Contacts of the helix formed by residues 1009 - 1037 (chain A) in PDB entry 3VF0
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 GLY1009 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007A GLY 3.4 1.0 + - - -
1008A SER* 1.3 73.0 + - - +
1010A THR* 1.4 62.2 + - - +
1011A LYS* 3.3 4.9 + - - -
1012A ARG 3.7 1.3 + - - -
1013A ALA* 3.3 13.9 + - - +
117B ARG* 3.0 43.9 + - - -
122B GLU* 3.9 11.2 + - - -
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Residues in contact with THR1010 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1002A ARG 5.4 0.2 - - - +
1003A LEU* 3.8 34.0 - - + +
1006A GLY* 3.5 19.2 - - - +
1007A GLY* 2.8 34.0 + - - +
1008A SER 4.0 5.2 - - - +
1009A GLY* 1.4 74.6 - - - +
1011A LYS* 1.4 56.9 + - - +
1013A ALA* 3.7 6.9 - - - +
1014A LEU* 2.8 36.6 + - - +
1073A LEU* 3.5 18.2 - - - +
3008B GOL 5.4 1.3 - - - +
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Residues in contact with LYS1011 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009A GLY* 3.3 2.1 - - - -
1010A THR* 1.4 80.8 + - - +
1012A ARG* 1.3 66.6 + - + +
1015A ILE* 3.3 37.1 + - + +
1070A ALA* 3.4 30.6 - - + +
1071A THR* 3.7 39.8 + - - +
1073A LEU* 4.6 3.2 - - + +
1074A GLY* 4.7 16.7 - - - +
1075A ARG* 6.1 0.8 - - - +
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Residues in contact with ARG1012 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009A GLY 3.7 2.0 + - - -
1011A LYS* 1.3 83.1 - - + +
1013A ALA* 1.3 59.2 + - - +
1015A ILE* 3.5 9.1 + - + +
1016A GLN* 3.1 28.8 + - - +
117B ARG* 3.4 58.8 - - - +
120B GLU* 2.8 47.7 + - - +
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Residues in contact with ALA1013 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1003A LEU* 3.7 25.0 - - + +
1009A GLY 3.3 18.3 + - - +
1010A THR* 3.7 3.8 - - - +
1012A ARG* 1.3 76.1 - - - +
1014A LEU* 1.3 59.6 + - - +
1016A GLN* 3.4 2.2 + - - +
1017A CYS* 2.9 31.0 + - - +
120B GLU 3.5 15.4 + - - +
121B ARG* 4.1 21.9 + - + +
122B GLU 5.0 0.7 - - - +
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Residues in contact with LEU1014 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000A MET* 3.6 34.8 - - + -
1003A LEU* 3.8 21.3 - - + +
1004A VAL* 4.1 15.3 - - + +
1010A THR 2.8 22.2 + - - +
1011A LYS 3.9 3.1 - - - +
1013A ALA* 1.3 69.7 - - - +
1015A ILE* 1.3 64.5 - - - +
1017A CYS* 3.4 0.7 + - - +
1018A ALA* 3.2 22.7 + - - +
1066A SER* 3.8 27.1 - - - +
1069A LYS* 4.0 25.1 - - + -
1070A ALA* 4.0 7.4 - - + +
1073A LEU* 4.1 13.2 - - + -
1090A LEU* 4.7 2.0 - - + -
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Residues in contact with ILE1015 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1011A LYS* 3.3 35.3 + - + +
1012A ARG* 3.8 9.2 - - + +
1013A ALA 3.3 0.2 - - - -
1014A LEU* 1.3 78.4 - - - +
1016A GLN* 1.3 60.4 + - - +
1018A ALA* 3.5 3.8 + - - +
1019A LYS* 3.2 47.3 + - - +
1066A SER* 4.7 5.8 - - - -
1067A THR* 4.0 33.9 - - + +
1070A ALA* 3.6 20.0 - - + -
1071A THR* 5.6 0.4 - - - +
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Residues in contact with GLN1016 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012A ARG 3.1 17.8 + - - +
