Contacts of the helix formed by residues 1012 - 1046 (chain G) in PDB entry 5F28
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 LEU1012 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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929E THR* 4.2 18.8 - - + +
932E VAL* 3.7 23.6 - - + -
933E LYS* 3.8 32.5 - - + +
936E ILE* 4.4 10.5 - - + -
1007G TYR* 3.6 31.9 - - + -
1010G THR* 2.9 14.9 + - + +
1011G SER* 1.3 84.3 - - - +
1013G GLN* 1.3 64.4 + - - +
1014G GLN 3.3 1.1 - - - -
1015G GLU* 3.1 28.7 + - + +
1016G TYR* 3.1 22.5 + - + -
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Residues in contact with GLN1013 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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945G ALA 4.4 3.2 + - - -
946G PRO* 5.4 1.2 - - - +
947G PRO* 3.9 6.9 - - - +
950G TYR* 3.9 10.1 + - - +
1004G ALA* 3.5 24.2 - - + +
1007G TYR* 3.2 24.0 + - - +
1008G VAL* 3.3 37.1 + - - +
1010G THR 3.5 7.1 + - - +
1011G SER 3.4 0.8 - - - -
1012G LEU* 1.3 77.6 - - - +
1014G GLN* 1.3 57.5 + - - +
1016G TYR* 3.2 3.1 + - - +
1017G LYS* 2.9 63.3 + - + +
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Residues in contact with GLN1014 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943G GLN* 5.1 6.3 - - - +
1010G THR 5.1 0.2 + - - -
1011G SER* 3.3 30.5 + - - +
1013G GLN* 1.3 79.2 - - - +
1015G GLU* 1.3 76.6 + - - +
1017G LYS* 3.5 16.0 + - + +
1018G LYS* 3.1 37.6 + - - +
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Residues in contact with GLU1015 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936E ILE* 3.1 44.0 - - + +
940E SER* 5.4 3.5 - - - -
1011G SER 4.1 13.7 - - - +
1012G LEU* 3.1 21.1 + - + +
1014G GLN* 1.3 88.0 + - + +
1016G TYR* 1.3 60.5 + - - +
1018G LYS* 3.2 48.6 + - - +
1019G GLN* 3.7 11.8 + - - +
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Residues in contact with TYR1016 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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932E VAL* 3.4 17.0 - - + +
935E VAL* 4.8 5.2 - - + +
936E ILE* 3.4 27.0 - - + +
1024F ALA 5.4 0.2 + - - -
1025F HIS* 5.9 0.4 - - - -
1028F ALA* 3.3 23.6 - - - +
1000G LYS* 3.9 6.4 - - + +
1003G LEU* 3.4 39.0 - - + -
1004G ALA* 3.7 24.2 - - + +
1007G TYR* 3.8 24.5 - + - -
1012G LEU* 3.1 22.7 + - + +
1013G GLN 4.1 0.2 - - - +
1015G GLU* 1.3 74.6 - - - +
1017G LYS* 1.3 61.0 + - - +
1018G LYS 3.2 0.9 - - - -
1019G GLN* 3.4 30.5 + - + +
1020G MET* 3.0 29.5 + - - +
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Residues in contact with LYS1017 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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942G ILE* 3.3 41.0 + - + +
943G GLN* 3.4 22.0 + - + +
944G PRO 4.2 0.4 - - - -
945G ALA 2.8 35.8 + - - +
950G TYR* 4.0 10.1 - - + -
1004G ALA* 4.7 2.2 - - + -
1013G GLN* 2.9 49.7 + - + +
1014G GLN* 3.7 13.1 - - - +
1016G TYR* 1.3 77.0 - - - +
1018G LYS* 1.3 62.6 + - - +
1020G MET* 3.0 18.1 + - - +
1021G LEU* 3.0 27.4 + - - +
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Residues in contact with LYS1018 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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946E PRO* 3.8 22.6 - - + +
949E GLU* 2.8 48.8 + - + +
943G GLN* 5.1 12.3 - - + +
