Contacts of the helix formed by residues 925 - 949 (chain A) in PDB entry 6C90
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 THR 925 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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923A LYS 4.1 1.6 + - - +
924A LEU* 1.3 74.2 - - - +
926A GLU* 1.3 65.4 + - - +
927A GLN* 3.9 16.5 + - - +
928A LEU* 3.0 15.0 + - - +
929A ALA* 2.9 19.6 + - - -
968A ASP* 6.3 0.4 - - - -
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Residues in contact with GLU 926 (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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924A LEU 3.9 0.2 + - - -
925A THR* 1.3 74.9 - - - +
927A GLN* 1.3 61.9 + - - +
929A ALA* 4.3 5.6 - - - +
930A GLY* 3.0 26.4 + - - -
931A PRO* 3.8 1.4 - - - +
933A ARG* 2.6 37.6 + - - -
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Residues in contact with GLN 927 (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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901A SER* 4.6 4.6 + - - -
904A GLN* 3.0 55.9 + - + +
925A THR* 3.0 12.6 + - - +
926A GLU* 1.3 78.9 - - - +
928A LEU* 1.3 63.9 + - + +
931A PRO* 3.1 11.2 - - - +
971A TYR* 3.0 35.6 + - + -
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Residues in contact with LEU 928 (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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904A GLN* 4.9 4.9 - - - +
907A ALA* 3.9 16.4 - - + -
924A LEU* 3.7 24.0 - - + -
925A THR* 3.0 16.3 + - - +
927A GLN* 1.3 85.1 - - + +
929A ALA* 1.3 65.2 + - - +
930A GLY 3.1 1.6 - - - -
931A PRO* 3.4 2.9 - - + +
932A LEU* 3.0 23.8 + - - +
967A MET* 3.6 21.0 - - + +
968A ASP* 3.7 38.6 - - + +
971A TYR* 3.7 36.8 - - + -
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Residues in contact with ALA 929 (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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924A LEU* 4.0 23.2 - - + +
925A THR 2.9 15.2 + - - +
926A GLU* 4.4 6.3 - - - +
928A LEU* 1.3 76.7 - - - +
930A GLY* 1.3 57.2 + - - +
932A LEU* 3.6 10.6 - - + +
933A ARG* 3.0 46.6 + - - +
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Residues in contact with GLY 930 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926A GLU* 3.0 20.7 + - - -
929A ALA* 1.3 73.1 - - - +
931A PRO* 1.3 71.2 - - - +
933A ARG* 2.9 34.2 + - - +
934A GLN* 3.1 21.1 + - - +
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Residues in contact with PRO 931 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900A LEU* 3.6 40.8 - - + -
904A GLN* 3.9 8.5 - - + +
908A LEU* 3.8 18.1 - - + +
926A GLU 3.8 1.6 - - - +
927A GLN 3.1 29.6 - - - +
928A LEU* 3.4 6.7 - - + +
930A GLY* 1.3 86.5 - - - +
932A LEU* 1.3 60.5 + - - +
934A GLN* 3.2 17.4 + - + +
935A MET* 3.0 24.1 + - - +
967A MET* 5.3 0.9 - - + -
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Residues in contact with LEU 932 (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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908A LEU* 4.0 7.3 - - - +
911A CYS* 4.4 1.6 - - - -
924A LEU* 3.9 20.2 - - + -
928A LEU 3.0 18.2 + - - +
929A ALA* 3.6 7.2 - - + +
930A GLY 3.1 0.2 - - - -
931A PRO* 1.3 77.6 - - - +
933A ARG* 1.3 63.4 + - + +
935A MET* 3.4 22.2 + - + +
936A GLN* 3.1 53.7 + - - +
962A PHE 5.1 1.6 - - - +
964A PRO* 3.8 37.0 - - + -
967A MET* 4.1 8.5 - - - -
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Residues in contact with ARG 933 (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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926A GLU* 2.6 40.4 + - - -
929A ALA* 3.0 25.9 + - - +
930A GLY* 2.9 16.6 + - - +
