Contacts of the helix formed by residues 922 - 947 (chain M) in PDB entry 3HOU
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 ASP 922 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901M LEU* 4.3 1.4 - - - +
902M LEU* 3.7 6.7 - - - +
918M GLU 5.1 5.2 - - - +
919M ILE* 2.9 22.3 + - - +
920M LEU 3.2 1.6 + - - -
921M GLY* 1.3 74.6 - - - +
923M LEU* 1.3 61.4 + - - +
924M LYS* 2.9 23.9 + - - +
925M LEU* 3.0 35.5 + - + +
926M GLN* 3.4 16.1 + - - +
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Residues in contact with LEU 923 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902M LEU* 3.3 40.4 - - + -
921M GLY 2.9 9.9 + - - +
922M ASP* 1.3 73.2 + - - +
924M LYS* 1.3 64.9 + - + +
925M LEU 3.3 0.5 + - - -
926M GLN* 3.4 9.2 + - + +
927M VAL* 3.1 17.7 + - - +
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Residues in contact with LYS 924 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922M ASP* 2.9 9.0 + - - +
923M LEU* 1.3 79.3 - - + +
925M LEU* 1.3 63.1 + - + +
927M VAL* 3.2 29.7 - - - +
928M LEU* 4.1 7.8 + - - +
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Residues in contact with LEU 925 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901M LEU* 3.3 15.0 - - + -
919M ILE* 3.1 44.0 - - + -
922M ASP* 3.0 27.8 + - - +
924M LYS* 1.3 77.0 - - + +
926M GLN* 1.3 54.2 + - - +
927M VAL 2.8 5.4 - - - -
928M LEU* 2.6 36.6 + - + +
929M LEU* 2.8 15.7 + - + +
982M THR* 6.0 3.1 - - + -
983M ILE* 4.0 16.8 - - + -
984M LYS* 4.8 17.9 - - + -
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Residues in contact with GLN 926 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898M ARG* 4.5 1.0 + - - -
899M VAL 3.3 13.0 + - - +
900M ASP* 3.4 15.2 - - - +
901M LEU* 2.7 48.9 + - + +
902M LEU* 3.3 41.3 - - + +
922M ASP 3.4 2.7 + - - +
923M LEU* 3.4 10.1 + - + +
925M LEU* 1.3 76.2 - - - +
927M VAL* 1.3 56.6 + - - +
928M LEU 3.2 0.2 - - - -
929M LEU* 3.4 9.1 - - - +
930M ASP* 2.8 60.8 + - - +
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Residues in contact with VAL 927 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
923M LEU 3.1 19.7 - - - +
924M LYS* 3.2 30.3 - - - +
925M LEU 2.7 0.8 + - - -
926M GLN* 1.3 77.9 - - - +
928M LEU* 1.3 61.1 + - + +
930M ASP* 4.1 3.2 - - - +
931M GLU* 3.0 32.2 + - - +
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Residues in contact with LEU 928 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924M LYS 4.5 7.6 - - - +
925M LEU* 2.6 23.2 + - + +
927M VAL* 1.3 73.5 - - + +
929M LEU* 1.3 60.2 + - + +
930M ASP 3.0 1.1 - - - -
931M GLU* 2.8 28.4 + - - +
932M GLU* 2.7 36.9 + - - +
983M ILE* 5.4 1.1 - - + +
984M LYS* 4.1 40.4 - - + -
987M VAL* 4.5 27.6 - - + +
988M LEU* 4.7 11.2 - - + -
991M LYS* 6.0 0.2 - - - +
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Residues in contact with LEU 929 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898M ARG* 4.1 1.8 + - - -
899M VAL* 3.2 44.4 + - + +
901M LEU* 4.2 1.1 - - + -
925M LEU 2.8 21.5 + - - +
926M GLN* 3.4 29.2 - - - +
928M LEU* 1.3 76.0 - - + +
930M ASP* 1.3 58.5 + - - +
932M GLU* 3.7 11.1 - - - +
933M TYR* 3.0 28.6 + - - +
983M ILE* 3.2 42.4 - - + -
987M VAL* 5.1 4.0 - - + -
1028M THR* 4.4 14.8 - - + +
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Residues in contact with ASP 930 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898M ARG* 2.6 43.9 + - - +
902M LEU* 5.6 1.9 - - - +
926M GLN* 2.8 41.5 + - - +
927M VAL* 4.1 3.8 - - - +
929M LEU* 1.3 75.0 - - - +
931M GLU* 1.3 65.7 + - - +
932M GLU 3.2 0.4 - - - -
933M TYR* 3.9 0.9 - - - +
934M LYS* 3.0 35.1 + - - +
