Contacts of the helix formed by residues 944 - 969 (chain B) in PDB entry 1SO2
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 VAL 944 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678B ASN* 2.9 35.7 + - + +
943B LYS* 1.3 72.7 - - - +
945B ARG* 1.3 71.2 + - + +
946B ASP* 3.6 26.5 - - + +
947B LEU* 2.8 35.3 + - + +
948B HIS 3.0 9.7 + - - -
1064B HIS* 3.6 18.5 + - + +
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Residues in contact with ARG 945 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B HG9 4.3 16.4 - - - +
943B LYS 3.6 1.8 + - - -
944B VAL* 1.3 76.0 - - + +
946B ASP* 1.3 69.6 + - - +
948B HIS* 3.6 1.1 - - - +
949B LEU* 3.0 56.3 + - + +
1064B HIS* 4.9 1.0 + - - -
1068B ASN* 3.5 20.6 + - - +
1071B ILE* 3.6 30.0 - - + +
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Residues in contact with ASP 946 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944B VAL* 2.9 27.0 + - + +
945B ARG* 1.3 83.2 - - - +
947B LEU* 1.3 69.7 + - + +
949B LEU* 3.9 5.9 + - - +
950B LYS* 3.5 19.6 + - - +
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Residues in contact with LEU 947 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678B ASN* 3.8 27.8 - - - +
679B PHE 3.7 24.5 - - - +
680B PRO* 4.8 9.0 - - + -
681B ILE* 4.9 3.4 - - + -
682B PHE* 3.9 25.8 - - + +
943B LYS* 3.9 22.9 - - + +
944B VAL* 2.8 21.2 + - + +
946B ASP* 1.3 80.8 - - + +
948B HIS* 1.3 65.1 + - - +
950B LYS* 3.0 14.9 + - - +
951B TRP* 3.2 29.9 + - + +
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Residues in contact with HIS 948 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B 666 3.0 16.6 + - - +
940B GLY* 3.6 20.3 + - - +
941B PRO* 3.6 17.8 - - + +
944B VAL 3.0 10.4 + - - +
945B ARG 3.6 6.3 - - - +
947B LEU* 1.3 78.1 - - - +
949B LEU* 1.3 66.4 + - + +
951B TRP 3.6 0.2 + - - -
952B THR* 2.6 51.8 + - - -
988B GLN* 3.6 17.7 - - - -
992B ILE* 4.8 0.9 - - + -
1068B ASN* 3.2 38.4 - - + +
1071B ILE* 4.4 1.8 - - + -
1072B TRP* 3.1 28.4 + + - -
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Residues in contact with LEU 949 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B HG9 3.9 15.8 - - + +
452B HG9 4.5 16.8 - - + -
945B ARG* 3.0 51.6 + - + +
946B ASP* 4.4 6.1 - - - +
947B LEU 3.3 0.2 - - - -
948B HIS* 1.3 84.2 - - + +
950B LYS* 1.3 60.6 + - - +
952B THR* 3.7 4.7 - - - -
953B GLU* 2.9 30.4 + - - +
1071B ILE* 4.4 8.1 - - + -
1072B TRP* 3.7 33.9 - - + -
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Residues in contact with LYS 950 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682B PHE* 3.4 48.3 - - + -
946B ASP 3.5 13.5 + - - +
947B LEU 3.0 10.8 + - - +
949B LEU* 1.3 80.6 - - - +
951B TRP* 1.3 62.7 + - - +
953B GLU* 3.5 31.0 + - - +
954B GLY* 3.3 16.1 + - - -
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Residues in contact with TRP 951 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B 666 3.6 25.6 - - + +
681B ILE* 4.3 5.9 - - + +
682B PHE* 3.4 32.7 - + - -
735B PRO 5.2 4.0 - - - -
736B TYR* 3.5 36.5 - + + -
738B ASN* 4.8 3.1 - - - -
740B ILE* 3.5 29.6 - - + -
741B HIS* 3.6 30.5 - - + -
744B ASP* 3.9 34.6 + - + -
939B ASN* 4.9 2.4 - - - +
940B GLY* 4.5 13.2 - - - -
943B LYS* 5.6 0.6 - - + +
947B LEU* 3.2 33.2 + - + +
948B HIS 4.0 1.3 - - - +
950B LYS* 1.3 76.8 - - - +
952B THR* 1.3 63.7 + - - +
954B GLY* 3.0 3.6 + - - -
955B ILE* 3.0 20.1 + - - +
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Residues in contact with THR 952 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B HG9 5.1 4.0 - - + -
462B 666 3.2 8.1 + - - -
