Contacts of the helix formed by residues 907 - 931 (chain A) in PDB entry 3NC0
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 907 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860A PHE* 6.2 2.0 - - + -
864A LEU* 5.0 13.9 - - + -
903A ASN 4.4 2.9 + - - +
904A VAL* 3.7 4.3 + - - +
906A GLN* 1.3 78.8 - - + +
908A GLU* 1.3 77.5 + - - +
909A ALA* 3.1 14.5 + - + +
910A ALA* 3.7 22.4 - - + +
911A ALA* 3.0 25.2 + - - +
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Residues in contact with GLU 908 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905A ALA 5.6 0.9 - - - -
906A GLN 3.0 10.6 + - - +
907A GLU* 1.3 77.5 + - - +
909A ALA* 1.3 65.2 + - - +
911A ALA* 3.4 15.4 - - - +
912A GLN* 3.8 17.4 + - - +
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Residues in contact with ALA 909 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907A GLU* 3.2 15.3 + - + +
908A GLU* 1.3 77.1 - - - +
910A ALA* 1.3 60.2 + - + +
911A ALA 2.8 10.4 + - - -
912A GLN* 3.7 9.9 + - - +
913A SER* 4.2 6.6 + - - -
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Residues in contact with ALA 910 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
864A LEU* 4.6 24.7 - - + +
904A VAL* 4.3 4.6 - - - +
907A GLU* 3.4 19.0 + - + +
909A ALA* 1.3 77.0 - - + +
911A ALA* 1.3 62.2 + - - +
913A SER* 4.3 10.1 - - - -
914A PHE* 3.9 14.0 + - - +
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Residues in contact with ALA 911 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904A VAL* 3.5 25.1 - - + +
905A ALA* 5.3 2.2 - - - +
907A GLU 3.0 19.1 + - - +
908A GLU* 3.4 11.9 - - - +
909A ALA 2.8 4.0 + - - -
910A ALA* 1.3 75.1 - - - +
912A GLN* 1.3 74.6 + - - +
913A SER 3.2 1.3 - - - -
914A PHE* 2.8 22.2 + - - +
915A TYR* 3.3 19.2 + - + +
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Residues in contact with GLN 912 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908A GLU* 3.8 19.0 + - - +
909A ALA 3.7 4.0 + - - +
911A ALA* 1.3 79.1 - - - +
913A SER* 1.3 64.7 + - - +
915A TYR* 2.8 35.4 + - - +
916A GLN* 2.9 15.3 + - - +
956A GLY 4.8 3.2 + - - -
957A LYS* 4.2 0.5 - - - +
958A ILE* 3.6 47.3 + - + +
959A SER* 3.9 17.3 + - - +
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Residues in contact with SER 913 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909A ALA 4.2 3.8 + - - -
910A ALA* 4.3 16.2 - - - -
911A ALA 3.2 0.4 - - - -
912A GLN* 1.3 78.7 - - - +
914A PHE* 1.3 63.8 + - - +
916A GLN* 3.2 8.0 + - - +
917A THR* 3.0 33.5 + - - -
918A TYR* 5.9 0.2 - - - -
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Residues in contact with PHE 914 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A PHE* 3.7 23.8 - + - -
875A LEU* 3.4 24.5 - - + -
897A LEU* 5.6 0.2 - - + -
900A LEU* 4.5 13.2 - - + -
901A LEU* 3.9 20.6 - - + -
904A VAL* 3.8 30.7 - - + -
910A ALA 3.9 5.5 + - - +
911A ALA 2.8 11.6 + - - +
913A SER* 1.3 78.1 - - - +
915A TYR* 1.3 68.4 + + - +
917A THR 3.2 0.2 + - - -
918A TYR* 2.7 54.1 + + + +
919A PHE* 5.2 1.8 - + - -
922A ILE* 3.4 33.7 - - + -
949A MET* 6.2 0.2 - - + -
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Residues in contact with TYR 915 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901A LEU* 5.1 8.5 + - + -
904A VAL* 4.7 6.0 - - + +
905A ALA* 4.5 18.5 + - - +
911A ALA* 3.8 20.0 - - + +
912A GLN* 2.8 36.6 + - - +
914A PHE* 1.3 93.7 - + - +
916A GLN* 1.3 63.5 + - - +
917A THR 3.1 0.9 + - - -
919A PHE* 3.0 47.1 + + + +
920A CYS* 4.7 0.7 + - - -
952A LEU* 3.5 34.2 - - + +
956A GLY* 4.9 1.9 - - - -
