Contacts of the helix formed by residues 867 - 893 (chain A) in PDB entry 3THW
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 867 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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866A MET* 1.3 75.2 - - - +
868A PRO* 1.3 77.9 - - + +
869A ALA* 3.1 4.5 - - + +
870A ALA* 3.0 21.0 + - + +
871A LYS* 3.0 25.1 + - - +
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Residues in contact with PRO 868 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867A GLU* 1.3 89.0 - - + +
869A ALA* 1.3 59.4 + - - +
871A LYS* 3.9 4.8 + - + +
872A LYS* 3.7 19.6 + - - +
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Residues in contact with ALA 869 (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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867A GLU* 3.1 4.6 - - + +
868A PRO* 1.3 79.5 - - + +
870A ALA* 1.3 63.7 + - - +
871A LYS 3.3 1.1 + - - -
872A LYS* 3.8 4.5 + - - +
873A CYS* 3.6 23.2 + - - +
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Residues in contact with ALA 870 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866A MET* 4.5 6.5 - - - +
867A GLU* 3.0 29.9 + - + +
869A ALA* 1.3 81.3 - - - +
871A LYS* 1.3 57.5 + - - +
873A CYS* 4.7 1.2 - - - +
874A TYR* 3.0 30.0 + - - +
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Residues in contact with LYS 871 (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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867A GLU 3.0 13.8 + - - +
868A PRO* 4.3 5.8 - - + +
869A ALA 3.3 0.2 - - - -
870A ALA* 1.3 77.1 - - - +
872A LYS* 1.3 64.3 + - - +
874A TYR* 4.7 3.1 - - - -
875A LEU* 3.0 39.7 + - + +
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Residues in contact with LYS 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868A PRO 3.7 15.7 + - - +
869A ALA* 3.8 5.1 + - - +
871A LYS* 1.3 80.6 - - - +
873A CYS* 1.3 62.4 + - - +
875A LEU* 4.2 3.5 - - - +
876A GLU* 3.4 22.5 + - - +
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Residues in contact with CYS 873 (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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869A ALA 3.6 15.2 + - - +
870A ALA* 4.7 0.9 - - - +
871A LYS 3.4 0.2 - - - -
872A LYS* 1.3 76.8 - - - +
874A TYR* 1.3 66.9 + - - +
876A GLU* 3.2 8.1 + - - +
877A ARG* 3.0 26.0 + - - +
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Residues in contact with TYR 874 (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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870A ALA 3.0 21.8 + - - +
871A LYS* 4.1 2.5 - - - +
873A CYS* 1.3 78.1 - - - +
875A LEU* 1.3 74.2 + - + +
877A ARG* 3.0 22.2 + - - +
878A GLU* 2.8 66.6 + - + +
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Residues in contact with LEU 875 (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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871A LYS* 3.0 24.9 + - + +
872A LYS* 4.2 3.6 - - - +
874A TYR* 1.3 97.0 - - + +
876A GLU* 1.3 64.0 + - - +
878A GLU* 3.4 17.7 + - - +
879A GLN* 2.9 37.4 + - + +
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Residues in contact with GLU 876 (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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872A LYS 3.4 14.2 + - - +
873A CYS* 3.2 14.3 + - - +
874A TYR 3.1 0.6 - - - -
875A LEU* 1.3 79.3 - - - +
877A ARG* 1.3 57.2 + - - +
879A GLN* 3.1 10.3 - - - +
880A GLY 3.0 22.3 + - - -
920A ASN* 3.0 33.9 + - - +
921A SER* 4.0 31.7 + - - +
922A PHE* 4.4 6.1 - - + +
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Residues in contact with ARG 877 (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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853A GLU* 3.5 31.9 + - - +
855A GLN* 3.0 44.5 + - - +
873A CYS* 3.0 13.7 + - - +
874A TYR* 3.0 22.1 + - - +
876A GLU* 1.3 72.6 - - - +
878A GLU* 1.3 66.1 + - - +
879A GLN 3.0 1.3 - - - -
880A GLY* 3.2 0.9 + - - -
881A GLU* 3.0 39.7 + - - +
922A PHE* 3.5 46.6 - - + +
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Residues in contact with GLU 878 (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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874A TYR* 2.8 56.3 + - + +
875A LEU* 3.6 18.2 - - - +
877A ARG* 1.3 72.4 - - - +
879A GLN* 1.3 70.0 + - - +
881A GLU* 3.8 11.4 + - - +
882A LYS* 3.2 52.5 + - - +
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Residues in contact with GLN 879 (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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875A LEU* 2.9 33.9 + - + +
876A GLU* 3.1 12.6 - - - +
877A ARG 3.0 0.2 - - - -
878A GLU* 1.3 80.8 + - - +
880A GLY* 1.3 68.1 + - - +
882A LYS* 2.7 25.7 + - - +
883A ILE* 2.9 18.5 + - + +
920A ASN* 3.5 12.6 - - - +
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Residues in contact with GLY 880 (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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876A GLU 3.0 7.3 + - - -
877A ARG 3.2 2.9 + - - -
879A GLN* 1.3 77.7 - - - +
881A GLU* 1.3 59.9 + - - +
883A ILE* 3.4 7.2 + - - +
884A ILE* 3.1 30.0 + - - +
920A ASN* 3.5 19.1 + - - +
922A PHE* 3.8 8.7 - - - -
923A VAL* 3.6 15.3 - - - +
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Residues in contact with GLU 881 (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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853A GLU* 3.5 20.6 - - - +
