Contacts of the helix formed by residues 942 - 972 (chain A) in PDB entry 3H2V
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 GLY 942 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941A SER* 1.3 79.6 + - - +
943A THR* 1.3 58.2 + - - +
944A LYS* 3.1 33.3 + - - +
946A ALA* 4.0 6.8 + - - +
117E ARG* 3.5 21.6 + - - -
122E GLU* 4.4 17.6 + - - +
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Residues in contact with THR 943 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
936A LEU* 3.6 34.8 - - + +
939A GLY* 3.0 39.5 - - - +
940A GLY 3.5 3.3 + - - -
941A SER* 2.8 3.7 - - - +
942A GLY 1.3 82.3 - - - +
944A LYS* 1.3 54.4 + - - +
945A ARG 3.5 0.2 - - - -
946A ALA* 4.4 4.7 - - - -
947A LEU* 2.6 39.6 + - - +
1006A LEU* 3.1 26.2 - - - +
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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
----------------------------------------------------------
941A SER* 3.5 22.0 - - - +
942A GLY* 3.1 31.8 + - - +
943A THR* 1.3 74.5 + - - +
945A ARG* 1.3 92.1 + - + +
947A LEU* 3.6 2.0 - - - +
948A ILE* 3.1 29.6 + - + +
1003A ALA* 4.2 29.4 - - + +
1006A LEU* 4.8 5.7 - - + +
117E ARG* 3.2 20.5 - - - +
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Residues in contact with ARG 945 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944A LYS* 1.3 100.6 - - + +
946A ALA* 1.3 63.9 + - - +
948A ILE* 3.2 8.4 + - + +
949A GLN* 2.9 22.0 + - - +
117E ARG* 2.8 54.5 - - - +
120E GLU* 3.1 41.2 + - - +
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Residues in contact with ALA 946 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932A GLU* 4.9 0.4 - - - +
936A LEU* 3.6 26.7 - - + -
942A GLY 4.0 11.0 + - - +
943A THR 3.4 4.4 + - - +
944A LYS 3.3 0.6 - - - -
945A ARG* 1.3 78.7 - - - +
947A LEU* 1.3 54.9 + - - +
949A GLN* 3.0 3.9 + - - +
950A CYS* 2.8 34.5 + - - +
120E GLU 3.3 17.5 + - - +
121E ARG* 4.1 23.0 + - + +
122E GLU 5.2 0.4 - - - +
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Residues in contact with LEU 947 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
933A MET* 3.1 44.9 - - + +
936A LEU* 3.5 31.0 - - + +
937A VAL* 4.9 7.4 - - + +
943A THR 2.6 22.8 + - - +
944A LYS* 3.6 5.2 - - - +
946A ALA* 1.3 71.4 - - - +
948A ILE* 1.3 60.6 + - - +
951A ALA* 3.2 19.1 + - - +
999A SER* 4.2 20.7 - - - +
1002A LYS* 4.0 27.8 - - + -
1003A ALA* 4.4 9.4 - - + +
1006A LEU* 4.7 7.2 - - + -
1023A LEU* 5.2 2.0 - - + -
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Residues in contact with ILE 948 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944A LYS* 3.1 23.7 + - + +
945A ARG* 3.5 8.7 - - - +
946A ALA 3.1 0.4 - - - -
947A LEU* 1.3 73.7 - - - +
949A GLN* 1.3 71.5 + - - +
951A ALA* 3.1 7.5 + - - +
952A LYS* 3.0 44.9 + - + +
999A SER* 4.9 3.6 - - - +
1000A THR* 4.2 26.9 - - + +
1003A ALA* 3.7 21.8 - - + -
1004A THR* 6.3 0.4 - - + -
120E GLU* 5.5 2.7 - - - +
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Residues in contact with GLN 949 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
945A ARG 2.9 7.3 + - - +
946A ALA* 3.5 6.7 - - - +
948A ILE* 1.3 78.1 - - - +
950A CYS* 1.3 52.0 + - - +
952A LYS* 3.1 40.1 + - - +
953A ASP* 2.7 45.4 + - - +
956A LYS* 5.6 0.3 + - - -
119E ARG* 3.3 10.1 - - + +
120E GLU* 3.1 48.8 + - + +
121E ARG* 3.6 12.6 - - - +
