Contacts of the helix formed by residues 942 - 979 (chain I) in PDB entry 6ALG
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 942 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
850I ILE* 5.2 5.2 - - - +
868I SER* 2.5 30.1 + - - +
870I ILE* 4.0 10.8 - - - +
933I VAL* 5.4 0.9 - - - +
940I GLU 3.9 1.4 + - - -
941I LYS* 1.3 78.3 - - - +
943I LYS* 1.3 64.1 + - - +
944I ARG 4.2 1.8 - - - -
945I ALA* 3.3 22.3 + - - +
946I LEU* 3.4 20.0 + - - +
1048I LYS* 3.7 24.9 + - - +
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Residues in contact with LYS 943 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867I GLU* 3.3 30.5 - - + +
868I SER* 4.6 6.6 + - - -
942I ASP* 1.3 78.4 - - - +
944I ARG* 1.3 59.3 + - - +
946I LEU* 3.2 11.7 + - + +
947I GLU* 2.9 29.4 + - + +
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Residues in contact with ARG 944 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866I ASP* 3.3 26.6 + - - +
868I SER* 3.7 21.8 + - - +
870I ILE* 3.7 38.4 - - + +
871I VAL 3.2 22.5 + - - -
872I TYR* 4.5 13.1 - - - -
873I ILE* 3.9 23.2 - - - +
931I VAL* 3.9 19.2 - - - +
933I VAL* 5.8 0.9 - - + -
942I ASP 3.4 0.6 - - - -
943I LYS* 1.3 78.3 - - - +
945I ALA* 1.3 59.4 + - - +
947I GLU* 3.0 24.2 + - - +
948I ILE* 2.9 47.4 + - + +
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Residues in contact with ALA 945 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
933I VAL* 3.8 28.8 - - + +
935I THR* 5.0 1.8 - - - +
941I LYS* 4.3 19.2 - - + +
942I ASP* 3.3 23.3 + - - +
943I LYS 3.3 0.4 - - - -
944I ARG* 1.3 77.7 - - - +
946I LEU* 1.3 59.9 + - - +
948I ILE* 3.9 8.9 - - - +
949I GLU* 2.9 31.2 + - - +
1048I LYS* 5.9 0.4 - - - +
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Residues in contact with LEU 946 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941I LYS* 4.0 22.9 - - + +
942I ASP 3.4 13.8 + - - +
943I LYS* 3.2 12.6 + - + +
945I ALA* 1.3 74.4 - - - +
947I GLU* 1.3 61.2 + - - +
949I GLU* 3.6 23.4 - - - +
950I GLU* 2.9 31.4 + - - +
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Residues in contact with GLU 947 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866I ASP* 4.8 3.1 - - - +
943I LYS* 2.9 17.2 + - + +
944I ARG* 3.0 30.5 + - - +
946I LEU* 1.3 78.3 - - - +
948I ILE* 1.3 58.8 + - + +
950I GLU* 3.3 14.8 + - - +
951I MET* 2.9 37.0 + - + +
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Residues in contact with ILE 948 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873I ILE* 6.2 3.8 - - + -
931I VAL* 4.1 24.2 - - + +
932I GLN* 6.0 0.2 - - - -
933I VAL* 4.0 30.3 - - + +
944I ARG* 2.9 48.8 + - + +
945I ALA* 4.0 4.5 - - - +
947I GLU* 1.3 75.5 - - + +
949I GLU* 1.3 62.2 + - - +
951I MET* 3.2 7.7 + - + +
952I GLN* 2.9 50.7 + - + +
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Residues in contact with GLU 949 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941I LYS* 2.6 42.4 + - - +
945I ALA 2.9 15.9 + - - +
946I LEU* 3.6 16.2 - - - +
948I ILE* 1.3 76.6 - - - +
950I GLU* 1.3 56.5 + - - +
952I GLN* 3.5 9.5 + - - +
953I LEU* 3.0 29.7 + - + +