957A LYS* 4.0 42.8 + - + -
959A SER* 6.4 0.9 - - - -
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Residues in contact with GLN 916 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912A GLN 2.9 9.7 + - - +
913A SER* 3.6 13.2 - - - +
915A TYR* 1.3 78.2 - - - +
917A THR* 1.3 61.2 + - - +
957A LYS* 4.5 6.1 - - - +
959A SER* 3.2 30.7 - - - -
960A THR* 2.8 35.7 + - - +
961A PRO* 4.0 5.6 - - - +
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Residues in contact with THR 917 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872A LYS* 6.2 0.7 - - - +
913A SER* 3.0 21.6 + - - -
916A GLN* 1.3 83.6 - - - +
918A TYR* 1.3 96.8 + - + +
919A PHE 3.8 0.2 - - - -
920A CYS 5.7 0.2 - - - -
921A ASP* 2.9 20.1 - - - +
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Residues in contact with TYR 918 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868A PRO* 4.1 6.6 + - - +
871A PHE* 3.7 28.0 - + - -
872A LYS* 3.6 44.1 + - + +
875A LEU* 3.8 17.0 - - + -
876A ASP* 5.0 5.2 - - - -
914A PHE* 2.7 41.2 + + + +
917A THR* 1.3 102.6 - - + +
919A PHE* 1.3 66.1 + - - +
920A CYS 3.5 2.2 - - - -
921A ASP* 3.1 12.4 + - + +
922A ILE* 2.7 45.2 + - + +
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Residues in contact with PHE 919 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901A LEU* 6.1 0.7 - - + -
914A PHE* 3.6 5.4 + + - -
915A TYR* 3.0 41.6 + + + +
917A THR 3.8 0.2 - - - -
918A TYR* 1.3 80.4 - - - +
920A CYS* 1.3 66.2 + - - +
922A ILE* 3.2 5.0 + - - +
923A LEU* 2.9 27.6 + - + +
949A MET* 3.3 47.0 - - + +
950A PHE* 6.2 0.2 - + - -
952A LEU* 4.8 13.9 - - + -
953A VAL* 3.5 28.5 - - + -
957A LYS* 3.8 28.7 - - + +
974A ILE* 3.5 31.4 - - + -
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Residues in contact with CYS 920 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915A TYR 4.7 0.6 + - - -
918A TYR 3.5 0.2 - - - -
919A PHE* 1.3 90.9 - - - +
921A ASP* 1.3 61.0 + - - +
923A LEU* 3.0 6.7 + - - +
924A GLN 2.8 27.7 + - - -
957A LYS* 4.8 5.4 - - - -
961A PRO* 5.4 0.9 - - - -
973A PHE* 3.9 29.6 - - - -
974A ILE* 4.6 2.9 - - - -
977A TYR* 3.4 41.8 + - + +
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Residues in contact with ASP 921 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917A THR 2.9 23.5 - - - +
918A TYR* 3.1 16.0 + - + +
920A CYS* 1.3 79.7 - - - +
922A ILE* 1.3 61.6 + - + +
924A GLN* 3.6 11.9 + - - +
925A HIS* 3.0 37.8 + - + -
977A TYR* 4.9 1.4 + - - -
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Residues in contact with ILE 922 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A LEU* 4.0 10.8 - - + -
879A ILE* 4.9 11.9 - - + -
882A PHE* 5.9 0.2 - - + -
897A LEU* 3.9 37.2 - - + -
901A LEU* 4.6 4.0 - - + -
914A PHE* 3.4 39.7 - - + -
918A TYR* 2.7 32.2 + - + +
919A PHE* 3.6 4.9 - - - +
921A ASP* 1.3 70.5 - - + +
923A LEU* 1.3 67.3 + - - +
925A HIS* 3.2 8.5 + - - +
926A ILE* 3.0 24.5 + - + +
949A MET* 4.4 18.8 - - + -
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Residues in contact with LEU 923 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919A PHE* 2.9 19.1 + - + +
920A CYS* 3.3 9.4 - - - +
922A ILE* 1.3 78.0 - - - +
924A GLN* 1.3 62.2 + - - +
926A ILE* 3.2 5.0 + - - +
927A PHE* 3.2 38.5 + - + -
946A LEU* 3.6 27.6 - - + -
949A MET* 4.2 22.2 - - + +
950A PHE* 4.2 11.9 - - + -
974A ILE* 3.5 33.9 - - + -
977A TYR* 4.5 7.0 - - + -
978A VAL* 3.7 22.0 - - + -
981A LEU* 5.1 0.7 - - + -
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Residues in contact with GLN 924 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
