Contacts of the helix formed by residues 818 - 839 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782C TYR* 3.7 56.4 - - + +
815C LEU* 3.6 25.5 + - + +
816C ASP 4.8 0.3 + - - -
817C GLU* 1.3 97.6 - - + +
819C ALA* 1.3 64.8 + - - +
820C GLU 3.5 0.2 - - - -
821C VAL* 3.7 9.0 + - - +
822C PHE* 3.0 24.4 + - - +
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Residues in contact with ALA 819 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808C LEU* 4.3 10.3 - - + +
811C VAL* 4.4 8.1 - - + -
812C ALA* 3.7 30.3 - - + +
815C LEU* 3.0 24.9 + - + +
816C ASP 4.6 3.8 - - - +
817C GLU 3.2 1.0 - - - -
818C GLU* 1.3 76.4 - - - +
820C GLU* 1.3 66.1 + - - +
822C PHE* 3.0 9.2 + - - +
823C ILE* 3.0 26.6 + - - +
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Residues in contact with GLU 820 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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749C LYS* 3.7 39.5 + - + +
753C PHE* 5.7 0.2 - - - -
808C LEU* 4.1 24.9 - - + +
816C ASP 5.7 0.2 + - - -
817C GLU 4.3 7.4 + - - +
818C GLU 3.5 0.2 - - - -
819C ALA* 1.3 78.3 - - - +
821C VAL* 1.3 65.6 + - + +
823C ILE* 3.4 1.9 + - - +
824C VAL* 3.0 28.2 + - + +
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Residues in contact with VAL 821 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782C TYR* 3.9 11.9 - - + +
817C GLU 4.9 4.0 + - - +
818C GLU* 3.7 10.4 + - - +
819C ALA 3.3 0.2 - - - -
820C GLU* 1.3 81.5 - - + +
822C PHE* 1.3 64.5 + - - +
824C VAL* 3.0 25.7 - - + +
825C LYS* 3.0 39.4 + - + +
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Residues in contact with PHE 822 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774C TRP* 3.5 32.7 - + - -
775C ILE* 4.1 15.9 - - + -
778C LYS* 3.7 14.4 - - + -
779C ILE* 4.0 21.1 - - + -
782C TYR* 3.4 30.7 - + + +
794C VAL* 4.1 18.6 - - + -
811C VAL* 4.0 23.8 - - + -
815C LEU* 4.4 5.6 - - + -
818C GLU 3.0 15.4 + - - +
819C ALA* 3.2 9.2 - - - +
821C VAL* 1.3 77.7 - - - +
823C ILE* 1.3 79.2 + - + +
825C LYS* 3.5 1.7 + - - -
826C MET* 2.9 29.9 + - + +
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Residues in contact with ILE 823 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753C PHE* 3.9 13.9 - - + -
804C PRO* 3.6 28.0 - - + +
807C ILE* 3.8 16.4 - - + -
808C LEU* 3.7 27.4 - - + +
811C VAL* 4.5 5.6 - - + -
819C ALA 3.0 15.3 + - - +
820C GLU 4.2 1.8 - - - +
822C PHE* 1.3 94.7 - - + +
824C VAL* 1.3 60.7 + - - +
826C MET* 3.3 30.9 - - + +
827C TRP* 2.8 30.7 + - + +
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Residues in contact with VAL 824 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747C THR 4.1 17.3 - - - +
749C LYS* 4.7 15.7 - - + +
752C LEU* 3.4 27.6 - - + +
753C PHE* 4.6 7.3 - - + -
820C GLU* 3.0 21.8 + - + +
821C VAL* 3.0 32.5 - - + +
823C ILE* 1.3 74.3 - - - +
825C LYS* 1.3 71.4 + - + +
826C MET 3.1 0.2 + - - -
827C TRP 3.2 0.2 + - - -
828C ARG* 3.0 33.2 + - + +
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Residues in contact with LYS 825 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774C TRP* 3.8 14.2 - - + -
778C LYS* 3.9 27.3 - - + +
781C GLU* 5.5 4.4 + - - -
782C TYR* 4.7 2.5 - - - +
821C VAL* 3.0 43.0 + - + +
822C PHE 3.7 4.0 - - - +
824C VAL* 1.3 80.8 - - + +
826C MET* 1.3 61.3 + - - +