1036I ILE* 4.1 18.9 - - + +
1037I THR* 3.3 32.6 + - - +
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Residues in contact with GLU 950 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946I LEU 2.9 22.0 + - - +
947I GLU* 3.3 13.8 - - - +
948I ILE 3.2 0.2 - - - -
949I GLU* 1.3 76.6 - - - +
951I MET* 1.3 58.7 + - - +
953I LEU* 3.3 10.0 + - + +
954I LYS* 3.0 29.0 + - + +
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Residues in contact with MET 951 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873I ILE* 5.3 15.3 - - + -
947I GLU* 2.9 25.3 + - + +
948I ILE* 3.7 7.2 - - + +
950I GLU* 1.3 74.0 - - - +
952I GLN* 1.3 62.3 + - + +
954I LYS* 3.3 9.0 + - + +
955I GLN* 2.9 39.0 + - + +
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Residues in contact with GLN 952 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931I VAL 5.7 0.8 + - - -
932I GLN* 4.7 17.8 + - - +
948I ILE* 2.9 36.7 + - + +
949I GLU* 3.9 5.5 - - - +
951I MET* 1.3 75.0 - - + +
953I LEU* 1.3 60.5 + - - +
955I GLN* 3.8 5.6 - - - +
956I ALA* 2.9 30.3 + - - +
1036I ILE* 3.7 28.6 - - + +
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Residues in contact with LEU 953 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
949I GLU* 3.0 18.9 + - + +
950I GLU* 3.3 9.2 + - + +
952I GLN* 1.3 77.9 - - - +
954I LYS* 1.3 57.1 + - - +
956I ALA* 3.4 3.6 + - + +
957I LYS* 2.9 35.2 + - + +
1032I LYS* 6.5 0.2 - - + -
1033I ARG* 3.7 48.5 - - + +
1036I ILE* 4.4 15.4 - - + +
1037I THR* 5.7 2.9 - - - +
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Residues in contact with LYS 954 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
950I GLU* 3.0 18.3 + - + +
951I MET* 3.3 10.5 + - + +
953I LEU* 1.3 76.5 - - - +
955I GLN* 1.3 65.1 + - - +
957I LYS* 3.9 6.6 - - - +
958I LYS* 2.9 37.9 + - + +
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Residues in contact with GLN 955 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
951I MET* 2.9 32.0 + - + +
952I GLN* 4.0 5.6 - - - +
954I LYS* 1.3 81.8 - - + +
956I ALA* 1.3 61.4 + - - +
958I LYS* 4.0 21.4 - - - +
959I ASP* 2.9 48.8 + - - +
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Residues in contact with ALA 956 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
952I GLN 2.9 18.7 + - - +
953I LEU* 3.8 6.1 - - + +
955I GLN* 1.3 78.3 - - - +
957I LYS* 1.3 57.5 + - - +
959I ASP* 3.4 4.2 + - - -
960I LEU* 3.0 38.0 + - + +
1032I LYS* 3.8 40.8 - - + +
1036I ILE* 4.0 7.6 - - + -
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Residues in contact with LYS 957 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953I LEU* 2.9 24.4 + - + +
954I LYS* 4.0 6.3 - - - +
956I ALA* 1.3 76.2 - - - +
958I LYS* 1.3 57.7 + - - +
960I LEU* 4.4 3.3 - - - +
961I SER* 2.8 36.2 + - - -
1025I PHE* 5.2 1.7 - - + -
1029I LEU* 4.7 24.2 - - + -
1033I ARG* 4.6 20.4 - - - +
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Residues in contact with LYS 958 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G GLU* 4.5 24.1 + - - +
731I ARG* 5.2 6.7 - - - +
954I LYS* 2.9 28.1 + - + +