948B HIS* 2.6 42.8 + - - -
949B LEU* 3.7 8.7 - - - -
951B TRP* 1.3 75.4 - - - +
953B GLU* 1.3 63.5 + - - +
955B ILE* 3.1 24.9 - - - +
956B VAL* 3.1 9.2 + - + +
984B LEU* 3.8 22.2 - - + -
988B GLN* 3.3 26.7 - - + +
1072B TRP* 4.5 9.0 - - + -
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Residues in contact with GLU 953 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B HG9 3.9 30.1 - - + +
949B LEU 2.9 18.5 + - - +
950B LYS* 3.6 30.7 + - - +
951B TRP 3.2 0.2 - - - -
952B THR* 1.3 78.4 - - - +
954B GLY* 1.3 59.1 + - - +
956B VAL* 2.9 26.4 - - - +
957B ASN* 3.2 26.3 + - - +
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Residues in contact with GLY 954 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735B PRO* 3.6 31.3 - - - +
736B TYR* 3.6 10.1 - - - +
950B LYS 3.3 7.7 + - - -
951B TRP* 3.0 8.6 + - - -
953B GLU* 1.3 80.3 - - - +
955B ILE* 1.3 61.0 + - - +
957B ASN* 3.4 2.1 + - - -
958B GLU* 3.1 22.7 + - - +
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Residues in contact with ILE 955 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B 666 4.0 32.5 - - + -
736B TYR* 3.7 33.2 - - + -
737B HIS* 4.1 14.4 - - + -
951B TRP 3.0 13.1 + - - +
952B THR* 3.1 25.4 - - - +
954B GLY* 1.3 76.3 - - - +
956B VAL* 1.3 65.0 + - + +
958B GLU* 3.3 3.6 + - + -
959B PHE* 3.0 56.0 + - + -
987B LEU* 5.1 2.9 - - + -
988B GLN* 4.2 14.6 - - - +
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Residues in contact with VAL 956 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B HG9 3.9 23.3 - - + -
952B THR* 3.1 15.1 + - + +
953B GLU* 2.9 30.7 - - - +
955B ILE* 1.3 78.6 - - + +
957B ASN* 1.3 70.0 + - - +
959B PHE* 3.3 7.4 + - - +
960B TYR* 3.1 43.1 + - + +
976B PHE 6.1 0.2 - - - -
984B LEU* 3.6 31.0 - - + -
987B LEU* 4.6 11.4 - - + -
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Residues in contact with ASN 957 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B HG9 3.1 63.1 + - - +
735B PRO* 4.0 17.3 - - + +
953B GLU* 3.2 36.8 + - - +
954B GLY* 4.0 5.8 - - - +
955B ILE 3.4 0.2 - - - -
956B VAL* 1.3 83.0 - - - +
958B GLU* 1.3 62.2 + - - +
960B TYR* 3.2 9.0 + - - +
961B GLU* 3.1 28.6 + - - +
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Residues in contact with GLU 958 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734B ILE* 3.6 9.4 - - + +
735B PRO* 3.6 15.0 - - + +
736B TYR* 3.0 13.9 + - - -
737B HIS* 2.5 57.4 + - - -
825B HIS* 4.1 0.2 - - - -
827B GLY* 3.3 35.9 - - - +
828B ARG* 5.7 1.1 - - - +
954B GLY 3.1 16.1 + - - +
955B ILE* 3.7 9.6 - - + +
956B VAL 3.2 0.2 - - - -
957B ASN* 1.3 77.9 - - - +
959B PHE* 1.3 65.7 + - + +
961B GLU* 3.2 8.8 + - - +
962B GLN* 3.1 20.4 + - - +
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Residues in contact with PHE 959 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462B 666 3.7 61.7 - + + -
737B HIS* 5.8 0.7 - + - -
829B THR* 4.8 4.5 - - + -
955B ILE* 3.0 43.2 + - + +
956B VAL* 3.3 6.5 + - - +
958B GLU* 1.3 80.0 - - + +
960B TYR* 1.3 57.9 + - + +
962B GLN* 3.3 4.6 + - - +
963B GLY 2.9 22.9 + - - -
976B PHE* 4.2 15.5 - - + +
977B MET* 3.3 49.8 - - + +
987B LEU* 4.1 25.4 - - + -
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Residues in contact with TYR 960 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B HG9 3.9 36.1 + - + +
956B VAL* 3.1 34.1 + - + +
957B ASN* 3.6 8.3 - - - +
958B GLU 3.1 0.2 - - - -
959B PHE* 1.3 74.9 - - + +
961B GLU* 1.3 66.6 + - - +
963B GLY* 3.3 0.5 + - - -
964B ASP* 3.0 29.5 + - - +
976B PHE 3.9 17.9 - - - -
977B MET* 3.7 10.7 - - - +
978B ASP 3.9 4.5 - - - -
979B ARG* 3.3 69.3 - - + +
