Contacts of the helix formed by residues 818 - 838 (chain E) 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 818 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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782E TYR* 3.7 48.5 - - + +
815E LEU* 3.7 36.5 - - + +
816E ASP* 5.0 3.0 - - - +
817E GLU* 1.3 85.7 - - + +
819E ALA* 1.3 57.5 + - - +
820E GLU 3.3 0.7 - - - -
821E VAL* 3.8 11.2 + - + +
822E PHE* 3.3 25.5 + - - +
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Residues in contact with ALA 819 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808E LEU* 4.0 7.0 - - - +
811E VAL* 4.0 10.1 - - + -
812E ALA* 3.5 30.1 - - + +
815E LEU* 3.2 29.5 + - + +
816E ASP 5.3 0.2 - - - +
817E GLU 3.1 1.4 - - - -
818E GLU* 1.3 76.3 - - - +
820E GLU* 1.3 64.3 + - - +
822E PHE* 3.8 7.6 - - - -
823E ILE* 3.4 28.1 + - - +
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Residues in contact with GLU 820 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749E LYS* 3.1 42.0 - - - +
808E LEU* 3.9 26.2 - - + +
817E GLU 3.5 13.5 + - - +
819E ALA* 1.3 80.3 - - - +
821E VAL* 1.3 67.1 + - + +
824E VAL* 3.2 32.4 + - + +
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Residues in contact with VAL 821 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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782E TYR* 4.5 7.4 - - + +
817E GLU 4.8 5.8 - - - +
818E GLU* 3.8 11.5 + - + +
820E GLU* 1.3 83.0 - - + +
822E PHE* 1.3 65.2 + - - +
824E VAL* 3.5 8.2 + - + +
825E LYS* 3.3 48.2 + - + +
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Residues in contact with PHE 822 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774E TRP* 4.0 12.0 - + - -
775E ILE* 4.3 19.1 - - + -
778E LYS* 3.6 28.3 - - + -
779E ILE* 4.5 11.9 - - + -
782E TYR* 3.5 32.0 + + + -
794E VAL* 4.3 10.8 - - + -
811E VAL* 4.0 25.4 - - + -
815E LEU* 4.9 2.0 - - + -
818E GLU 3.3 17.5 + - - +
819E ALA* 3.7 6.3 - - - +
820E GLU 3.3 0.4 - - - -
821E VAL* 1.3 80.8 - - - +
823E ILE* 1.3 76.2 + - + +
825E LYS* 3.6 3.6 + - - +
826E MET* 3.2 44.8 + - + +
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Residues in contact with ILE 823 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753E PHE* 3.8 18.2 - - + -
804E PRO* 3.5 26.7 - - + +
807E ILE* 3.7 25.8 - - + -
808E LEU* 3.9 25.6 - - + -
811E VAL* 4.5 3.1 - - + -
819E ALA 3.4 16.3 + - - +
820E GLU 4.6 0.2 - - - +
822E PHE* 1.3 97.4 - - + +
824E VAL* 1.3 66.8 - - - +
826E MET* 3.5 15.4 - - + +
827E TRP* 2.9 32.0 + - + +
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Residues in contact with VAL 824 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747E THR 6.1 0.4 - - - +
749E LYS* 4.7 15.3 - - + -
752E LEU* 4.2 22.8 - - + +
753E PHE* 4.8 15.7 - - + -
808E LEU* 5.6 0.2 - - + -
820E GLU* 3.2 33.3 + - + +
821E VAL* 3.5 10.3 + - + +
822E PHE 3.4 0.6 - - - -
823E ILE* 1.3 79.3 - - - +
825E LYS* 1.3 67.2 + - + +
827E TRP* 3.6 3.0 + - - +
828E ARG* 3.3 22.8 + - - +