955I GLN* 4.0 23.6 - - - +
956I ALA 3.3 0.2 - - - -
957I LYS* 1.3 75.9 - - - +
959I ASP* 1.3 60.8 + - - +
961I SER* 2.9 7.5 + - - +
962I GLU* 2.9 49.9 + - + +
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Residues in contact with ASP 959 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731I ARG* 3.6 21.0 + - - +
752I ASN* 5.8 1.5 - - - +
955I GLN* 2.9 40.0 + - - +
956I ALA* 3.8 5.8 - - - +
958I LYS* 1.3 77.3 + - - +
960I LEU* 1.3 63.7 + - + +
962I GLU* 3.3 6.0 + - - +
963I GLU* 2.9 33.1 + - + +
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Residues in contact with LEU 960 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956I ALA* 3.0 29.2 + - + +
957I LYS* 4.4 2.5 - - - +
959I ASP* 1.3 83.3 - - + +
961I SER* 1.3 57.6 + - - +
963I GLU* 3.3 13.7 + - + +
964I LEU 3.0 21.3 + - - -
1025I PHE* 3.3 31.9 - - + +
1028I LYS* 4.0 47.8 - - + +
1029I LEU* 4.2 10.1 - - + +
1032I LYS* 4.7 19.7 - - + +
----------------------------------------------------------
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Residues in contact with SER 961 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
957I LYS* 2.8 27.4 + - - -
958I LYS* 2.9 16.8 + - - +
960I LEU* 1.3 79.3 - - - +
962I GLU* 1.3 60.1 + - - +
964I LEU* 3.3 4.2 + - - +
965I GLN* 2.9 38.1 + - - +
1025I PHE* 3.7 15.8 - - - -
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Residues in contact with GLU 962 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731I ARG* 4.8 18.4 + - - +
958I LYS* 2.9 44.6 + - + +
959I ASP* 3.8 4.7 - - - +
961I SER* 1.3 77.3 + - - +
963I GLU* 1.3 61.3 + - - +
965I GLN* 3.0 25.3 + - - +
966I ILE* 2.9 54.3 + - + +
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Residues in contact with GLU 963 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731I ARG* 5.3 3.1 + - - -
750I ILE* 3.3 46.8 - - - +
752I ASN* 4.2 14.4 + - - +
959I ASP* 2.9 21.7 + - + +
960I LEU* 3.3 17.3 - - + +
962I GLU* 1.3 76.0 - - - +
964I LEU* 1.3 57.4 + - - +
966I ILE* 4.5 0.2 - - - +
967I LEU* 2.9 40.0 + - + +
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Residues in contact with LEU 964 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
960I LEU 3.0 15.6 + - - +
961I SER* 3.3 5.1 + - - +
963I GLU* 1.3 77.4 - - - +
965I GLN* 1.3 51.8 + - - +
967I LEU* 4.7 2.2 - - + -
968I GLU* 2.6 43.2 + - - +
1018I TYR* 4.7 11.7 - - + +
1021I LEU* 3.7 44.4 - - + +
1022I LYS* 4.3 21.5 - - + +
1025I PHE* 3.6 40.2 - - + -
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Residues in contact with GLN 965 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961I SER* 2.9 23.9 + - - +
962I GLU* 3.0 32.8 + - - +
963I GLU 3.3 0.4 - - - -
964I LEU* 1.3 77.6 - - - +
966I ILE* 1.3 62.3 + - + +
968I GLU* 3.5 12.2 - - - +
969I ALA* 2.9 27.5 + - - +
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Residues in contact with ILE 966 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725I GLN* 4.9 6.6 + - - +
726I TYR* 5.4 7.0 - - + -
731I ARG* 4.8 13.9 - - - +
733I VAL* 3.9 30.1 - - + -
748I ILE* 3.7 23.8 - - + +
750I ILE* 4.1 13.7 - - + -