1013A ALA* 3.9 3.6 - - - +
1015A ILE* 1.3 74.3 - - - +
1017A CYS* 1.3 53.7 + - - +
1019A LYS* 3.1 29.5 + - - +
1020A ASP* 2.8 55.9 + - - +
119B ARG* 3.4 24.8 - - + +
120B GLU* 3.6 23.6 - - + +
121B ARG* 3.6 10.5 - - - +
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Residues in contact with CYS1017 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996A LEU* 3.2 29.6 - - - -
999A GLU* 3.7 15.3 - - - -
1000A MET* 4.0 18.2 - - + -
1003A LEU* 3.8 11.9 - - + -
1013A ALA 2.9 21.7 + - - +
1014A LEU* 3.7 4.9 - - - +
1016A GLN* 1.3 70.4 - - - +
1018A ALA* 1.3 57.3 + - - +
1020A ASP* 3.3 4.1 + - - +
1021A ILE* 3.0 40.8 + - - +
121B ARG* 3.6 15.2 - - - +
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Residues in contact with ALA1018 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1000A MET* 5.2 2.1 - - - -
1014A LEU 3.2 6.4 + - - +
1015A ILE 3.8 5.2 - - - +
1017A CYS* 1.3 72.3 - - - +
1019A LYS* 1.3 60.6 + - - +
1021A ILE* 3.5 9.9 + - - +
1022A ALA* 3.0 27.7 + - - +
1062A LEU* 3.9 20.3 - - + +
1063A LYS* 3.8 13.6 - - - +
1066A SER* 3.1 37.5 - - - +
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Residues in contact with LYS1019 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015A ILE* 3.2 38.2 + - - +
1016A GLN* 3.1 33.1 + - - +
1018A ALA* 1.3 76.0 - - - +
1020A ASP* 1.4 56.5 + - - +
1022A ALA* 3.3 3.6 + - - +
1023A LYS* 3.0 28.1 + - - +
1063A LYS* 4.1 24.5 - - + -
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Residues in contact with ASP1020 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996A LEU* 3.8 21.8 - - + +
1016A GLN* 2.8 36.2 + - - -
1017A CYS 3.6 7.9 - - - +
1019A LYS* 1.4 73.6 - - - +
1021A ILE* 1.3 61.3 + - - +
1023A LYS* 3.3 9.6 + - - +
1024A ALA* 3.1 23.0 + - - +
69B ASP* 4.3 3.1 - - - +
119B ARG* 3.3 17.6 + - - -
121B ARG* 2.9 34.7 + - - -
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Residues in contact with ILE1021 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993A MET* 4.2 15.1 - - + +
996A LEU* 3.5 23.8 - - + +
997A MET* 3.8 42.0 - - + +
1000A MET* 4.3 5.6 - - - -
1017A CYS* 3.0 34.7 + - - +
1018A ALA 3.8 4.5 - - - +
1020A ASP* 1.3 73.9 - - - +
1022A ALA* 1.4 55.8 + - - +
1024A ALA* 3.3 6.0 + - - +
1025A SER* 2.9 30.0 + - - -
1062A LEU* 3.7 14.6 - - + -
1097A LEU* 3.5 31.0 - - + -
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Residues in contact with ALA1022 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018A ALA 3.0 17.3 + - - +
1019A LYS 3.5 5.6 - - - +
1021A ILE* 1.4 73.7 - - - +
1023A LYS* 1.3 58.5 + - - +
1025A SER* 3.3 2.9 - - - -
1026A ASP* 3.0 36.6 + - - +
1059A SER* 3.9 27.0 - - - +
1063A LYS* 3.9 31.6 - - + +
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Residues in contact with LYS1023 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019A LYS 3.0 12.9 + - - +
1020A ASP* 3.3 11.9 + - - +
1022A ALA* 1.3 75.4 - - - +
1024A ALA* 1.3 62.8 + - - +
1026A ASP* 3.3 14.7 + - + +
1027A GLU* 3.3 19.5 + - - +