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Residues in contact with CYS 950 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929A LEU* 3.5 28.0 - - - -
932A GLU* 4.1 17.9 - - - -
933A MET* 3.6 20.2 - - + -
936A LEU* 4.0 11.2 - - + -
946A ALA 2.8 19.4 + - - +
947A LEU 3.6 5.6 - - - +
949A GLN* 1.3 74.4 - - - +
951A ALA* 1.3 57.5 + - - +
953A ASP* 3.2 4.0 + - - +
954A ILE* 3.0 30.7 + - - +
121E ARG* 3.9 16.1 - - - +
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Residues in contact with ALA 951 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
933A MET* 3.6 14.3 - - + +
947A LEU 3.2 10.2 + - - +
948A ILE* 3.1 5.6 + - - +
950A CYS* 1.3 78.1 - - - +
952A LYS* 1.3 63.9 + - - +
954A ILE* 3.3 10.4 + - - +
955A ALA* 3.1 22.5 + - - +
992A SER 5.3 0.3 - - - +
995A LEU* 4.2 12.3 - - + +
996A LYS* 4.2 11.9 - - + +
999A SER* 3.3 27.1 - - - +
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Residues in contact with LYS 952 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948A ILE* 3.0 31.8 + - + +
949A GLN* 3.2 40.9 - - - +
951A ALA* 1.3 74.2 - - + +
953A ASP* 1.3 66.7 + - - +
955A ALA* 3.2 5.1 + - - +
956A LYS* 3.0 21.5 + - - +
996A LYS* 4.5 20.2 - - + -
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Residues in contact with ASP 953 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929A LEU* 3.6 22.5 - - + +
949A GLN* 2.7 31.1 + - - +
950A CYS 3.2 9.6 - - - +
952A LYS* 1.3 71.8 - - - +
954A ILE* 1.3 60.0 + - - +
956A LYS* 2.9 49.1 + - - +
957A ALA* 3.1 7.8 + - - +
69E ASP* 3.7 14.7 - - - +
119E ARG* 4.0 3.4 + - - -
121E ARG* 3.0 31.6 + - - -
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Residues in contact with ILE 954 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926A MET* 4.2 9.8 - - + +
929A LEU* 3.8 23.3 - - + +
930A MET* 3.2 33.0 - - + -
933A MET* 4.0 21.3 - - - -
950A CYS* 3.0 24.2 + - - +
951A ALA* 3.5 6.5 - - - +
952A LYS 3.2 0.2 - - - -
953A ASP* 1.3 77.7 - - - +
955A ALA* 1.3 59.4 + - - +
957A ALA* 2.9 16.2 + - - +
958A SER* 2.8 24.1 + - - +
992A SER* 5.1 1.3 - - - -
995A LEU* 3.8 12.3 - - + -
1030A LEU* 3.5 31.2 - - + -
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Residues in contact with ALA 955 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951A ALA 3.1 12.7 + - - +
952A LYS 3.2 7.6 + - - +
954A ILE* 1.3 75.4 - - - +
956A LYS* 1.3 63.4 + - - +
958A SER* 3.3 8.7 + - - -
959A ASP* 2.9 35.5 + - - +
992A SER* 4.1 17.9 + - - +
996A LYS* 4.0 32.1 - - + +
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Residues in contact with LYS 956 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925A ARG* 5.8 0.2 - - - -
949A GLN* 5.6 0.6 + - - -
952A LYS 3.0 10.7 + - - +
953A ASP* 2.9 37.7 + - - +
955A ALA* 1.3 79.1 - - - +
957A ALA* 1.3 59.5 + - - +
959A ASP* 3.2 9.9 + - - +
960A GLU* 3.0 32.2 + - + +
69E ASP* 5.4 3.8 + - - -
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Residues in contact with ALA 957 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922A ALA* 4.0 9.9 - - + +
925A ARG* 4.4 20.6 - - + +
926A MET* 3.2 35.2 - - + +
929A LEU* 4.9 4.3 - - + -
953A ASP 3.1 6.9 + - - +
954A ILE* 2.9 7.5 + - - +
956A LYS* 1.3 76.7 - - - +
958A SER* 1.3 61.9 + - - +
960A GLU* 3.3 7.0 + - - +
961A VAL* 3.1 24.3 + - - +