920A CYS 2.8 17.0 + - - +
921A ASP* 3.8 13.0 + - - +
923A LEU* 1.3 72.5 - - - +
925A HIS* 1.3 68.2 + - + +
927A PHE* 3.3 4.7 + - - +
928A SER* 3.0 22.9 + - - -
977A TYR* 3.1 19.3 + - - +
981A LEU* 3.6 43.9 - - + +
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Residues in contact with HIS 925 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876A ASP* 5.0 6.8 + - - -
879A ILE* 3.4 46.8 - - + +
882A PHE* 3.8 17.1 - - + -
883A LYS* 3.7 22.5 + - - -
921A ASP* 3.0 25.8 + - + +
922A ILE 3.2 8.0 + - - +
924A GLN* 1.3 83.4 - - + +
926A ILE* 1.3 62.9 + - - +
928A SER* 3.1 20.9 + - - -
929A VAL* 3.4 5.2 + - - +
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Residues in contact with ILE 926 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882A PHE* 3.6 27.6 - - + -
894A LEU* 4.2 15.3 - - + -
897A LEU* 3.9 20.0 - - + -
922A ILE* 3.0 21.8 + - + +
923A LEU* 3.2 6.9 + - - +
925A HIS* 1.3 76.2 - - - +
927A PHE* 1.3 62.4 + - - +
929A VAL* 3.0 7.5 - - - +
930A VAL* 3.0 36.7 + - + +
942A HIS* 4.6 13.9 - - - +
945A ILE* 4.7 11.4 - - + -
946A LEU* 3.7 35.4 - - + +
949A MET* 5.6 0.9 - - - -
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Residues in contact with PHE 927 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923A LEU* 3.2 33.8 + - + +
924A GLN* 3.7 9.4 - - - +
926A ILE* 1.3 79.1 - - - +
928A SER* 1.3 62.8 + - - +
930A VAL* 4.1 9.6 - - + -
931A THR* 3.0 34.3 + - + +
946A LEU* 3.5 40.2 - - + -
950A PHE* 3.9 8.7 - + - -
978A VAL* 4.1 10.3 - - + -
981A LEU* 4.9 10.3 - - + -
982A LEU* 3.6 32.5 - - + -
997A PHE* 3.8 26.9 - + - -
1001A LEU* 3.8 18.8 - - + -
1015A LEU* 5.5 0.9 - - + -
1018A PHE* 6.0 0.2 - + - -
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Residues in contact with SER 928 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883A LYS* 4.3 18.8 + - - +
924A GLN* 3.0 15.7 + - - -
925A HIS* 3.1 20.6 - - - -
926A ILE 3.1 0.2 - - - -
927A PHE* 1.3 78.3 - - - +
929A VAL* 1.3 58.0 + - - +
931A THR* 3.6 11.8 + - - -
932A ASP* 3.9 10.9 - - - +
----------------------------------------------------------
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Residues in contact with VAL 929 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882A PHE* 3.8 32.8 - - + +
883A LYS* 3.9 24.0 - - + -
925A HIS 3.9 5.8 - - - +
926A ILE* 3.0 19.1 - - - +
928A SER* 1.3 80.6 - - - +
930A VAL* 1.3 66.0 + - - +
931A THR 3.3 1.6 - - - -
932A ASP* 3.3 24.1 + - - +
935A HIS* 3.7 28.0 - - + +
942A HIS* 3.5 28.1 + - + -
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Residues in contact with VAL 930 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926A ILE* 3.0 38.5 + - + +
927A PHE* 3.3 11.9 + - + +
929A VAL* 1.3 79.0 - - - +
931A THR* 1.3 61.5 + - + +
932A ASP 3.2 8.3 + - - +
935A HIS 5.8 0.2 - - - -
939A LEU* 6.1 2.5 - - + -
942A HIS* 4.1 28.0 - - + -
946A LEU* 4.9 8.1 - - + -
997A PHE* 6.1 0.7 - - + -
1015A LEU* 4.0 31.2 - - + +
1018A PHE* 6.3 1.1 - - + -
1019A LEU* 3.0 33.5 - - + +
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Residues in contact with THR 931 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927A PHE* 3.0 20.9 + - + +
928A SER* 3.6 9.7 + - - -
930A VAL* 1.3 79.2 - - + +
932A ASP* 1.3 58.8 + - - +
933A THR* 3.9 4.2 + - - +
982A LEU* 4.8 8.1 - - + -
986A PHE* 3.7 37.7 - - + -
1018A PHE* 4.3 22.7 - - + -
1019A LEU* 3.7 11.0 - - + -
1022A ILE* 3.6 17.5 - - + +
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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