1014G GLN* 3.1 25.5 + - - +
1015G GLU* 3.2 43.4 + - - +
1016G TYR 3.2 0.6 - - - -
1017G LYS* 1.3 77.6 - - - +
1019G GLN* 1.3 58.1 + - + +
1021G LEU* 3.1 22.6 + - + +
1022G THR* 3.2 12.1 + - - +
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Residues in contact with GLN1019 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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936E ILE* 3.8 21.6 - - - +
939E SER* 3.9 21.2 + - - -
943E GLN* 4.1 15.5 + - - +
1021F LEU* 5.9 1.4 - - - +
1000G LYS* 2.9 46.1 + - + +
1015G GLU 3.7 9.0 + - - +
1016G TYR* 3.4 27.8 + - - +
1017G LYS 3.3 0.4 - - - -
1018G LYS* 1.3 76.2 - - + +
1020G MET* 1.3 64.8 + - - +
1022G THR* 3.1 19.7 + - - +
1023G ALA* 3.2 13.7 + - - +
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Residues in contact with MET1020 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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938G MET* 5.1 1.8 - - - -
942G ILE* 3.6 28.9 - - + -
950G TYR* 4.4 8.7 - - + -
954G VAL* 3.6 24.7 - - + -
997G LEU* 3.4 20.7 - - + +
1000G LYS* 3.6 22.0 - - + +
1001G MET* 3.6 37.0 - - + +
1004G ALA* 4.0 14.4 - - - -
1016G TYR 3.0 18.1 + - - +
1017G LYS* 3.0 12.7 + - - +
1019G GLN* 1.3 77.0 - - - +
1021G LEU* 1.3 57.0 + - - +
1023G ALA 3.3 0.5 + - - -
1024G ALA* 2.9 27.3 + - - +
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Residues in contact with LEU1021 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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946E PRO* 4.0 16.6 - - + -
948E GLU* 3.4 36.3 - - + +
938G MET* 5.0 6.7 - - - -
939G SER* 3.7 29.8 - - - +
942G ILE* 3.6 24.5 - - + -
943G GLN* 4.4 18.8 - - + +
1017G LYS 3.0 17.0 + - - +
1018G LYS* 3.1 12.3 + - + +
1020G MET* 1.3 77.9 - - - +
1022G THR* 1.3 57.4 + - - +
1024G ALA* 3.4 3.1 + - + +
1025G HIS* 2.9 38.7 + - + -
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Residues in contact with THR1022 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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943E GLN* 3.4 28.2 + - + +
944E PRO 3.9 13.7 - - - +
946E PRO* 3.7 36.6 - - + -
1018G LYS 3.2 3.5 + - - +
1019G GLN* 3.1 16.3 + - - -
1021G LEU* 1.3 77.5 - - - +
1023G ALA* 1.3 56.3 + - - +
1025G HIS* 4.0 5.9 - - - +
1026G ALA* 3.1 27.7 + - - +
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Residues in contact with ALA1023 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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993G ASP* 4.4 8.3 - - - +
996G GLU* 4.2 17.7 - - + +
997G LEU* 3.8 31.6 - - - +
1000G LYS* 4.7 1.6 - - + -
1019G GLN 3.2 14.6 + - - +
1020G MET* 3.7 5.2 - - - +
1021G LEU 3.2 0.8 - - - -
1022G THR* 1.3 81.1 + - - +
1024G ALA* 1.3 58.3 + - - +
1026G ALA* 3.5 6.3 + - - +
1027G LEU* 3.2 23.0 + - - +
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Residues in contact with ALA1024 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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935G VAL* 3.5 30.1 - - + +
938G MET* 4.0 22.2 - - + -
939G SER* 5.6 1.1 - - - +
997G LEU* 4.2 15.9 - - + +
1020G MET 2.9 16.7 + - - +
1021G LEU* 4.0 4.0 - - - +
1023G ALA* 1.3 75.2 - - - +
1025G HIS* 1.3 64.3 + - - +
1027G LEU* 3.1 9.7 + - - +
1028G ALA 3.1 17.3 + - - -