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Residues in contact with SER 958 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926A MET* 3.8 20.5 - - - +
954A ILE* 2.8 17.3 + - - +
955A ALA* 3.4 10.8 - - - -
957A ALA* 1.3 72.8 - - - +
959A ASP* 1.3 68.0 + - - +
961A VAL* 2.8 6.1 + - - +
962A THR* 2.8 28.3 + - - -
988A ILE* 3.4 25.5 - - - +
989A PRO* 5.4 0.7 - - - -
992A SER* 3.6 16.3 - - - -
1030A LEU* 4.6 0.8 - - - +
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Residues in contact with ASP 959 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955A ALA* 2.9 26.9 + - - +
956A LYS* 3.4 12.2 - - - +
958A SER* 1.3 75.4 - - - +
960A GLU* 1.3 67.7 + - - +
962A THR* 3.8 6.5 - - - -
963A ARG* 3.0 28.2 + - - +
989A PRO* 4.8 17.2 - - - +
992A SER* 4.9 2.8 + - - -
996A LYS* 5.9 0.3 + - - -
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Residues in contact with GLU 960 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922A ALA* 4.9 9.2 - - + -
925A ARG* 5.6 6.3 - - - +
956A LYS* 3.0 30.0 + - + +
957A ALA* 3.7 9.4 - - - +
958A SER 3.0 0.8 - - - -
959A ASP* 1.3 87.7 - - - +
961A VAL* 1.3 64.2 + - - +
962A THR 3.2 0.2 - - - -
963A ARG* 3.2 39.8 + - - +
964A LEU* 3.1 35.1 + - + +
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Residues in contact with VAL 961 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919A ILE* 4.0 24.6 - - + +
922A ALA* 3.8 19.5 - - + -
923A ALA 4.6 1.3 - - - +
926A MET* 4.3 2.9 - - - -
957A ALA 3.1 17.4 + - - +
958A SER* 2.8 13.3 + - - +
960A GLU* 1.3 72.8 - - - +
962A THR* 1.3 58.4 + - - +
964A LEU* 3.8 0.3 - - - -
965A ALA* 2.8 32.6 + - + +
988A ILE* 4.2 11.4 - - + -
1034A VAL* 4.2 28.3 - - + +
1037A THR* 3.9 24.9 - - + -
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Residues in contact with THR 962 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
958A SER 2.8 16.5 + - - -
959A ASP* 3.8 6.3 - - - -
961A VAL* 1.3 75.0 - - - +
963A ARG* 1.3 68.4 + - - +
965A ALA* 3.0 6.6 + - - +
966A LYS* 2.9 47.7 + - - +
985A CYS* 3.2 29.2 - - + +
986A GLU* 5.1 0.2 - - - +
988A ILE* 3.6 19.7 - - - +
989A PRO* 4.1 16.3 - - + +
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Residues in contact with ARG 963 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918A ASP* 5.3 3.6 + - - -
959A ASP 3.0 19.8 + - - +
960A GLU* 3.2 30.3 + - - +
962A THR* 1.3 76.3 - - - +
964A LEU* 1.3 99.9 + - - +
966A LYS* 3.4 9.6 + - - +
967A GLU* 3.3 23.6 + - + +
73F GLN* 5.5 7.1 - - - +
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Residues in contact with LEU 964 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918A ASP* 3.4 43.5 - - + +
919A ILE* 3.8 17.0 - - + +
960A GLU* 3.1 23.0 + - + +
963A ARG* 1.3 109.3 - - - +
965A ALA* 1.3 67.2 + - - +
966A LYS 3.0 2.0 - - - -
967A GLU* 3.1 7.6 + - + +
968A VAL* 3.0 27.5 + - - +
1054A PHE* 3.9 30.8 - - + -
1056A LEU* 5.3 3.8 - - + -
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Residues in contact with ALA 965 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919A ILE* 3.9 8.4 - - - +
961A VAL 2.8 23.8 + - - +
962A THR 3.0 5.4 + - - +
964A LEU* 1.3 72.8 - - - +
966A LYS* 1.3 57.0 + - - +
968A VAL* 3.3 4.7 + - - +
969A ALA* 3.0 23.3 + - - +
981A LEU* 3.4 19.0 - - + +
985A CYS* 4.1 19.7 - - + -
1037A THR* 4.0 24.5 - - + -
1041A ALA* 5.5 0.7 - - - -
