Contacts of the helix formed by residues 817 - 840 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816A ASP* 1.3 90.0 - - - +
818A GLU* 1.3 61.2 + - - +
819A ALA 3.2 1.1 - - - -
820A GLU* 3.6 19.1 + - + +
821A VAL* 3.5 17.2 - - - +
773E PRO 5.4 0.3 - - - +
774E TRP* 6.0 1.2 - - - -
777E LYS* 4.0 22.5 - - + +
778E LYS* 5.7 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 818 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A TYR* 3.7 34.4 + - + -
815A LEU* 3.1 15.2 + - + +
816A ASP* 4.4 1.3 - - + +
817A GLU* 1.3 78.5 - - - +
819A ALA* 1.3 56.0 + - - +
820A GLU 3.2 0.4 - - - -
821A VAL* 3.3 12.6 + - - +
822A PHE* 3.1 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 819 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
808A LEU* 4.1 3.9 - - - +
811A VAL* 3.6 42.4 - - + +
812A ALA* 3.8 4.5 - - + +
815A LEU* 3.1 14.6 + - + +
816A ASP 3.4 13.5 - - - +
817A GLU 3.2 0.2 - - - -
818A GLU* 1.3 74.5 - - - +
820A GLU* 1.3 61.9 + - - +
822A PHE* 3.2 21.4 + - - +
823A ILE* 3.4 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 820 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749A LYS* 4.1 21.3 - - - +
808A LEU* 3.8 33.3 - - + +
816A ASP 4.2 1.2 + - - +
817A GLU* 3.6 19.4 + - + +
818A GLU 3.2 0.6 - - - -
819A ALA* 1.3 75.7 - - - +
821A VAL* 1.3 70.0 + - - +
822A PHE 3.1 0.6 + - - -
823A ILE 3.8 0.3 + - - -
824A VAL* 3.4 38.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 821 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
782A TYR* 4.5 10.0 + - + +
817A GLU 3.5 17.7 - - - +
818A GLU* 3.3 10.7 + - - +
820A GLU* 1.3 83.9 - - - +
822A PHE* 1.3 64.5 + - - +
824A VAL* 3.9 7.8 + - + +
825A LYS* 3.5 20.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 822 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774A TRP* 3.6 25.1 - + - -
775A ILE* 4.0 26.7 - - + -
778A LYS* 3.9 20.0 - - + -
779A ILE* 5.5 7.9 - - + -
782A TYR* 4.0 27.4 - + + +
794A VAL* 4.6 12.6 - - + -
811A VAL* 4.4 17.0 - - + -
815A LEU* 5.1 5.6 - - + -
818A GLU 3.1 12.3 + - - +
819A ALA* 3.2 13.2 - - - +
820A GLU 3.1 0.2 - - - -
821A VAL* 1.3 79.6 - - - +
823A ILE* 1.3 80.5 + - + +
825A LYS* 3.5 4.1 + - - +
826A MET* 3.1 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 823 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753A PHE* 4.2 9.4 - - + -
794A VAL* 5.2 0.2 - - + -
804A PRO* 3.8 19.3 - - + +
807A ILE* 4.4 14.4 - - + -
808A LEU* 3.9 28.9 - - + -
811A VAL* 4.4 16.8 - - + -
819A ALA 3.4 13.3 + - - +
820A GLU 3.8 0.2 + - - -
822A PHE* 1.3 95.8 - - + +
824A VAL* 1.3 56.7 + - - +
826A MET* 3.0 15.9 + - + -
827A TRP* 2.7 56.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 824 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749A LYS* 4.1 13.5 - - + -
752A LEU* 4.0 10.4 - - + +
753A PHE* 4.0 24.6 - - + -
820A GLU* 3.4 33.5 + - - +
821A VAL* 3.9 8.1 - - + +
822A PHE 3.4 0.2 - - - -
823A ILE* 1.3 78.9 - - - +
825A LYS* 1.3 62.8 + - + +
827A TRP* 3.3 2.8 + - - +
828A ARG* 3.1 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 825 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774A TRP* 4.1 17.5 - - + -