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Residues in contact with GLU 931 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927M VAL* 3.0 23.4 + - - +
928M LEU* 2.8 29.2 + - - +
930M ASP* 1.3 75.8 - - - +
932M GLU* 1.3 62.4 + - - +
934M LYS* 3.4 12.5 + - - +
935M GLN* 3.2 20.8 + - - +
991M LYS* 2.9 33.0 + - - +
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Residues in contact with GLU 932 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897M TYR 4.1 14.7 - - - +
899M VAL* 5.3 0.2 - - - +
928M LEU 2.7 19.4 + - - +
929M LEU* 3.7 13.8 - - - +
931M GLU* 1.3 69.3 - - - +
933M TYR* 1.3 66.0 + - - +
934M LYS 3.0 5.0 + - - -
935M GLN* 3.0 17.1 + - - +
936M LEU* 3.0 26.6 + - + +
986M ILE* 5.0 0.3 - - - +
987M VAL* 3.0 24.2 - - + +
1026M LEU 4.9 1.9 - - - +
1027M ALA* 4.2 9.6 - - - +
1028M THR* 2.7 48.1 + - - -
1029M ARG 4.5 0.2 + - - -
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Residues in contact with TYR 933 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893M PHE* 3.6 25.0 - + - -
894M GLU* 3.2 33.3 - - + +
897M TYR* 3.5 15.9 - - + +
898M ARG* 3.3 68.0 - - + +
899M VAL 5.5 0.7 - - - +
929M LEU 3.0 16.0 + - - +
930M ASP 4.3 1.6 - - - +
932M GLU* 1.3 79.8 - - + +
934M LYS* 1.3 61.2 + - - +
936M LEU* 4.0 8.7 - - + -
937M VAL* 3.3 26.0 + - + +
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Residues in contact with LYS 934 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930M ASP* 3.0 27.1 + - - +
931M GLU* 3.4 11.6 - - - +
932M GLU 3.0 1.0 + - - -
933M TYR* 1.3 76.1 - - - +
935M GLN* 1.3 60.7 + - - +
937M VAL* 2.9 30.2 - - + +
938M LYS* 2.9 11.0 + - + +
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Residues in contact with GLN 935 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931M GLU 3.2 8.3 + - - +
932M GLU* 3.0 10.5 + - - +
934M LYS* 1.3 77.2 - - - +
936M LEU* 1.3 69.9 + - + +
938M LYS* 2.7 32.8 + - - +
939M ASP* 2.7 46.9 + - - -
1023M ARG* 3.1 37.1 - - - +
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Residues in contact with LEU 936 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885M THR* 3.7 9.1 - - + +
893M PHE* 3.8 11.4 - - + -
897M TYR* 3.1 52.9 - - + +
932M GLU* 3.0 32.9 + - + +
933M TYR* 4.0 10.8 - - - +
935M GLN* 1.3 76.2 - - + +
937M VAL* 1.3 58.3 + - - +
939M ASP* 3.3 9.1 + - - +
940M ARG* 3.0 26.0 + - - +
1023M ARG* 3.9 35.0 - - + +
1024M SER* 5.7 0.4 - - - -
1027M ALA* 3.9 11.0 - - + -
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Residues in contact with VAL 937 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893M PHE* 3.7 26.7 - - + -
933M TYR* 3.3 20.6 + - + +
934M LYS* 2.9 26.0 - - + +
935M GLN 3.1 0.6 - - - -
936M LEU* 1.3 77.5 - - - +
938M LYS* 1.3 66.2 + - + +
940M ARG* 3.4 4.3 - - - +
941M LYS* 3.3 44.8 + - + +
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Residues in contact with LYS 938 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934M LYS* 2.9 14.1 + - + +
935M GLN* 2.7 39.5 + - - +
937M VAL* 1.3 71.7 - - + +
939M ASP* 1.3 70.6 + - - +
941M LYS* 3.1 9.6 + - - +
942M PHE* 2.9 23.7 + - + +
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Residues in contact with ASP 939 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885M THR* 4.4 8.1 - - + +
935M GLN* 2.7 31.3 + - - +
936M LEU* 3.3 12.0 - - - +
938M LYS* 1.3 73.7 - - - +
940M ARG* 1.3 53.1 + - - +
942M PHE* 2.7 29.4 + - - +
943M LEU* 2.8 21.7 + - + +
1020M CYS* 3.9 29.4 - - + +
1023M ARG* 2.6 50.2 + - - +
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Residues in contact with ARG 940 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885M THR* 3.1 39.8 + - + +