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Residues in contact with LYS 825 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805A GLN* 4.9 7.7 - - - +
809A ASP* 4.0 30.5 + - + +
813A MET* 5.2 2.1 - - - +
774E TRP* 3.7 20.9 - - + -
778E LYS* 4.8 13.8 - - - +
781E GLU* 5.1 6.9 + - - -
782E TYR* 4.8 10.9 + - - +
821E VAL* 3.3 34.5 + - + +
822E PHE 4.0 0.9 - - - +
824E VAL* 1.3 83.6 - - + +
826E MET* 1.3 62.3 + - - +
828E ARG* 3.4 15.2 + - - +
829E LEU* 3.2 19.2 + - - +
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Residues in contact with MET 826 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771E ILE* 5.7 2.5 - - + -
774E TRP* 3.5 21.9 - - + -
775E ILE* 3.8 15.3 - - + -
794E VAL* 3.3 30.3 - - + -
798E VAL* 3.9 23.8 - - - -
822E PHE* 3.2 38.2 + - + +
823E ILE* 3.1 19.1 + - + +
825E LYS* 1.3 74.0 - - - +
827E TRP* 1.3 65.6 + - - +
828E ARG 3.1 1.8 - - - -
829E LEU* 2.8 26.4 + - + +
830E LEU* 3.0 26.7 + - + +
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Residues in contact with TRP 827 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752E LEU* 3.8 37.6 + - + +
753E PHE* 4.5 9.9 + + + -
755E TYR* 4.5 13.5 + - + -
757E LEU* 4.7 16.8 - - + +
798E VAL* 5.0 9.0 - - + -
801E HIS* 5.6 3.1 - - - -
802E SER 3.7 18.2 - - - -
804E PRO* 3.6 44.1 - - + +
807E ILE* 3.9 20.4 - - + -
823E ILE* 2.9 22.4 + - + +
824E VAL 4.1 0.4 - - - +
826E MET* 1.3 80.7 - - - +
828E ARG* 1.3 56.9 + - - +
830E LEU* 3.6 29.0 - - + +
831E ILE* 3.0 32.1 + - + +
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Residues in contact with ARG 828 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806A SER 4.7 0.4 + - - -
809A ASP* 3.4 39.0 + - - +
810A ASP* 2.6 31.5 + - - +
813A MET* 3.2 28.6 - - + +
742E ILE* 4.8 8.5 - - - +
745E ILE* 4.4 22.4 - - + +
746E PRO* 4.8 5.6 - - + -
752E LEU* 4.2 21.9 - - + +
824E VAL* 3.3 14.0 + - - +
825E LYS* 3.4 18.8 + - - +
826E MET 3.1 0.2 - - - -
827E TRP* 1.3 79.6 - - - +
829E LEU* 1.3 56.6 + - - +
831E ILE* 3.6 5.4 + - - +
832E TYR 3.0 22.2 + - - -
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Residues in contact with LEU 829 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812A ALA 6.0 0.2 - - - -
813A MET* 3.8 22.4 - - + +
770E ARG* 3.8 43.7 - - + +
771E ILE* 4.7 15.7 - - + +
774E TRP* 3.7 47.8 - - + +
775E ILE* 6.3 0.2 - - + -
825E LYS 3.2 12.2 + - - +
826E MET* 2.8 17.5 + - + +
828E ARG* 1.3 74.9 - - - +
830E LEU* 1.3 59.5 + - + +
832E TYR* 3.2 2.8 + - - +
833E GLU* 2.8 41.1 + - + +
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Residues in contact with LEU 830 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757E LEU* 5.7 6.7 - - + -
762E VAL* 5.4 10.5 - - + -
771E ILE* 3.9 34.1 - - + -
798E VAL* 4.2 22.0 - - + -
826E MET* 3.0 25.5 + - + +
827E TRP* 3.6 44.9 - - + +
829E LEU* 1.3 77.5 - - + +
831E ILE* 1.3 54.9 + - - +
833E GLU* 3.1 5.1 + - - +
834E THR* 2.7 41.8 + - - +
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Residues in contact with ILE 831 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741E LEU* 5.4 0.5 - - - +
744E LYS 5.9 0.2 - - - +
745E ILE* 5.2 12.6 - - + -