828C ARG* 3.5 11.1 + - - +
829C LEU* 3.0 22.0 + - - +
805D GLN* 4.7 9.7 - - - +
808D LEU* 5.9 4.0 - - - +
809D ASP* 4.7 13.6 + - - +
813D MET* 5.3 2.3 - - - +
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Residues in contact with MET 826 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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771C ILE* 5.1 3.1 - - - -
774C TRP* 3.2 32.5 - - + -
775C ILE* 4.2 9.9 - - - -
794C VAL* 3.8 27.4 - - + -
798C VAL* 4.0 20.6 - - + -
807C ILE* 4.3 9.6 - - + -
822C PHE* 2.9 22.2 + - + +
823C ILE* 3.3 36.3 - - + +
824C VAL 3.1 0.4 - - - -
825C LYS* 1.3 77.4 - - - +
827C TRP* 1.3 63.7 + - + +
829C LEU* 3.1 9.3 - - + +
830C LEU* 3.0 36.9 + - - +
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Residues in contact with TRP 827 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752C LEU* 3.7 40.2 + - + -
753C PHE* 4.5 5.1 + + + +
755C TYR 4.9 3.8 + - - -
757C LEU* 3.8 27.7 - - + +
759C TRP* 3.6 20.6 - + - -
798C VAL* 5.2 0.7 - - + -
802C SER 3.5 21.1 - - - -
804C PRO* 3.4 47.2 - - + +
807C ILE* 4.2 15.3 - - + -
823C ILE* 2.8 25.1 + - + +
826C MET* 1.3 75.1 - - + +
828C ARG* 1.3 66.7 + - - +
830C LEU* 3.2 22.4 + - + +
831C ILE* 2.9 42.5 + - + +
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Residues in contact with ARG 828 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742C ILE* 4.2 3.8 + - - +
745C ILE* 3.1 43.3 + - + +
746C PRO 2.9 13.7 + - - -
747C THR* 3.5 22.8 - - - +
752C LEU* 3.9 17.7 - - + +
824C VAL* 3.0 26.0 + - - +
825C LYS* 3.6 10.3 - - - +
827C TRP* 1.3 76.8 - - - +
829C LEU* 1.3 56.9 + - - +
831C ILE* 3.3 2.3 + - - +
832C TYR* 2.9 31.4 + - - +
809D ASP* 3.3 19.7 + - - +
810D ASP* 3.1 27.9 + - - -
813D MET* 3.1 40.5 - - + +
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Residues in contact with LEU 829 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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770C ARG* 3.9 28.9 - - + +
771C ILE* 4.5 21.3 - - + -
774C TRP* 3.7 56.8 - - + +
825C LYS 3.0 14.2 + - - +
826C MET* 3.1 11.6 + - + +
828C ARG* 1.3 75.0 - - - +
830C LEU* 1.3 63.2 + - + +
832C TYR* 3.2 5.8 + - + +
833C GLU* 3.0 38.8 + - + +
812D ALA 5.5 4.9 - - - +
813D MET* 4.9 12.7 - - + +
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Residues in contact with LEU 830 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757C LEU* 3.8 23.1 - - + -
759C TRP* 4.8 0.9 - - + -
762C VAL* 4.8 9.9 - - + -
766C LEU* 5.8 0.8 - - + +
771C ILE* 3.8 40.6 - - + -
798C VAL* 4.0 31.9 - - + -
826C MET* 3.0 19.4 + - - +
827C TRP* 3.2 41.5 + - + +
829C LEU* 1.3 75.3 - - + +
831C ILE* 1.3 63.0 + - - +
833C GLU* 4.3 2.6 - - - +
834C THR* 3.0 31.2 + - - +
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Residues in contact with ILE 831 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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744C LYS* 5.6 1.3 - - + -
745C ILE* 4.0 19.5 - - + +
746C PRO* 4.3 2.9 - - + -
752C LEU* 3.5 32.1 - - + -
755C TYR* 3.6 63.0 - - + +
757C LEU* 3.8 14.8 - - + -
827C TRP* 2.9 28.1 + - + +
828C ARG 3.7 3.8 - - - +
830C LEU* 1.3 75.9 - - - +
832C TYR* 1.3 63.2 + - - +
834C THR* 3.7 0.6 - - - -
835C GLU* 2.9 33.5 + - + +