877A ARG* 3.0 37.4 + - - +
878A GLU* 3.9 10.4 - - - +
879A GLN 2.8 3.8 + - - -
880A GLY* 1.3 72.6 - - - +
882A LYS* 1.3 62.2 + - + +
883A ILE 3.0 1.6 + - - -
884A ILE* 3.1 16.3 + - - +
885A GLN* 3.1 14.7 + - - +
922A PHE* 4.2 16.1 - - + -
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Residues in contact with LYS 882 (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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878A GLU* 3.2 43.5 + - + +
879A GLN* 2.7 19.8 + - - +
881A GLU* 1.3 76.5 - - + +
883A ILE* 1.3 59.3 + - + +
885A GLN* 4.0 6.5 + - - +
886A GLU* 3.6 17.3 + - - +
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Residues in contact with ILE 883 (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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879A GLN* 2.9 29.2 - - + +
880A GLY* 3.4 10.1 - - - +
882A LYS* 1.3 76.2 - - + +
884A ILE* 1.3 66.0 + - + +
885A GLN 3.2 0.2 - - - -
886A GLU* 3.1 8.1 + - - +
887A PHE* 2.9 26.7 + - - +
915A VAL* 4.3 28.7 - - + +
918A LYS* 4.2 41.3 - - + +
920A ASN* 4.9 6.7 - - + +
923A VAL* 3.8 21.3 - - + -
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Residues in contact with ILE 884 (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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880A GLY 3.1 18.6 + - - +
881A GLU* 3.1 7.2 + - - +
883A ILE* 1.3 82.3 - - + +
885A GLN* 1.3 53.0 + - - +
887A PHE* 3.3 9.6 + - + +
888A LEU* 2.8 56.3 + - + +
915A VAL* 6.1 0.9 - - + -
922A PHE* 4.9 5.2 - - + -
923A VAL* 3.8 28.7 - - + -
926A ILE* 4.9 19.7 - - + -
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Residues in contact with GLN 885 (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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881A GLU 3.1 14.5 + - - +
882A LYS* 4.2 7.4 - - - +
884A ILE* 1.3 76.4 - - - +
886A GLU* 1.3 57.1 + - - +
888A LEU* 3.8 12.5 - - - +
889A SER* 2.8 40.0 + - - +
892A LYS* 5.4 7.5 - - - +
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Residues in contact with GLU 886 (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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882A LYS 3.6 12.7 + - - +
883A ILE* 3.1 12.0 + - - +
885A GLN* 1.3 76.2 - - - +
887A PHE* 1.3 65.2 + - - +
889A SER* 2.7 21.7 + - - -
890A LYS* 3.0 53.1 + - - +
918A LYS* 6.3 1.3 - - - +
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Residues in contact with PHE 887 (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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883A ILE 2.9 12.3 + - - +
884A ILE* 3.6 12.6 - - + +
886A GLU* 1.3 78.0 - - - +
888A LEU* 1.3 81.0 + - + +
890A LYS* 3.2 16.0 + - - +
891A VAL* 3.1 37.3 + - + +
908A LEU* 4.6 5.8 - - + -
911A LEU* 3.4 48.7 - - + -
912A LYS* 3.7 24.0 - - + -
915A VAL* 3.7 21.8 - - + -
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Residues in contact with LEU 888 (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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884A ILE* 2.8 42.5 + - + +
885A GLN* 3.9 15.5 - - - +
887A PHE* 1.3 88.9 - - + +
889A SER* 1.3 60.7 + - - +
891A VAL* 3.5 7.8 + - + +
892A LYS* 3.3 33.6 + - - +
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Residues in contact with SER 889 (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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885A GLN* 2.8 24.8 + - - -
886A GLU* 2.7 30.1 + - - -
888A LEU* 1.3 75.7 - - - +
890A LYS* 1.3 61.5 + - - +
892A LYS* 3.9 12.7 - - - +
893A GLN* 3.0 30.0 + - - +
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Residues in contact with LYS 890 (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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886A GLU* 3.0 53.5 + - - +
887A PHE* 3.2 9.2 + - - +
889A SER* 1.3 76.6 - - - +
891A VAL* 1.3 64.2 + - - +
893A GLN* 3.3 14.6 + - - +
894A MET* 3.3 16.6 + - - +
911A LEU* 3.8 31.5 - - + +
914A GLU* 4.0 16.5 + - - -
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Residues in contact with VAL 891 (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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887A PHE* 3.1 41.0 + - + +
888A LEU* 3.8 10.1 - - + +
889A SER 3.3 0.2 - - - -
890A LYS* 1.3 75.8 - - - +
892A LYS* 1.3 60.3 + - + +
894A MET* 3.6 13.9 - - + +
896A PHE* 3.1 33.3 - - + -
908A LEU* 4.9 15.9 - - + -
911A LEU* 4.0 15.3 - - + -
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Residues in contact with LYS 892 (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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885A GLN* 5.4 7.1 - - - +
888A LEU* 3.3 22.6 + - - +
889A SER* 4.1 11.4 - - - +
890A LYS 3.2 0.2 - - - -
891A VAL* 1.3 79.1 - - + +
893A GLN* 1.3 55.9 + - - +
894A MET 2.9 17.7 + - - +
896A PHE* 4.8 3.2 - - - -
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Residues in contact with GLN 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A SER 3.0 20.5 + - - +
890A LYS* 3.3 9.1 + - - +
892A LYS* 1.3 74.5 - - - +
894A MET* 1.3 57.8 + - - +
895A PRO* 4.0 5.2 - - - +
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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
------------------------------------------------------------
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