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Residues in contact with ALA1024 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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989A ALA* 4.0 10.4 - - + +
992A ARG* 4.3 19.7 - - - +
993A MET* 3.4 31.4 - - + +
996A LEU* 5.0 3.6 - - + -
1020A ASP 3.1 13.2 + - - +
1021A ILE* 3.7 4.7 - - - +
1023A LYS* 1.3 74.8 - - - +
1025A SER* 1.3 56.6 + - - +
1027A GLU* 3.3 9.6 + - - +
1028A VAL* 3.1 29.8 + - - +
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Residues in contact with SER1025 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
993A MET* 3.6 24.8 - - - +
1021A ILE 2.9 15.4 + - - -
1022A ALA 3.3 10.3 - - - -
1024A ALA* 1.3 73.6 - - - +
1026A ASP* 1.4 62.7 + - - +
1028A VAL* 3.3 5.1 + - - +
1029A THR* 3.0 29.6 + - - -
1055A ILE* 3.7 12.8 - - - +
1056A PRO* 5.7 1.1 - - - -
1059A SER* 2.9 29.2 + - - -
1097A LEU* 3.7 6.1 - - - +
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Residues in contact with ASP1026 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022A ALA* 3.0 21.5 + - - +
1023A LYS* 3.3 17.1 + - + +
1025A SER* 1.4 75.5 - - - +
1027A GLU* 1.3 57.8 + - - +
1029A THR* 3.5 1.2 + - - -
1030A ARG* 3.0 21.1 + - - +
1056A PRO* 4.7 9.2 - - - +
1059A SER* 6.0 1.0 - - - -
1063A LYS* 5.7 2.3 + - - -
2003A GOL 2.7 46.8 + - - +
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Residues in contact with GLU1027 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985A ASP* 3.9 23.6 - - - +
988A ALA* 6.1 0.2 - - - +
989A ALA* 4.2 9.0 - - + -
992A ARG* 2.8 33.3 + - - -
1023A LYS 3.3 7.9 + - - +
1024A ALA* 3.3 9.8 + - - +
1025A SER 3.3 0.4 - - - -
1026A ASP* 1.3 75.8 - - - +
1028A VAL* 1.4 64.6 + - - +
1030A ARG* 3.2 33.3 + - - +
1031A LEU* 3.0 37.7 + - + +
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Residues in contact with VAL1028 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
986A ILE* 3.8 31.5 - - + +
989A ALA* 3.7 19.5 - - + -
990A ALA 4.3 5.2 - - - +
993A MET* 4.4 11.9 - - - -
1024A ALA 3.1 16.7 + - - +
1025A SER* 3.3 9.8 + - - +
1027A GLU* 1.4 73.5 - - - +
1029A THR* 1.3 56.2 + - - +
1031A LEU* 4.7 0.4 - - - -
1032A ALA* 2.9 29.2 + - - +
1055A ILE* 4.0 16.2 - - + -
1101A VAL* 4.5 13.7 - - + -
1104A THR* 3.9 23.8 - - + -
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Residues in contact with THR1029 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1025A SER 3.0 17.6 + - - -
1026A ASP* 3.6 5.2 - - - -
1028A VAL* 1.3 75.7 - - - +
1030A ARG* 1.3 61.7 + - - +
1032A ALA* 4.0 5.1 - - - +
1033A LYS* 3.1 39.8 + - - +
1052A CYS* 3.6 25.2 + - - +
1053A GLU* 5.0 0.2 - - - -
1055A ILE* 3.5 20.3 - - - +
1056A PRO* 4.0 9.9 - - + +
2003A GOL 3.6 26.5 - - - +
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Residues in contact with ARG1030 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026A ASP 3.0 15.4 + - - +
1027A GLU* 3.4 38.7 + - - +
1029A THR* 1.3 75.8 - - - +
1031A LEU* 1.3 81.5 + - - +
1033A LYS* 3.4 5.2 + - - +
1034A GLU* 3.1 35.9 + - + +
2003A GOL 3.8 23.7 - - - +
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Residues in contact with LEU1031 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