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Residues in contact with HIS1025 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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946E PRO* 4.8 1.3 - - + -
947E PRO* 4.0 24.9 - - + +
948E GLU* 3.2 26.3 + - - -
1008E VAL* 4.3 7.4 - - + -
1009E MET* 3.4 32.3 - - + +
1013E GLN* 5.9 3.8 - - - +
935G VAL* 3.5 11.5 - - + +
936G ILE* 5.4 0.9 - - - -
939G SER* 3.1 26.0 + - - -
1021G LEU* 2.9 28.9 + - + +
1022G THR* 4.2 6.3 - - - +
1024G ALA* 1.3 75.5 - - - +
1026G ALA* 1.3 58.1 + - - +
1028G ALA* 3.4 2.8 + - - +
1029G VAL* 3.1 33.0 + - + +
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Residues in contact with ALA1026 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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993G ASP* 3.3 18.1 - - - +
1022G THR 3.1 20.0 + - - +
1023G ALA* 3.7 8.3 - - - +
1024G ALA 3.2 0.2 - - - -
1025G HIS* 1.3 74.6 - - - +
1027G LEU* 1.3 65.5 + - - +
1029G VAL* 3.4 6.6 + - - +
1030G ASP* 3.1 23.2 + - - +
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Residues in contact with LEU1027 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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931G LEU* 4.0 20.6 - - + -
935G VAL* 4.7 3.4 - - + -
957G VAL* 3.5 32.3 - - + -
961G LEU* 4.3 14.1 - - + -
990G LEU* 3.4 41.7 - - + +
993G ASP* 3.7 18.4 + - + +
994G LEU* 4.2 9.0 - - + +
997G LEU* 5.4 3.6 - - + -
1023G ALA 3.2 12.4 + - - +
1024G ALA* 3.1 11.2 + - - +
1026G ALA* 1.3 76.6 - - - +
1028G ALA* 1.3 57.0 + - - +
1030G ASP* 3.3 2.1 + - - +
1031G ALA* 2.8 27.7 + - - +
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Residues in contact with ALA1028 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009E MET* 3.6 28.5 - - + -
931G LEU* 5.5 1.8 - - - -
932G VAL* 4.0 20.1 - - + +
935G VAL* 4.2 14.8 - - + +
1024G ALA 3.1 12.5 + - - +
1025G HIS 3.4 3.8 + - - +
1027G LEU* 1.3 77.2 - - - +
1029G VAL* 1.3 61.7 + - - +
1031G ALA* 3.6 7.6 - - - +
1032G LYS* 3.2 28.2 + - - +
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Residues in contact with VAL1029 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1008E VAL 5.7 0.2 - - - +
1009E MET* 4.4 22.7 - - + +
1013E GLN* 5.6 8.5 - - - +
1025G HIS* 3.1 19.2 + - + +
1026G ALA* 3.7 8.3 - - - +
1027G LEU 3.2 0.2 - - - -
1028G ALA* 1.3 78.8 - - - +
1030G ASP* 1.3 70.2 + - - +
1032G LYS* 3.2 9.8 + - - +
1033G ASN* 3.1 30.5 + - - +
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Residues in contact with ASP1030 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986G ALA* 5.6 1.8 - - - +
989G LEU* 3.2 35.9 - - + +
990G LEU* 3.6 23.2 - - + +
993G ASP* 2.7 25.6 - - - +
1026G ALA* 3.1 12.1 + - - +
1027G LEU 3.9 0.7 - - - +
1029G VAL* 1.3 83.7 - - - +
1031G ALA* 1.3 63.6 + - - +
1033G ASN* 3.4 15.9 + - + +
1034G LEU* 3.2 19.9 + - - +
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Residues in contact with ALA1031 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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928G VAL* 4.0 21.6 - - + +
931G LEU* 3.8 27.1 - - + -
932G VAL* 4.9 1.8 - - + -
964G LEU* 4.5 5.1 - - + +
990G LEU* 3.6 11.8 - - + +
1027G LEU 2.8 17.4 + - - +
1028G ALA* 3.6 9.4 - - - +
1029G VAL 3.2 0.4 - - - -
1030G ASP* 1.3 77.1 - - - +
1032G LYS* 1.3 60.1 + - - +
1034G LEU* 3.3 5.4 + - - +