962I GLU* 2.9 38.8 + - + +
965I GLN* 1.3 74.7 - - + +
967I LEU* 1.3 59.9 + - - +
969I ALA* 3.1 8.5 + - - +
970I GLY* 2.9 23.4 + - - -
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Residues in contact with LEU 967 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747I GLY* 3.8 28.9 - - - -
748I ILE* 4.0 18.4 - - + +
750I ILE* 4.8 8.0 - - + +
963I GLU* 2.9 25.4 + - + +
964I LEU* 4.7 3.4 - - + +
966I ILE* 1.3 74.8 - - - +
968I GLU* 1.3 59.7 + - - +
970I GLY* 4.3 1.1 - - - +
971I LEU* 2.9 31.0 + - + +
1021I LEU* 3.7 39.7 - - + +
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Residues in contact with GLU 968 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964I LEU* 2.6 31.8 + - - +
965I GLN* 3.5 15.4 - - - +
967I LEU* 1.3 76.7 - - - +
969I ALA* 1.3 56.8 + - - +
971I LEU* 4.1 2.6 - - - +
972I PHE* 2.9 53.9 + - + +
994I ARG* 5.6 2.7 - - - +
1018I TYR* 3.1 41.9 + - + -
1021I LEU* 5.3 0.6 - - - +
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Residues in contact with ALA 969 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725I GLN* 5.2 11.4 - - - +
735I LYS* 6.1 0.2 - - - -
965I GLN 2.9 14.9 + - - +
966I ILE* 3.1 11.4 + - - +
968I GLU* 1.3 75.5 - - - +
970I GLY* 1.3 50.7 + - - +
973I SER* 2.3 41.6 + - - -
994I ARG* 3.8 19.9 + - - +
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Residues in contact with GLY 970 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725I GLN* 6.1 0.2 - - - +
735I LYS* 5.2 4.3 - - - -
747I GLY* 5.2 5.4 - - - -
748I ILE* 4.7 22.9 - - - -
966I ILE 2.9 13.8 + - - -
967I LEU* 3.3 3.8 + - - -
968I GLU 3.3 0.2 - - - -
969I ALA* 1.3 76.8 - - - +
971I LEU* 1.3 57.0 + - - +
973I SER* 3.0 7.0 + - - -
974I ARG* 2.9 35.2 + - - +
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Residues in contact with LEU 971 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746I ALA* 6.3 1.8 - - + +
747I GLY* 5.2 9.3 - - - +
967I LEU* 2.9 19.6 + - + +
968I GLU* 4.1 4.5 - - - +
970I GLY* 1.3 74.2 - - - +
972I PHE* 1.3 67.4 + - + +
974I ARG* 3.0 9.7 + - - +
975I ILE* 2.9 48.6 + - + +
1014I LEU* 3.3 42.9 - - + +
1017I GLN* 3.9 11.9 - - + -
1018I TYR* 3.9 28.0 - - + +
1021I LEU* 4.0 15.7 - - + -
----------------------------------------------------------
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Residues in contact with PHE 972 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
968I GLU* 2.9 49.1 + - + +
971I LEU* 1.3 88.3 - - + +
973I SER* 1.3 57.5 + - - +
975I ILE* 3.2 26.0 + - + +
976I ARG 3.0 23.0 + - - -
994I ARG* 3.6 62.1 - - + +
995I ASP* 4.0 17.7 - - + -
997I TRP* 3.5 12.7 - + + -
998I LEU* 6.2 0.2 - - + -
1015I ALA* 6.5 0.7 - - - -
1018I TYR* 3.9 30.1 - + + -
----------------------------------------------------------
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Residues in contact with SER 973 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735I LYS* 4.6 11.2 + - - -
969I ALA* 2.3 29.3 + - - -
970I GLY* 3.0 14.0 + - - -
972I PHE* 1.3 77.2 - - - +
974I ARG* 1.3 56.6 + - - +
976I ARG* 3.8 10.7 - - - +
977I ALA* 2.9 25.6 + - - +