932A LEU* 1.3 74.5 - - + +
934A GLN* 1.3 65.2 + - + +
936A GLN* 3.3 16.2 + - - +
937A GLU* 3.0 31.2 + - + +
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Residues in contact with GLN 934 (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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896A LEU* 3.5 42.6 - - + +
899A ASP* 6.4 0.4 - - - +
900A LEU* 5.2 6.0 - - - +
930A GLY* 3.1 18.6 + - - +
931A PRO* 3.6 18.6 - - + +
933A ARG* 1.3 77.5 - - + +
935A MET* 1.3 61.1 - - - +
937A GLU* 3.2 9.6 + - - +
938A CYS* 3.1 18.7 + - - +
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Residues in contact with MET 935 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A LEU* 4.3 9.0 - - + +
891A MET* 3.7 29.2 - - + -
896A LEU* 3.6 10.4 - - - +
908A LEU* 4.0 11.2 - - + -
911A CYS* 4.1 13.7 - - + -
912A PHE* 3.7 18.2 - - + -
931A PRO 3.0 16.1 + - - +
932A LEU* 3.7 27.6 - - + +
934A GLN* 1.3 76.6 - - - +
936A GLN* 1.3 67.2 + - + +
938A CYS* 3.3 4.9 + - - +
939A ALA* 2.9 27.4 + - - +
962A PHE* 3.8 30.1 - - + +
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Residues in contact with GLN 936 (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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932A LEU* 3.1 50.3 + - + +
933A ARG* 3.8 17.2 - - - +
934A GLN 3.2 0.2 - - - -
935A MET* 1.3 83.3 - - + +
937A GLU* 1.3 61.7 + - - +
939A ALA* 3.2 6.1 + - - +
940A LYS* 2.9 37.9 + - - +
959A LEU* 3.9 29.4 + - + +
962A PHE 5.4 3.2 + - - -
964A PRO* 5.5 2.6 - - - +
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Residues in contact with GLU 937 (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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933A ARG* 3.0 22.1 + - + +
934A GLN* 3.2 9.6 + - - +
936A GLN* 1.3 76.4 - - + +
938A CYS* 1.3 62.1 + - - +
940A LYS* 3.1 41.0 + - - +
941A ARG* 3.2 13.0 + - - +
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Residues in contact with CYS 938 (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 LEU* 3.6 17.9 - - + -
890A GLU* 3.6 33.4 - - - -
891A MET* 4.0 14.4 - - + -
894A ASN* 3.8 12.3 - - - +
896A LEU* 4.7 6.3 - - + -
934A GLN 3.1 12.0 + - - +
935A MET 3.5 8.3 - - - +
937A GLU* 1.3 75.8 - - - +
939A ALA* 1.3 63.8 + - - +
941A ARG* 3.1 14.3 + - - +
942A ILE* 3.1 21.5 + - - +
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Residues in contact with ALA 939 (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 LEU* 3.8 25.9 - - + +
935A MET* 2.9 21.0 + - - +
936A GLN* 3.2 8.9 + - - +
938A CYS* 1.3 76.5 - - - +
940A LYS* 1.3 61.8 + - - +
942A ILE* 3.4 2.0 + - - -
943A ALA* 3.0 20.3 + - - +
958A TYR* 3.5 19.7 - - + -
959A LEU* 3.6 17.3 - - + -
962A PHE* 4.6 4.3 - - + -
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Residues in contact with LYS 940 (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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936A GLN* 2.9 19.2 + - - +
937A GLU* 3.1 34.6 + - - +
939A ALA* 1.3 77.7 - - - +
941A ARG* 1.3 57.2 + - - +
943A ALA* 3.1 6.1 + - - +
944A LYS* 2.8 27.8 + - - +
955A GLU* 3.2 29.2 - - - +
959A LEU* 3.6 31.4 - - + -
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Residues in contact with ARG 941 (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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861A LEU* 3.9 15.2 - - - +
890A GLU* 2.9 30.9 + - - +
894A ASN* 2.8 34.1 + - - +
937A GLU 3.2 6.9 + - - +
938A CYS* 3.1 17.3 + - - +
940A LYS* 1.3 80.0 - - - +
942A ILE* 1.3 57.2 + - - +
944A LYS* 3.0 14.9 + - + +
945A VAL* 2.8 40.8 + - + +
