Contacts of the helix formed by residues 817 - 839 (chain A) in PDB entry 1S0V
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 ILE 817 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A LEU* 3.3 11.2 - - + -
448A LYS* 3.9 14.1 - - + +
449A GLY* 4.9 0.2 - - - -
450A LYS* 3.7 33.0 - - + +
530A CYS 3.8 0.7 - - - +
531A SER* 3.2 39.7 - - - +
532A LEU 3.9 2.0 - - - -
806A SER* 4.7 8.1 - - - -
816A THR* 1.3 81.7 - - + +
818A PRO* 1.3 75.8 - - + +
819A ALA* 2.7 8.5 + - + -
820A ASP* 2.9 38.6 + - - +
821A ALA* 2.8 19.3 + - - +
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Residues in contact with PRO 818 (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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450A LYS* 5.9 0.7 - - + +
452A ILE* 4.6 13.2 - - + -
456A GLY* 3.5 33.9 - - - +
459A TRP* 4.4 1.4 - - - -
460A LEU* 4.9 2.9 - - + -
530A CYS* 2.8 50.7 - - + +
532A LEU 3.8 11.3 - - - +
534A LEU* 3.8 21.5 - - + -
816A THR 3.8 1.6 - - - -
817A ILE* 1.3 89.2 - - + -
819A ALA* 1.3 60.5 + - + +
821A ALA* 2.7 20.9 - - + +
822A ALA* 4.1 1.7 + - - +
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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
----------------------------------------------------------
450A LYS* 3.6 42.0 - - + +
451A PRO 4.2 13.2 - - - +
452A ILE* 4.5 10.1 - - - +
456A GLY* 4.6 1.7 - - - -
817A ILE* 2.7 6.7 + - + -
818A PRO* 1.3 76.9 - - + +
820A ASP* 1.3 60.1 + - - +
821A ALA 2.9 8.1 + - - -
822A ALA* 3.8 12.0 + - - +
823A ASN* 5.2 1.6 - - - +
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Residues in contact with ASP 820 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A LYS* 3.3 26.4 + - - +
803A GLY 4.3 2.9 - - - +
804A ILE* 3.2 46.3 - - + +
805A GLU* 3.9 6.9 + - - +
806A SER* 4.8 1.4 + - - -
816A THR* 3.6 13.6 - - + +
817A ILE* 2.9 31.8 + - - +
819A ALA* 1.3 71.0 - - - +
821A ALA* 1.3 64.6 + - - +
822A ALA 3.3 0.4 - - - -
823A ASN* 3.0 16.2 - - - +
824A LEU 2.9 19.1 + - - -
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Residues in contact with ALA 821 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A TRP* 4.0 17.7 - - + -
534A LEU* 4.7 5.6 - - + +
536A PHE* 3.8 18.2 - - + -
816A THR* 4.5 5.8 - - - +
817A ILE 2.8 11.3 + - - +
818A PRO* 2.7 27.4 - - + +
819A ALA 2.9 1.6 - - - -
820A ASP* 1.3 76.9 - - - +
822A ALA* 1.3 63.5 + - - +
823A ASN 2.8 1.2 + - - -
824A LEU* 2.9 15.7 + - - +
825A PHE* 3.2 14.0 + - - +
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Residues in contact with ALA 822 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A GLU* 4.4 19.1 - - + +
456A GLY* 6.4 0.2 - - - -
459A TRP* 3.2 26.1 + - + +
818A PRO 4.1 0.4 + - - +
819A ALA 3.8 10.4 + - - +
821A ALA* 1.3 79.6 - - - +
823A ASN* 1.3 65.7 - - - +
825A PHE* 3.4 15.2 - - - +
826A LYS* 3.8 7.3 + - - +
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Residues in contact with ASN 823 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A TYR* 3.1 46.4 - - + +
804A ILE* 3.6 13.1 - - + +
819A ALA 5.2 0.7 - - - +
820A ASP* 3.0 18.0 - - - +
822A ALA* 1.3 80.3 - - - +
824A LEU* 1.3 75.0 + - - +
825A PHE 3.1 1.3 - - - -
826A LYS* 2.6 18.6 + - - +
827A ALA* 2.7 11.5 + - - -
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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
----------------------------------------------------------
536A PHE* 4.5 10.8 - - + -
794A THR* 3.6 29.6 - - + -
798A ALA* 4.4 9.9 - - + -
804A ILE* 3.6 5.7 - - + +
807A PHE* 4.6 11.9 - - + -