1035G LEU* 3.2 18.9 + - - +
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Residues in contact with LYS1032 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009E MET* 3.4 46.0 + - + +
1010E THR* 4.1 11.7 - - - +
928G VAL* 4.4 12.1 - - + -
932G VAL* 4.1 19.8 - - + +
1028G ALA 3.2 11.1 + - - +
1029G VAL* 3.2 10.6 + - - +
1031G ALA* 1.3 73.4 - - - +
1033G ASN* 1.3 65.9 + - - +
1035G LEU* 3.4 14.3 + - + +
1036G ASP* 3.2 29.5 + - - +
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Residues in contact with ASN1033 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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986G ALA* 6.3 1.1 - - + -
989G LEU* 6.2 0.6 - - - +
1029G VAL* 3.1 24.3 + - - +
1030G ASP* 3.6 21.0 + - + +
1031G ALA 3.2 0.4 - - - -
1032G LYS* 1.3 76.5 - - - +
1034G LEU* 1.3 59.9 + - - +
1036G ASP* 3.2 9.9 + - - +
1037G VAL* 2.9 34.6 + - + +
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Residues in contact with LEU1034 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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924G VAL* 6.0 0.7 - - + -
964G LEU* 4.9 5.2 - - + -
965G LEU* 5.0 0.4 - - + -
968G VAL* 3.7 29.2 - - + -
983G ILE* 3.9 28.0 - - + -
986G ALA* 3.7 28.8 - - + +
987G GLN* 4.2 9.2 - - + -
990G LEU* 3.9 24.7 - - + -
1030G ASP 3.2 9.8 + - - +
1031G ALA 3.3 8.0 + - - +
1033G ASN* 1.3 79.1 - - - +
1035G LEU* 1.3 57.9 + - - +
1037G VAL* 3.5 5.8 + - + -
1038G ILE* 2.9 48.5 + - + +
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Residues in contact with LEU1035 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919G ARG* 4.0 16.6 - - - +
922G ASP* 4.8 0.7 - - - +
924G VAL* 3.9 25.6 - - + -
925G TYR* 3.9 34.1 - - + +
928G VAL* 4.3 21.0 - - + +
1031G ALA 3.2 12.9 + - - +
1032G LYS* 3.5 15.7 - - + +
1033G ASN 3.1 0.6 - - - -
1034G LEU* 1.3 77.7 - - - +
1036G ASP* 1.3 61.3 + - - +
1038G ILE* 3.3 4.3 + - + +
1039G ASP* 2.8 51.2 + - - +
1042G ARG* 4.9 0.9 - - - +
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Residues in contact with ASP1036 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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919G ARG* 5.4 0.5 + - - -
1032G LYS* 3.2 16.5 + - - +
1033G ASN* 3.8 11.4 - - - +
1035G LEU* 1.3 80.3 - - - +
1037G VAL* 1.3 61.6 + - - +
1039G ASP* 3.6 14.9 - - - +
1040G GLN* 2.9 42.1 + - + +
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Residues in contact with VAL1037 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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979G THR* 5.4 4.4 - - + +
982G GLU* 4.1 35.7 - - + +
983G ILE* 3.9 27.6 - - + +
986G ALA* 5.8 3.8 - - + -
1033G ASN* 2.9 24.1 + - + +
1034G LEU* 3.8 9.9 - - + +
1036G ASP* 1.3 77.0 - - + +
1038G ILE* 1.3 62.0 + - - +
1040G GLN* 3.4 14.9 + - - +
1041G ALA* 3.1 21.1 + - - +
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Residues in contact with ILE1038 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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924G VAL* 4.0 29.2 - - + -
968G VAL* 4.1 20.6 - - + -
971G THR* 4.8 10.3 - - + -
975G LEU* 4.7 7.9 - - + -
983G ILE* 4.2 13.9 - - + -
1034G LEU* 2.9 44.6 + - + +
1035G LEU* 3.7 4.7 - - - +
1037G VAL* 1.3 73.0 - - - +
1039G ASP* 1.3 66.8 + - - +
1041G ALA* 3.2 8.5 + - - +
