + - - +
670A LEU* 4.7 6.2 - - - +
690A ILE* 4.4 14.8 - - - +
821A TYR 3.3 1.8 + - - -
822A SER* 3.0 12.2 + - - -
824A LEU* 1.3 78.0 - - - +
826A TYR* 1.3 63.1 + - - -
828A THR* 3.2 2.8 + - - -
829A ALA* 2.9 20.9 + - - +
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Residues in contact with TYR 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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648A LEU* 4.9 6.5 - - + -
649A PRO 2.5 30.0 + - - -
650A LEU* 3.3 24.9 - - + -
652A ASP* 3.1 27.7 + - + +
655A THR* 3.7 23.3 - - + +
656A PHE* 3.5 37.7 - + - -
687A LEU* 3.8 25.1 - - + -
690A ILE* 4.7 7.3 - - + +
822A SER 2.9 5.5 + - - -
823A LEU* 3.5 9.9 - - + +
825A SER* 1.3 75.7 - - - +
827A GLN* 1.3 63.6 + - + +
829A ALA* 3.1 7.9 + - - +
830A TYR* 2.6 49.3 + + + +
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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
----------------------------------------------------------
628A LEU* 3.7 20.4 - - + +
645A TYR* 3.3 49.2 + - + +
646A ASP* 4.4 6.3 + - - +
648A LEU* 4.5 10.8 - - + -
823A LEU* 2.9 44.7 + - + +
824A LEU* 3.6 24.2 - - - +
826A TYR* 1.3 78.4 - - + +
828A THR* 1.3 64.3 + - - +
830A TYR* 3.3 6.6 + - - +
831A VAL* 3.0 27.5 + - - +
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Residues in contact with THR 828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A THR* 3.9 12.3 + - - +
627A PHE* 4.6 8.7 - - + -
628A LEU* 4.0 12.7 - - - +
666A GLY 3.0 29.6 - - - +
667A VAL* 3.3 15.5 - - + -
668A PHE* 3.6 16.4 - - - +
824A LEU 2.9 16.0 + - - -
825A SER 3.4 8.5 - - - -
827A GLN* 1.3 75.6 - - - +
829A ALA* 1.3 57.9 + - - +
832A LYS 3.2 0.2 + - - -
839A PHE* 2.6 44.8 - - + -
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Residues in contact with ALA 829 (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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655A THR* 4.0 13.9 - - + -
658A LEU* 4.2 9.3 - - + +
659A LEU* 3.7 32.3 - - + -
667A VAL* 3.8 13.0 - - + +
825A SER 2.9 17.0 + - - +
826A TYR 3.5 6.5 - - - +
828A THR* 1.3 73.5 - - - +
830A TYR* 1.3 52.0 + - - +
832A LYS* 3.2 6.3 + - - +
833A ALA* 2.8 35.3 + - - +
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Residues in contact with TYR 830 (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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643A LEU* 4.1 15.8 - - + +
648A LEU* 3.6 44.5 - - + +
649A PRO* 4.9 10.3 - - + +
652A ASP* 3.6 20.2 - - + -
655A THR* 3.2 29.5 - - + +
826A TYR* 2.6 33.1 + + + +
827A GLN* 3.5 7.6 - - - +
829A ALA* 1.3 72.1 - - - +
831A VAL* 1.3 69.8 + - + +
833A ALA* 3.2 2.6 + - - +
834A HIS* 3.0 47.5 + + + +
835A TYR* 5.0 5.0 - + - -
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Residues in contact with VAL 831 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A LEU* 4.5 3.8 - - + -
631A ALA* 4.3 10.5 - - + -
635A VAL* 5.3 2.5 - - + -
643A LEU* 4.2 13.0 - - + -
645A TYR* 3.8 32.1 - - + +
827A GLN 3.0 18.4 + - - +
830A TYR* 1.3 81.7 - - + +
832A LYS* 1.3 53.6 + - - +
834A HIS 3.6 0.2 - - - -
835A TYR* 2.7 44.4 + - + +
839A PHE* 1.7 63.9 - - + -
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Residues in contact with LYS 832 (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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658A LEU* 3.9 14.2 - - + +
663A GLU 2.9 27.8 + - - +
665A LYS* 3.0 60.6 - - - +
666A GLY 3.5 5.3 - - - +
667A VAL* 4.2 9.6 - - + -
828A THR 3.2 1.5 + - - +
829A ALA* 3.5 8.3 - - - +
831A VAL* 1.3 73.5 - - - +
833A ALA* 1.3 62.1 + - - +
835A TYR 4.2 7.8 + - - -
836A PRO* 4.6 3.8 - - - +
839A PHE* 2.4 49.1 - - + -
840A MET* 4.1 17.9 - - + +
864A LEU* 5.3 8.0 - - + +
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Residues in contact with ALA 833 (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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654A LYS* 3.5 38.3 - - + +
655A THR* 3.9 9.4 - - - +
658A LEU* 3.7 13.7 - - + -
829A ALA 2.8 20.0 + - - +
830A TYR 3.5 4.5 - - - +
831A VAL 3.2 0.2 - - - -
832A LYS* 1.3 75.7 - - - +
834A HIS* 1.3 66.5 + - + +
835A TYR 3.9 0.2 + - - -
836A PRO* 5.2 1.9 - - - +
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Residues in contact with HIS 834 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A ASP* 2.8 39.9 + - - -
654A LYS* 4.0 25.2 - - + +
830A TYR* 3.0 46.3 + + + +
833A ALA* 1.3 84.5 + - + +
835A TYR* 1.3 86.1 + - + +
836A PRO* 3.2 10.9 - - - +
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Residues in contact with TYR 835 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A VAL* 4.0 26.7 - - + -
639A LYS* 3.7 36.1 - - + -
641A VAL* 3.6 29.5 - - + +
643A LEU* 4.6 23.1 - - + -
830A TYR* 5.0 5.4 - + - -
831A VAL* 2.7 24.4 + - + +
832A LYS 4.3 3.6 - - - -
833A ALA 3.6 0.6 - - - -
834A HIS* 1.3 90.9 - - + +
836A PRO* 1.1 111.0 - - + +
838A GLU* 4.8 2.2 - - + -
839A PHE* 2.5 28.8 + - + +
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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
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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