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Residues in contact with ILE 942 (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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857A VAL* 5.9 0.2 - - + -
861A LEU* 4.3 19.5 - - + -
886A LEU* 4.0 20.2 - - + +
887A LEU* 3.4 48.5 - - + +
890A GLU* 4.0 20.6 - - + -
938A CYS 3.1 10.7 + - - +
939A ALA 3.8 6.1 - - - +
940A LYS 3.3 0.2 - - - -
941A ARG* 1.3 76.1 - - + +
943A ALA* 1.3 58.5 + - - +
945A VAL* 3.2 6.9 + - - +
946A SER* 2.8 43.5 + - - +
953A ILE* 5.8 0.2 - - + -
958A TYR* 3.7 22.7 - - + +
1104A MLI 5.3 2.7 - - - +
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Residues in contact with ALA 943 (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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939A ALA 3.0 14.5 + - - +
940A LYS 3.1 9.8 + - - +
942A ILE* 1.3 78.7 - - - +
944A LYS* 1.3 56.1 + - - +
946A SER* 3.4 1.7 + - - -
947A ALA* 2.9 29.8 + - - +
953A ILE* 4.1 23.7 - - + +
955A GLU* 4.2 27.4 - - + -
958A TYR* 4.1 14.1 - - + -
959A LEU* 5.3 0.2 - - + -
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Residues in contact with LYS 944 (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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940A LYS 2.8 13.1 + - - +
941A ARG* 3.3 16.6 - - + +
943A ALA* 1.3 73.0 - - - +
945A VAL* 1.3 72.1 + - + +
947A ALA* 3.1 7.4 + - - +
948A GLU* 2.9 64.8 + - + +
955A GLU* 6.2 0.2 - - - -
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Residues in contact with VAL 945 (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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857A VAL* 4.2 14.4 - - + -
860A ARG* 4.3 24.4 + - + -
861A LEU* 4.1 39.5 - - + -
941A ARG* 2.8 32.6 + - + +
942A ILE* 3.7 6.3 - - - +
944A LYS* 1.3 76.1 - - + +
946A SER* 1.3 57.3 + - - +
948A GLU* 3.3 14.2 + - - +
949A ALA* 2.9 27.9 + - - +
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Residues in contact with SER 946 (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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567A TYR* 4.5 5.5 + - - -
857A VAL* 4.0 18.7 - - - +
886A LEU* 5.1 0.7 - - - +
942A ILE* 2.8 38.4 + - - +
943A ALA* 3.6 6.2 - - - -
945A VAL* 1.3 73.0 - - - +
947A ALA* 1.3 63.0 + - - +
949A ALA* 3.0 11.8 + - - +
951A LEU* 3.1 33.3 + - - +
953A ILE* 4.0 19.8 - - - +
1104A MLI 4.7 6.2 + - - -
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Residues in contact with ALA 947 (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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943A ALA 2.9 17.2 + - - +
944A LYS* 3.1 6.7 + - - +
946A SER* 1.3 76.3 - - - +
948A GLU* 1.3 59.1 + - + +
950A LYS* 2.8 28.6 + - - +
951A LEU 4.0 10.7 - - - +
953A ILE* 4.0 10.7 - - + +
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Residues in contact with GLU 948 (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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856A ARG* 5.3 0.2 + - - -
860A ARG* 3.3 21.5 + - - +
944A LYS* 2.9 61.5 + - + +
945A VAL* 3.7 11.0 - - - +
947A ALA* 1.3 76.4 - - + +
949A ALA* 1.3 59.9 + - - +
950A LYS* 3.1 21.6 + - - +
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Residues in contact with ALA 949 (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 CYS* 3.3 21.7 - - - +
856A ARG* 3.1 25.7 + - + +
857A VAL* 3.4 35.0 - - + +
860A ARG* 3.4 13.6 - - - +
945A VAL 2.9 8.9 + - - +
946A SER 3.0 6.2 + - - +
948A GLU* 1.3 74.5 - - - +
950A LYS* 1.3 67.8 + - - +
951A LEU* 3.4 1.3 - - + +
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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) + - + + + + + -
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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