994I ARG* 3.7 9.7 - - - +
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Residues in contact with ARG 974 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735I LYS* 5.6 2.4 - - - +
736I VAL* 5.3 5.1 + - - +
738I GLU* 5.5 2.2 - - - +
741I MET* 2.8 42.8 - - - +
743I PRO 5.7 0.2 - - - -
746I ALA* 3.5 25.6 - - - +
747I GLY* 2.7 32.5 + - - +
748I ILE* 4.4 8.7 - - - +
970I GLY 2.9 21.0 + - - +
971I LEU* 3.0 7.5 + - - +
973I SER* 1.3 76.5 - - - +
975I ILE* 1.3 60.6 + - - +
977I ALA* 3.2 9.9 + - + +
978I VAL* 2.8 37.9 + - + +
1010I GLN* 5.7 4.9 - - - +
1014I LEU* 3.7 19.3 - - + -
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Residues in contact with ILE 975 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971I LEU* 2.9 25.9 + - + +
972I PHE* 3.2 37.2 + - + +
974I ARG* 1.3 76.8 - - - +
976I ARG* 1.3 57.4 + - - +
978I VAL* 3.0 23.0 + - - +
979I LEU* 3.0 17.2 + - + +
989I LEU* 5.9 0.2 - - + -
995I ASP 5.7 0.4 - - - +
997I TRP* 3.7 34.1 - - + +
998I LEU* 4.1 20.6 - - + -
1011I LEU* 3.7 20.9 - - + -
1014I LEU* 3.6 20.4 - - + -
1015I ALA* 5.6 0.4 - - - -
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Residues in contact with ARG 976 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
972I PHE 3.0 15.6 + - - +
973I SER* 3.8 10.3 - - - +
975I ILE* 1.3 75.8 - - - +
977I ALA* 1.3 60.6 + - - +
979I LEU 3.6 3.0 + - - +
980I VAL* 3.3 23.2 + - + +
989I LEU* 3.5 43.8 - - + +
990I ASP* 4.5 19.8 + - - +
994I ARG* 6.1 1.8 - - - +
997I TRP* 3.6 28.5 - - + -
----------------------------------------------------------
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Residues in contact with ALA 977 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738I GLU* 6.1 0.9 - - - +
973I SER 2.9 18.8 + - - +
974I ARG* 3.2 13.2 + - + +
976I ARG* 1.3 74.5 - - - +
978I VAL* 1.3 64.0 + - + +
980I VAL* 3.7 20.2 - - - +
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Residues in contact with VAL 978 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
974I ARG* 2.8 26.0 + - + +
975I ILE* 3.0 12.1 + - - +
977I ALA* 1.3 75.7 - - + +
979I LEU* 1.3 68.3 + - + +
980I VAL 3.1 7.6 + - - -
981I ALA* 2.9 20.8 + - - +
1002I LEU* 5.3 2.2 - - + -
1007I LYS* 4.6 24.4 - - + +
1010I GLN* 4.6 26.7 - - + +
1011I LEU* 4.1 17.7 - - + -
1014I LEU* 5.5 4.3 - - + -
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Residues in contact with LEU 979 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
975I ILE* 3.0 21.6 + - + +
976I ARG* 3.6 6.0 + - - +
977I ALA 3.5 0.2 - - - -
978I VAL* 1.3 75.9 - - + +
980I VAL* 1.3 61.4 + - - +
981I ALA 3.3 7.0 - - - -
983I GLY 4.4 12.3 - - - +
984I VAL* 3.3 22.4 - - - +
985I GLU 4.4 5.2 + - - +
989I LEU* 4.5 19.0 - - + +
997I TRP* 4.0 12.6 - - + +
1000I LEU* 3.7 36.8 - - + -
1001I GLY 5.8 0.2 - - - +
1002I LEU* 4.0 17.3 - - + -
1011I LEU* 3.7 36.8 - - + -
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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) + - + + + + + -
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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