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Residues in contact with LYS 966 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962A THR* 2.9 30.9 + - + +
963A ARG* 3.6 8.7 - - - +
965A ALA* 1.3 77.1 - - - +
967A GLU* 1.3 61.0 + - - +
969A ALA* 3.2 5.1 + - - +
970A LYS* 2.8 30.9 + - - +
982A LEU* 3.9 14.3 - - + +
985A CYS* 3.2 27.1 - - - -
986A GLU* 3.3 29.0 + - - -
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Residues in contact with GLU 967 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963A ARG* 3.3 14.5 + - - +
964A LEU* 3.1 12.4 + - + +
966A LYS* 1.3 79.3 - - - +
968A VAL* 1.3 60.6 + - - +
970A LYS* 2.9 39.7 + - - +
971A GLN* 3.2 42.4 + - - +
1054A PHE* 4.0 32.8 + - + +
----------------------------------------------------------
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Residues in contact with VAL 968 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919A ILE* 5.0 1.6 - - + -
964A LEU 3.0 16.7 + - - +
965A ALA* 3.4 10.1 - - - +
966A LYS 3.1 0.2 - - - -
967A GLU* 1.3 75.0 - - - +
969A ALA* 1.3 60.3 + - - +
971A GLN* 3.1 9.1 + - - +
972A CYS* 3.0 24.1 + - - +
981A LEU* 3.8 16.2 - - + -
1041A ALA* 3.9 22.0 - - + +
1044A ALA* 4.0 16.3 - - + +
1045A SER* 4.6 6.3 - - - +
1048A ILE* 6.1 2.0 - - + -
1054A PHE* 5.1 10.1 - - + -
1055A THR* 6.4 0.2 - - - -
1056A LEU* 4.3 28.5 - - + +
----------------------------------------------------------
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Residues in contact with ALA 969 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
965A ALA 3.0 17.1 + - - +
966A LYS 3.6 4.7 - - - +
968A VAL* 1.3 77.4 - - - +
970A LYS* 1.3 61.3 + - - +
972A CYS* 3.3 11.5 + - - +
978A ARG* 3.0 36.6 + - + +
981A LEU* 3.7 17.5 - - + +
982A LEU* 3.7 32.3 - - + -
----------------------------------------------------------
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Residues in contact with LYS 970 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
966A LYS 2.8 17.5 + - - +
967A GLU* 2.9 36.6 + - - +
968A VAL 3.2 0.2 - - - -
969A ALA* 1.3 76.3 - - - +
971A GLN* 1.3 68.1 + - - +
972A CYS 4.6 1.6 - - - +
978A ARG* 5.5 0.9 - - - +
1049A ARG* 4.4 10.6 - - - -
----------------------------------------------------------
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Residues in contact with GLN 971 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967A GLU* 3.2 29.7 + - - +
968A VAL* 3.1 11.3 + - - +
970A LYS* 1.3 93.7 + - - +
972A CYS* 1.3 64.6 + - - +
1047A LYS 4.7 0.2 - - - -
1048A ILE* 3.9 25.5 - - + -
1049A ARG* 3.1 39.1 + - + +
1050A THR* 3.6 21.9 - - - +
1053A GLY* 3.9 4.5 - - - -
1054A PHE 3.8 32.5 - - - +
----------------------------------------------------------
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Residues in contact with CYS 972 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968A VAL 3.0 11.6 + - - +
969A ALA* 3.3 14.3 + - - +
970A LYS 4.6 2.4 - - - +
971A GLN* 1.3 80.8 - - - +
973A THR* 1.3 61.5 + - - +
974A ASP* 3.4 31.9 - - - -
977A ILE* 4.3 0.9 - - - -
978A ARG* 2.8 33.8 + - + -
1044A ALA* 3.8 30.5 - - + +
1047A LYS* 3.8 18.2 - - - -
1049A ARG* 5.0 2.8 - - - +
----------------------------------------------------------
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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).
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