821A VAL* 3.5 15.2 + - + +
822A PHE* 3.8 4.9 - - + +
823A ILE 3.2 0.6 - - - -
824A VAL* 1.3 81.5 - - + +
826A MET* 1.3 61.1 + - - +
828A ARG* 3.6 16.8 + - - +
829A LEU* 3.3 18.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 826 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771A ILE* 5.7 3.6 - - + -
774A TRP* 3.7 19.0 - - + -
775A ILE* 3.6 33.2 - - + -
794A VAL* 3.8 23.3 - - + -
798A VAL* 4.1 19.7 - - + -
807A ILE* 5.6 2.2 - - - -
822A PHE* 3.1 29.9 + - + +
823A ILE* 3.0 18.9 + - + +
825A LYS* 1.3 73.7 - - - +
827A TRP* 1.3 69.7 + - - +
829A LEU* 2.9 10.7 + - + +
830A LEU* 2.8 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 827 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752A LEU* 3.2 40.4 + - + -
753A PHE* 4.4 6.1 + + + -
755A TYR* 4.7 8.9 + - - +
757A LEU* 4.3 14.8 - - + +
759A TRP* 3.6 33.4 - + - -
798A VAL* 5.5 1.1 - - + -
802A SER 3.8 3.4 - - - -
804A PRO* 3.4 56.0 - - + +
807A ILE* 4.2 13.5 - - + -
823A ILE* 2.7 29.0 + - + +
824A VAL 3.7 4.5 - - - +
826A MET* 1.3 78.2 - - - +
828A ARG* 1.3 56.6 + - - +
830A LEU* 3.2 23.9 + - + +
831A ILE* 2.9 53.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 828 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742A ILE* 4.5 21.8 - - - +
745A ILE* 3.4 32.4 - - + +
746A PRO 5.4 1.9 + - - -
752A LEU* 3.7 20.8 - - + +
824A VAL* 3.1 26.0 + - - +
825A LYS* 3.6 17.6 + - - +
827A TRP* 1.3 75.8 - - - +
829A LEU* 1.3 60.2 + - - +
831A ILE* 4.5 0.9 - - - -
832A TYR* 3.3 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 829 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770A ARG* 3.5 41.5 - - + +
771A ILE* 4.6 17.0 - - + -
774A TRP* 3.7 44.2 - - + +
825A LYS 3.3 9.8 + - - +
826A MET* 2.9 15.7 + - + +
828A ARG* 1.3 77.4 - - - +
830A LEU* 1.3 63.6 + - + +
832A TYR* 3.2 5.4 + - + +
833A GLU* 2.8 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 830 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757A LEU* 3.8 20.6 - - + -
762A VAL* 4.4 16.4 - - + -
771A ILE* 3.8 33.9 - - + -
798A VAL* 4.2 24.5 - - + -
826A MET* 2.8 26.7 + - + +
827A TRP* 3.2 45.1 + - + +
829A LEU* 1.3 74.2 - - + +
831A ILE* 1.3 56.9 + - - +
833A GLU* 3.2 4.4 + - + -
834A THR* 2.8 35.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 831 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741A LEU 5.7 0.2 - - - +
744A LYS* 4.8 2.9 - - + +
745A ILE* 3.8 21.8 - - + +
746A PRO* 4.1 6.5 - - + -
752A LEU* 3.8 28.3 - - + -
755A TYR* 3.7 55.0 - - + +
757A LEU* 3.8 13.9 - - + +
827A TRP* 2.9 34.5 + - + +
828A ARG* 4.5 1.3 - - - +
830A LEU* 1.3 75.2 - - - +
832A TYR* 1.3 57.5 + - - +
834A THR* 4.1 0.6 - - - -
835A GLU* 2.8 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 832 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734A LYS* 2.9 54.4 + - + -
737A HIS 3.8 5.7 + - - -
738A ILE* 3.9 15.1 - - - +
741A LEU* 3.7 34.2 - - + +
742A ILE* 3.8 24.0 - - + -
745A ILE* 3.7 21.3 - - + +
828A ARG 3.3 17.7 + - - +
829A LEU* 3.2 7.0 + - + +