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Residues in contact with TYR 832 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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738C ILE* 4.1 17.9 - - - +
741C LEU* 3.4 46.4 - - + +
742C ILE* 4.1 15.5 - - + -
745C ILE* 3.5 27.8 - - + +
828C ARG 2.9 14.0 + - - +
829C LEU* 3.8 3.6 - - + +
831C ILE* 1.3 76.2 - - - +
833C GLU* 1.3 72.6 + - - +
836C ALA* 2.8 44.4 + - + +
813D MET* 3.5 40.6 - - + -
814D VAL* 4.0 17.8 - - + +
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Residues in contact with GLU 833 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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766C LEU* 3.8 32.8 - - + +
770C ARG* 3.2 54.0 + - + +
771C ILE* 5.8 4.0 - - + -
829C LEU* 3.0 26.1 + - + +
830C LEU* 4.3 2.7 - - - +
832C TYR* 1.3 92.1 - - - +
834C THR* 1.3 57.1 + - - +
836C ALA* 3.7 5.1 - - + +
837C LYS* 3.0 30.8 + - - +
813D MET 5.0 0.2 - - - +
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Residues in contact with THR 834 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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757C LEU* 4.0 7.5 - - + +
758C ASP* 3.7 29.6 + - + +
761C ILE* 4.1 21.1 - - + +
762C VAL* 3.7 23.7 - - - +
766C LEU* 4.5 6.5 - - - +
830C LEU 3.0 23.5 + - - -
831C ILE 3.7 2.0 - - - +
833C GLU* 1.3 77.3 - - - +
835C GLU* 1.3 77.8 + - - +
837C LYS* 3.3 4.7 + - - +
838C LYS* 3.2 22.2 + - - +
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Residues in contact with GLU 835 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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741C LEU* 3.7 20.2 - - + +
744C LYS* 5.1 19.1 + - + +
755C TYR* 3.5 34.1 + - - +
756C PRO 5.0 1.0 - - - +
758C ASP* 4.4 11.4 + - - +
831C ILE* 2.9 29.4 + - + +
834C THR* 1.3 86.5 - - + +
836C ALA* 1.3 56.9 + - - +
838C LYS* 3.9 10.4 + - - +
839C ILE* 3.2 26.5 + - - +
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Residues in contact with ALA 836 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736C LYS* 5.7 1.9 - - - -
741C LEU* 3.8 21.9 - - + +
832C TYR* 2.8 28.8 + - + +
833C GLU* 3.7 8.3 - - + +
835C GLU* 1.3 75.6 - - - +
837C LYS* 1.3 64.1 - - - +
839C ILE* 3.0 24.6 + - - +
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Residues in contact with LYS 837 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761C ILE* 3.6 25.5 + - + +
763C ASP* 3.1 38.0 + - - -
765C ILE* 3.9 13.1 - - - +
766C LEU* 4.1 21.1 - - + +
833C GLU 3.0 17.5 + - - +
834C THR 3.6 4.7 - - - +
836C ALA* 1.3 75.6 - - - +
838C LYS* 1.3 63.0 + - - +
839C ILE 4.2 2.6 - - - -
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Residues in contact with LYS 838 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761C ILE* 3.9 21.4 - - + +
834C THR 3.2 13.0 + - - +
835C GLU* 4.0 12.3 - - - +
836C ALA 3.3 0.2 - - - -
837C LYS* 1.3 79.9 - - - +
839C ILE* 1.3 61.9 + - - +
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Residues in contact with ILE 839 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736C LYS* 4.4 20.8 + - - +
737C HIS* 5.4 12.7 - - + -
741C LEU* 5.2 7.2 - - + -
744C LYS* 6.1 2.2 - - - +
835C GLU 3.2 15.8 + - - +
836C ALA* 3.0 20.1 + - - +
837C LYS 4.2 3.1 - - - -
838C LYS* 1.3 82.7 - - - +
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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