982B PRO* 3.4 25.8 - - + +
983B GLN 5.0 0.7 + - - -
984B LEU* 5.3 5.7 + - - +
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Residues in contact with GLU 961 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B HG9 6.1 0.7 - - - -
734B ILE* 5.0 6.9 - - - +
735B PRO* 4.1 25.7 - - - +
828B ARG* 3.7 23.8 + - - +
957B ASN* 3.1 19.7 + - - +
958B GLU* 3.2 9.4 + - - +
960B TYR* 1.3 75.7 - - - +
962B GLN* 1.3 63.0 + - - +
964B ASP* 3.4 9.8 + - - +
965B GLU* 3.3 16.8 + - - +
979B ARG* 4.8 6.7 - - - +
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Residues in contact with GLN 962 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827B GLY 4.2 2.5 - - - +
828B ARG* 3.3 39.5 - - + +
829B THR* 2.9 46.0 + - - +
832B PHE* 3.6 13.3 - - + +
958B GLU 3.1 12.6 + - - +
959B PHE* 3.6 9.9 - - - +
961B GLU* 1.3 78.0 - - - +
963B GLY* 1.3 57.0 + - - +
965B GLU* 3.3 4.2 + - - +
966B GLU* 3.0 52.1 + - + +
974B SER* 3.9 3.0 + - - -
977B MET* 3.4 22.4 - - - +
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Residues in contact with GLY 963 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
959B PHE 2.9 10.9 + - - -
960B TYR 3.3 0.6 + - - -
962B GLN* 1.3 74.2 - - - +
964B ASP* 1.3 66.5 + - - +
966B GLU* 3.3 17.8 + - - +
967B ALA* 3.0 24.4 + - - +
973B ILE* 4.1 11.0 - - - +
977B MET* 3.5 22.0 - - - +
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Residues in contact with ASP 964 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
960B TYR 3.0 16.3 + - - +
961B GLU* 3.6 10.4 - - - +
962B GLN 3.2 0.2 - - - -
963B GLY* 1.3 75.2 - - - +
965B GLU* 1.3 59.4 + - - +
967B ALA* 3.2 6.8 + - - +
968B ASN* 2.8 41.5 + - - +
977B MET 5.5 0.5 - - - +
979B ARG* 2.6 47.6 + - - +
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Residues in contact with GLU 965 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828B ARG* 2.6 48.2 + - - +
832B PHE* 3.6 22.2 - - + -
961B GLU 3.3 3.2 + - - +
962B GLN 3.3 9.2 + - - +
964B ASP* 1.3 79.4 - - - +
966B GLU* 1.3 56.9 + - - +
968B ASN* 3.1 9.3 + - + +
969B LEU* 2.9 42.7 + - + +
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Residues in contact with GLU 966 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832B PHE* 3.9 25.3 - - + +
962B GLN* 3.0 41.6 + - - +
963B GLY* 3.5 14.6 - - - +
965B GLU* 1.3 75.3 - - - +
967B ALA* 1.3 56.7 + - - +
969B LEU* 3.1 7.2 + - - -
971B LEU* 2.7 43.9 + - + +
972B PRO 4.0 14.7 - - - +
973B ILE* 3.3 5.1 - - - -
974B SER* 2.4 51.6 + - - -
977B MET* 4.5 0.9 - - - +
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Residues in contact with ALA 967 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963B GLY 3.0 17.2 + - - +
964B ASP* 3.6 6.7 - - - +
966B GLU* 1.3 73.4 - - - +
968B ASN* 1.3 67.4 + - - +
970B GLY* 2.9 14.7 + - - -
971B LEU 4.0 8.7 + - - -
973B ILE* 4.0 20.8 - - + +
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Residues in contact with ASN 968 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964B ASP* 2.8 32.0 + - - +
965B GLU* 3.1 13.8 + - + +
967B ALA* 1.3 79.2 - - - +
969B LEU* 1.3 62.4 + - + +
970B GLY 3.2 2.8 + - - -
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Residues in contact with LEU 969 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832B PHE* 4.4 3.8 - - + -
836B THR* 3.9 28.7 - - + -
965B GLU* 2.9 40.2 + - + +
966B GLU 3.7 4.9 - - - +
967B ALA 3.1 0.8 - - - -
968B ASN* 1.3 78.7 - - + +
970B GLY* 1.3 59.6 + - - +
971B LEU* 3.0 21.7 + - + +
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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