814A PHE* 3.7 20.0 - - + +
815A GLY* 3.6 27.4 - - - +
816A THR* 2.7 30.7 - - - +
820A ASP 2.9 8.6 + - - +
821A ALA* 2.9 9.1 + - - +
823A ASN* 1.3 77.2 - - - +
825A PHE* 1.3 54.7 + - - +
826A LYS 2.6 3.1 + - - -
827A ALA* 2.4 31.4 + - - -
828A VAL* 3.0 14.7 + - + +
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Residues in contact with PHE 825 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A TRP* 3.0 42.4 - + + -
475A PHE* 3.8 13.5 - + - -
536A PHE* 4.0 32.0 - + + -
821A ALA 3.2 7.1 + - - +
822A ALA 3.4 14.6 - - - +
824A LEU* 1.3 78.2 - - - +
826A LYS* 1.3 58.1 + - + +
828A VAL* 2.7 21.1 - - - +
829A ARG* 2.4 80.0 + - - +
879A ASP* 3.3 13.0 - - - -
882A PHE* 5.2 5.2 - + + -
883A ALA 5.8 0.2 - - - +
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Residues in contact with LYS 826 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802A TYR* 3.5 15.0 - - + +
822A ALA 4.2 7.0 - - - +
823A ASN* 2.6 13.0 + - - +
824A LEU 2.6 3.2 + - - -
825A PHE* 1.3 76.6 - - + +
827A ALA* 1.3 68.5 + - - +
828A VAL 2.9 2.1 + - - -
829A ARG* 3.2 7.8 + - + +
830A GLU* 2.8 52.9 + - + +
876A LEU* 6.1 3.8 - - + +
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Residues in contact with ALA 827 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
794A THR* 4.1 5.4 - - + -
797A TRP* 3.5 21.1 - - + +
798A ALA* 3.2 35.0 - - + -
802A TYR* 4.5 6.6 + - + -
823A ASN 2.7 10.3 + - - +
824A LEU* 2.4 23.3 + - - +
826A LYS* 1.3 68.5 - - - +
828A VAL* 1.3 48.9 + - - +
830A GLU* 2.8 6.6 - - - +
831A THR* 2.5 36.9 + - - -
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Residues in contact with VAL 828 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A PHE* 6.0 2.0 - - + -
790A HIS* 4.2 3.1 - - + -
794A THR* 3.5 23.3 - - + +
814A PHE* 3.7 19.5 - - + -
824A LEU* 3.0 9.9 + - + +
825A PHE* 2.7 38.6 - - - +
827A ALA* 1.3 69.3 - - - +
829A ARG* 1.3 56.9 + - - +
830A GLU 2.6 7.2 + - - -
831A THR* 2.8 8.3 + - - +
832A MET* 2.6 36.9 + - - +
883A ALA* 3.4 43.5 - - + +
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Residues in contact with ARG 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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825A PHE* 2.4 66.5 + - - +
826A LYS* 3.2 8.2 + - + +
828A VAL* 1.3 82.7 - - + +
830A GLU* 1.3 55.8 + - - +
832A MET* 4.1 3.4 - - - -
833A VAL* 2.9 30.3 - - - +
875A ILE* 2.7 38.4 - - + +
876A LEU* 2.9 23.3 - - + +
877A GLU 4.8 0.4 - - - -
878A SER* 2.4 35.4 + - - +
879A ASP* 2.6 14.8 + - - +
881A ALA* 4.6 2.3 - - - -
882A PHE* 4.1 16.5 - - - +
883A ALA* 4.2 10.7 - - - +
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Residues in contact with GLU 830 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797A TRP* 2.6 42.8 + - + +
802A TYR* 2.2 27.5 + - - -
826A LYS* 2.8 40.3 + - + +
827A ALA 2.8 13.5 - - - +
828A VAL 2.6 0.6 + - - -
829A ARG* 1.3 77.0 - - - +
831A THR* 1.3 64.7 + - - +
832A MET 2.5 4.7 + - - -
833A VAL* 3.0 13.9 + - - +
834A ASP* 3.2 11.8 + - - +
876A LEU* 4.0 14.1 - - + -
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Residues in contact with THR 831 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
790A HIS* 3.2 21.6 - - + +
793A LYS* 3.1 18.2 - - + +
794A THR* 2.5 48.1 + - - +
797A TRP* 4.4 11.0 - - - +
827A ALA 2.5 14.2 + - - -
828A VAL* 2.8 11.9 + - - +
830A GLU* 1.3 72.0 - - - +
832A MET* 1.3 70.4 + - - +
834A ASP* 3.6 7.9 - - - +
835A THR* 3.2 20.8 + - - -