746E PRO* 5.3 4.9 - - + -
752E LEU* 5.8 1.6 - - + -
755E TYR* 5.0 30.1 + - + -
757E LEU* 5.3 9.2 - - + +
827E TRP* 3.0 21.0 + - + +
828E ARG* 3.8 8.1 - - - +
830E LEU* 1.3 76.6 - - - +
832E TYR* 1.3 60.6 + - - +
834E THR* 3.8 6.2 - - - -
835E GLU* 3.7 18.2 + - - +
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Residues in contact with TYR 832 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813A MET* 3.2 51.4 - - + -
814A VAL* 3.3 22.7 - - + +
738E ILE* 4.8 3.8 - - + +
741E LEU* 3.6 45.2 - - + +
742E ILE* 3.7 30.3 - - + -
828E ARG 3.0 18.8 + - - +
829E LEU* 3.5 4.5 - - + +
830E LEU 3.1 0.2 - - - -
831E ILE* 1.3 77.7 - - - +
833E GLU* 1.3 78.1 + - - +
834E THR 3.2 0.8 + - - -
836E ALA* 3.1 32.8 + - + +
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Residues in contact with GLU 833 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813A MET 4.1 0.9 - - - +
761E ILE* 4.7 1.4 - - - +
766E LEU* 5.4 9.4 - - + -
770E ARG* 3.3 49.3 + - + +
771E ILE* 6.3 2.9 - - + -
829E LEU* 2.8 24.7 + - + +
830E LEU* 4.1 4.3 - - - +
832E TYR* 1.3 91.4 - - - +
834E THR* 1.3 63.5 + - - +
836E ALA* 3.9 13.4 - - + +
837E LYS* 3.6 17.7 + - - +
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Residues in contact with THR 834 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755E TYR* 6.5 0.9 - - + -
757E LEU* 4.9 4.9 - - - +
758E ASP* 3.7 47.7 + - + +
761E ILE* 3.4 26.8 - - + +
762E VAL* 5.4 5.4 - - - +
830E LEU* 2.7 26.7 + - - +
831E ILE* 3.8 8.3 + - - -
832E TYR 3.2 0.2 - - - -
833E GLU* 1.3 77.9 - - - +
835E GLU* 1.3 65.1 + - + +
837E LYS 3.3 3.5 + - - -
838E LYS* 3.2 18.4 + - + +
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Residues in contact with GLU 835 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741E LEU* 3.6 23.3 - - + +
744E LYS* 6.3 3.4 - - + -
755E TYR* 5.8 4.0 - - - +
831E ILE 3.7 8.4 + - - +
832E TYR 3.6 1.8 + - - -
834E THR* 1.3 79.3 - - + +
836E ALA* 1.3 62.9 + - - +
837E LYS 3.3 0.4 - - - -
838E LYS* 3.3 25.7 - - - +
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Residues in contact with ALA 836 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736E LYS* 5.3 9.9 + - - +
741E LEU* 3.5 15.7 - - + +
832E TYR* 3.1 29.5 + - + +
833E GLU* 4.0 21.8 - - - +
834E THR 3.2 0.4 - - - -
835E GLU* 1.3 77.4 - - - +
837E LYS* 1.3 59.6 + - - +
838E LYS 4.7 1.7 - - - +
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Residues in contact with LYS 837 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761E ILE* 3.9 14.8 - - + +
833E GLU 3.6 10.1 + - - +
834E THR 3.3 9.7 + - - +
835E GLU 3.3 0.2 - - - -
836E ALA* 1.3 81.6 - - - +
838E LYS* 1.3 60.8 + - - +
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Residues in contact with LYS 838 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761E ILE* 4.5 18.8 - - + -
834E THR* 3.2 14.1 + - + +
835E GLU* 3.3 22.1 - - - +
836E ALA 3.5 1.6 - - - +
837E LYS* 1.3 81.7 - - - +
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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