831A ILE* 1.3 79.8 - - - +
833A GLU* 1.3 61.7 + - + +
835A GLU* 4.0 3.5 - - - +
836A ALA* 3.1 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 833 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734A LYS* 2.7 40.6 + - - +
761A ILE* 5.4 0.9 - - - -
766A LEU* 6.2 3.4 - - + -
770A ARG* 3.6 31.0 + - + +
771A ILE* 5.4 9.6 - - + -
829A LEU* 2.8 40.8 + - + +
830A LEU* 3.8 5.4 - - + +
832A TYR* 1.3 72.9 - - + +
834A THR* 1.3 66.1 + - - +
836A ALA* 2.9 16.8 + - - +
837A LYS* 3.3 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 834 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
757A LEU* 4.6 10.3 - - - -
758A ASP* 4.1 23.6 - - - -
761A ILE* 3.3 41.3 - - - +
762A VAL* 4.8 7.6 - - - -
830A LEU 2.8 21.8 + - - -
831A ILE* 4.1 1.6 - - - -
833A GLU* 1.3 73.2 - - - +
835A GLU* 1.3 60.5 + - - +
837A LYS 3.6 6.6 + - - -
838A LYS* 3.7 4.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 835 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741A LEU* 3.8 23.3 - - + +
744A LYS* 4.6 14.4 - - + -
755A TYR* 2.6 34.6 + - - -
831A ILE* 2.8 22.0 + - + +
832A TYR* 4.1 0.9 - - - +
834A THR* 1.3 77.1 - - - +
836A ALA* 1.3 61.0 + - - +
838A LYS* 3.2 32.2 + - - +
839A ILE* 3.3 9.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 836 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A MET* 4.6 10.7 - - + +
734A LYS* 4.0 26.7 - - + +
741A LEU* 3.7 24.0 - - + +
832A TYR 3.1 19.0 + - - +
833A GLU* 2.9 7.2 + - - +
835A GLU* 1.3 78.7 - - - +
837A LYS* 1.3 61.1 + - + +
838A LYS 3.1 0.2 - - - -
839A ILE* 3.2 19.6 + - - +
840A GLY 3.9 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 837 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761A ILE* 3.8 33.8 + - + -
763A ASP* 4.4 11.7 + - - +
765A ILE* 5.1 4.6 - - - +
766A LEU* 4.3 26.2 - - - +
769A ARG* 6.3 0.6 - - - +
833A GLU* 3.3 10.4 + - - +
834A THR 3.6 0.6 + - - +
835A GLU 3.4 0.2 - - - -
836A ALA* 1.3 79.2 - - + +
838A LYS* 1.3 60.3 + - - +
839A ILE 3.4 0.2 - - - -
840A GLY* 4.0 12.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 838 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
758A ASP* 3.3 29.6 + - - +
761A ILE* 3.7 29.4 - - + -
834A THR 3.7 3.3 + - - +
835A GLU* 3.2 28.3 + - - +
836A ALA 3.1 0.8 - - - -
837A LYS* 1.3 77.3 - - - +
839A ILE* 1.3 63.7 + - - +
840A GLY 3.1 11.7 + - - +
841A LEU* 4.3 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 839 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A MET* 5.1 9.7 - - + +
737A HIS* 3.6 45.5 - - + +
741A LEU* 5.3 5.8 - - + -
835A GLU 3.3 7.0 + - - +
836A ALA* 3.2 18.0 + - - +
838A LYS* 1.3 79.0 - - - +
840A GLY* 1.3 60.7 + - - +
841A LEU* 3.1 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 840 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733A MET* 5.0 19.2 - - - +
836A ALA 3.9 5.1 + - - -
837A LYS* 4.0 8.9 + - - +
838A LYS* 3.1 9.0 - - - +
839A ILE* 1.3 74.9 - - - +
841A LEU* 1.3 60.9 + - - +
----------------------------------------------------------
Back to top of page
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