985A ASP* 3.6 37.0 - - + +
986A ILE* 3.5 33.2 - - + +
1027A GLU* 3.0 31.5 + - + +
1030A ARG* 1.3 97.9 - - - +
1032A ALA* 1.4 66.0 + - - +
1034A GLU* 3.1 10.5 + - + +
1035A VAL* 3.1 24.4 + - - +
1121A PHE* 3.5 32.3 - - + -
1123A LEU* 4.9 1.3 - - + -
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Residues in contact with ALA1032 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
986A ILE* 3.7 9.1 - - + +
1028A VAL 2.9 20.6 + - - +
1029A THR 4.0 0.4 - - - +
1030A ARG 3.5 0.2 - - - -
1031A LEU* 1.4 73.7 - - - +
1033A LYS* 1.4 56.5 + - - +
1035A VAL* 3.3 8.8 + - - +
1036A ALA* 3.0 27.8 + - - +
1048A LEU* 3.7 15.4 - - + +
1052A CYS* 3.9 18.8 - - + -
1104A THR* 3.6 26.2 - - + -
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Residues in contact with LYS1033 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1029A THR* 3.1 30.7 + - - +
1030A ARG* 3.6 5.2 - - - +
1032A ALA* 1.4 73.0 - - - +
1034A GLU* 1.3 62.2 + - - +
1036A ALA* 3.8 7.3 - - - +
1037A LYS* 3.2 45.5 + - - +
1049A LEU* 4.0 21.8 - - + +
1052A CYS* 4.1 10.1 - - - -
1053A GLU* 5.0 18.2 - - - +
1056A PRO* 6.0 1.6 - - - +
2003A GOL 2.7 33.2 + - - +
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Residues in contact with GLU1034 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1030A ARG* 3.1 22.6 + - - +
1031A LEU* 3.1 14.4 + - + +
1033A LYS* 1.3 72.3 - - - +
1035A VAL* 1.3 63.7 + - - +
1037A LYS* 3.6 30.5 + - - +
1038A GLN* 3.5 26.7 + - - +
1121A PHE* 3.5 36.3 - - + +
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Residues in contact with VAL1035 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1031A LEU 3.1 14.8 + - - +
1032A ALA* 3.3 9.6 + - - +
1034A GLU* 1.3 72.4 - - - +
1036A ALA* 1.3 65.1 + - - +
1038A GLN* 3.0 15.8 + - - +
1039A CYS* 3.3 10.4 + - - +
1048A LEU* 3.7 17.5 - - + -
1108A ALA* 4.2 12.3 - - + +
1111A ALA* 4.0 17.7 - - + -
1112A SER* 6.0 0.4 - - - -
1115A ILE* 4.2 8.9 - - + +
1121A PHE* 3.8 19.5 - - + +
1122A THR* 5.5 0.7 - - - -
1123A LEU* 3.6 34.3 - - + +
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Residues in contact with ALA1036 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032A ALA 3.0 16.3 + - - +
1033A LYS 3.8 5.2 - - - +
1034A GLU 3.5 0.4 - - - -
1035A VAL* 1.3 75.1 - - - +
1037A LYS* 1.4 62.5 + - + +
1038A GLN 3.3 1.2 + - - -
1039A CYS* 3.3 12.7 + - - +
1045A ARG* 3.3 33.6 + - + +
1048A LEU* 3.8 15.2 - - + +
1049A LEU* 3.7 34.3 - - + -
----------------------------------------------------------
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Residues in contact with LYS1037 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1033A LYS* 3.2 40.3 + - - +
1034A GLU* 3.7 28.0 + - - +
1035A VAL 3.2 0.4 - - - -
1036A ALA* 1.4 74.8 - - + +
1038A GLN* 1.4 66.6 + - - +
1039A CYS 5.1 1.0 - - - +
1045A ARG* 5.7 0.4 - - - +
1049A LEU* 6.2 1.5 - - + +
1116A ARG* 5.0 3.3 - - - -
----------------------------------------------------------
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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