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Residues in contact with MET 832 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A GLN* 4.9 3.4 - - + +
545A HIS* 4.7 20.9 - - + +
548A ALA* 4.0 25.6 - - + -
561A LEU* 4.3 14.1 - - + -
790A HIS* 3.2 38.1 - - + +
828A VAL 2.6 16.1 + - - +
829A ARG* 4.2 8.5 - - - +
830A GLU 2.5 4.0 + - - -
831A THR* 1.3 75.6 - - - +
833A VAL* 1.3 56.9 - - - +
834A ASP 2.5 16.2 + - - -
835A THR* 2.7 12.8 + - - -
836A TYR* 3.4 22.2 + - + -
875A ILE* 3.9 24.0 - - + -
883A ALA* 4.2 14.8 - - - +
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Residues in contact with VAL 833 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829A ARG 2.9 21.3 - - - +
830A GLU* 3.0 5.2 + - - +
832A MET* 1.3 78.3 - - - +
834A ASP* 1.3 55.3 + - - +
836A TYR* 4.0 1.1 - - - +
837A GLU* 3.0 50.7 + - + +
872A LEU* 3.3 42.0 - - + +
873A ARG* 3.7 11.0 - - + +
875A ILE* 3.5 30.1 - - + -
876A LEU* 3.9 13.2 - - + -
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Residues in contact with ASP 834 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793A LYS* 4.6 13.7 + - - +
797A TRP* 6.2 0.2 - - - -
830A GLU 3.2 10.1 + - - +
831A THR* 3.6 14.3 - - - +
832A MET 2.5 5.7 + - - -
833A VAL* 1.3 73.7 - - - +
835A THR* 1.3 58.4 + - - +
837A GLU* 3.8 5.1 - - - +
838A SER* 3.0 43.1 + - - -
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Residues in contact with THR 835 (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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730A PRO* 3.5 35.0 - - + -
786A GLN* 6.1 1.1 - - + -
789A SER* 4.5 5.2 - - - +
790A HIS* 5.3 8.2 - - + +
793A LYS* 3.3 30.4 + - + +
831A THR 3.2 11.8 + - - -
832A MET* 2.7 13.1 + - - -
834A ASP* 1.3 73.6 - - - +
836A TYR* 1.3 79.6 + - + +
838A SER* 4.9 2.0 - - - -
839A CYS* 3.3 27.2 + - - +
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Residues in contact with TYR 836 (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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545A HIS* 3.3 25.8 + + + -
548A ALA* 3.9 6.5 - - + -
549A MET* 3.4 52.8 - - + +
551A ARG* 2.9 21.0 + - - +
730A PRO* 6.5 0.2 - - + -
786A GLN* 3.1 31.0 - - + +
790A HIS* 5.2 4.0 - + + -
832A MET* 3.4 32.2 + - + +
833A VAL 4.5 0.4 - - - +
835A THR* 1.3 94.1 - - + +
837A GLU* 1.3 58.7 + - - +
839A CYS 2.9 20.7 - - - +
841A VAL* 4.7 9.4 - - + -
872A LEU* 3.3 26.9 - - + -
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Residues in contact with GLU 837 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A ARG* 4.5 2.6 + - - +
833A VAL* 3.0 36.5 + - + +
834A ASP* 3.8 5.1 - - - +
836A TYR* 1.3 77.9 - - - +
838A SER* 1.3 64.8 + - - +
839A CYS* 3.4 2.3 + - - +
871A ASN* 5.4 1.6 - - - +
872A LEU* 3.8 20.2 - - + +
873A ARG* 3.9 36.3 + - - +
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Residues in contact with SER 838 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793A LYS* 6.2 0.9 - - - -
834A ASP* 3.0 28.4 + - - -
835A THR* 4.4 2.7 - - - -
837A GLU* 1.3 81.4 - - - +
839A CYS* 1.3 67.1 + - - +
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Residues in contact with CYS 839 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A ARG* 4.8 2.1 + - - -
730A PRO* 4.2 29.4 - - + -
793A LYS* 6.3 0.7 - - - -
835A THR* 3.3 19.0 + - - +
836A TYR* 2.9 23.7 - - - +
837A GLU 3.3 1.8 - - - +
838A SER* 1.3 86.6 - - - +
840A ASP* 1.3 62.5 + - - +
841A VAL* 3.8 4.4 + - - +
844A ASP* 3.4 16.6 - - - +
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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