1042G ARG* 2.9 50.9 + - + +
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Residues in contact with ASP1039 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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917G LEU* 4.1 12.3 - - + +
919G ARG* 2.7 43.7 + - - -
1035G LEU* 2.8 28.3 + - - +
1036G ASP* 3.6 17.0 - - - +
1037G VAL 3.3 0.2 - - - -
1038G ILE* 1.3 73.0 - - - +
1040G GLN* 1.3 63.5 + - + +
1042G ARG* 3.2 23.0 + - - +
1043G LEU* 3.1 20.8 + - - +
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Residues in contact with GLN1040 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1036G ASP* 2.9 28.6 + - - +
1037G VAL* 3.6 13.8 - - - +
1039G ASP* 1.3 74.7 - - - +
1041G ALA* 1.3 63.9 + - - +
1043G LEU* 3.1 11.1 + - - +
1044G LYS* 3.1 39.5 + - - +
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Residues in contact with ALA1041 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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975G LEU* 4.2 20.4 - - + -
976G PRO* 3.7 8.7 - - + +
979G THR* 3.9 32.8 - - + +
983G ILE* 5.0 0.9 - - + -
1037G VAL 3.1 14.3 + - - +
1038G ILE* 3.2 11.2 + - - +
1040G GLN* 1.3 75.4 - - - +
1042G ARG* 1.3 62.5 + - - +
1044G LYS* 3.3 9.4 + - - +
1045G MET* 3.0 21.8 + - - +
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Residues in contact with ARG1042 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
919G ARG* 3.9 0.4 - - - +
921G ASN 5.4 0.6 + - - -
922G ASP* 2.5 51.0 + - - +
923G LYS 4.8 1.0 - - - +
924G VAL* 4.1 17.2 - - - +
971G THR* 5.1 8.1 + - - +
975G LEU* 4.5 13.5 - - + -
1035G LEU* 4.9 1.0 - - - +
1038G ILE* 2.9 32.3 + - - +
1039G ASP* 3.2 25.5 + - - +
1041G ALA* 1.3 76.3 - - - +
1043G LEU* 1.3 62.9 + - - +
1045G MET* 3.1 17.7 + - - +
1046G LEU* 3.3 17.0 + - - +
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Residues in contact with LEU1043 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1039G ASP 3.1 10.2 + - - +
1040G GLN* 3.1 13.5 + - - +
1042G ARG* 1.3 73.6 - - - +
1044G LYS* 1.3 70.5 + - + +
1046G LEU* 3.2 30.7 + - + +
1047G GLY 3.9 1.7 + - - -
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Residues in contact with LYS1044 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976G PRO* 4.3 13.9 - - + +
1040G GLN* 3.1 28.1 + - - +
1041G ALA* 3.6 8.7 - - - +
1043G LEU* 1.3 80.8 - - + +
1045G MET* 1.3 62.3 + - - +
1047G GLY* 3.1 19.8 + - - +
1048G GLN* 4.7 2.1 - - - +
----------------------------------------------------------
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Residues in contact with MET1045 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
974G ALA 3.3 27.8 - - - +
975G LEU* 4.2 2.2 - - + -
976G PRO* 3.7 24.7 - - + -
1041G ALA 3.0 13.4 + - - +
1042G ARG* 3.4 13.9 - - - +
1043G LEU 3.1 0.4 - - - -
1044G LYS* 1.3 73.0 - - - +
1046G LEU* 1.3 64.3 + - + +
1047G GLY 3.0 6.3 + - - -
1048G GLN* 3.4 61.3 + - + +
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Residues in contact with LEU1046 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1042G ARG 3.7 12.6 - - - +
1043G LEU* 3.2 24.7 + - + +
1045G MET* 1.3 77.8 - - + +
1047G GLY* 1.3 56.2 + - - +
1048G GLN 3.4 3.4 + - - -
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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