886M ILE* 4.5 3.3 - - - +
887M GLY 3.3 4.8 + - - -
888M GLY 2.3 34.6 + - - -
889M SER 3.7 11.7 + - - -
890M ASP* 2.9 24.7 + - - +
893M PHE* 3.4 34.2 - - - +
936M LEU 3.0 6.4 + - - +
937M VAL 3.4 11.2 - - - +
939M ASP* 1.3 78.4 - - - +
941M LYS* 1.3 81.2 + - - +
943M LEU* 4.0 4.5 - - - +
944M ARG* 2.9 52.9 + - - +
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Residues in contact with LYS 941 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890M ASP* 4.4 6.2 + - - -
893M PHE* 6.1 0.2 - - - -
937M VAL* 3.3 35.7 + - + +
938M LYS* 3.1 8.8 + - - +
940M ARG* 1.3 119.6 - - - +
942M PHE* 1.3 65.4 + - - +
944M ARG* 3.2 15.1 + - + +
945M GLU* 3.1 24.2 + - - +
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Residues in contact with PHE 942 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938M LYS* 2.9 16.4 + - + +
939M ASP* 2.7 15.3 + - - +
941M LYS* 1.3 73.7 - - - +
943M LEU* 1.3 77.5 + - + +
945M GLU* 3.1 20.4 - - - +
946M VAL* 3.1 30.4 + - + +
1016M THR* 3.9 20.4 - - + -
1017M LEU* 5.3 0.9 - - + -
1020M CYS* 4.4 10.8 - - - -
201Q LYS* 4.0 12.1 - - + -
206Q GLY* 3.7 19.7 - - - -
207Q ARG* 3.4 44.4 - - + -
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Residues in contact with LEU 943 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883M LEU* 3.6 34.3 - - + -
885M THR* 4.5 9.9 - - - -
886M ILE* 3.6 36.0 - - + +
939M ASP 2.8 23.6 + - - +
940M ARG 4.0 2.5 - - - +
942M PHE* 1.3 75.3 - - + +
944M ARG* 1.3 58.6 + - - +
945M GLU 2.8 10.2 + - - -
946M VAL* 2.9 4.5 + - + +
947M PHE* 2.8 30.4 + - + +
1017M LEU* 3.8 26.9 - - + -
1020M CYS* 3.9 24.9 - - + -
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Residues in contact with ARG 944 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886M ILE* 3.0 31.9 + - + -
887M GLY 4.1 0.2 + - - -
888M GLY 3.2 5.3 + - - -
890M ASP* 5.1 0.6 + - - -
940M ARG* 2.9 55.7 + - - +
941M LYS* 3.2 14.9 + - - +
943M LEU* 1.3 77.2 - - - +
945M GLU* 1.3 57.1 + - - +
947M PHE 4.4 2.5 - - - -
948M VAL* 3.6 19.3 - - - +
1292M PRO* 3.7 23.9 - - - +
1296M GLY* 2.8 31.5 + - - -
1298M TYR* 3.1 39.0 + - - +
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Residues in contact with GLU 945 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941M LYS* 3.1 14.0 + - - +
942M PHE* 3.1 22.8 - - - +
943M LEU 2.8 0.2 - - - -
944M ARG* 1.3 80.2 - - - +
946M VAL* 1.3 62.5 + - - +
948M VAL* 3.9 14.7 - - - +
201Q LYS* 2.5 37.0 + - - +
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Residues in contact with VAL 946 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
942M PHE* 3.1 24.6 + - + +
943M LEU* 2.9 9.2 + - + +
945M GLU* 1.3 78.7 - - - +
947M PHE* 1.3 91.7 + - + +
948M VAL* 3.5 4.4 + - - +
1017M LEU* 6.2 0.4 - - + -
201Q LYS* 3.3 43.6 - - + +
202Q SER 3.9 14.8 - - - +
203Q GLU 4.8 0.4 - - - +
206Q GLY* 3.5 13.0 - - - +
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Residues in contact with PHE 947 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883M LEU* 4.2 18.4 - - + -
886M ILE* 3.9 13.5 - - + +
943M LEU* 2.8 18.0 + - + +
944M ARG 4.2 1.5 - - - +
946M VAL* 1.3 101.5 - - + +
948M VAL* 1.3 50.7 + - - +
949M ASP* 3.0 5.6 - - + -
950M GLY* 2.6 32.4 + - - -
951M GLU* 3.8 16.6 - - + +
954M TRP* 3.3 60.8 - + + -
1017M LEU* 4.0 14.4 - - + -
1298M TYR* 4.5 0.3 + - - -
203Q GLU* 3.5 35.2 - - + -
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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
------------------------------------------------------------
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