Contacts of the helix formed by residues 998 - 1026 (chain A) in PDB entry 6CNC
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 TYR 998 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
974A LEU* 3.2 48.4 - - + +
976A ARG* 6.5 0.4 - - - -
996A ASP* 3.5 24.5 - - - +
997A GLN* 1.3 104.1 + - + +
999A ASP* 1.3 57.2 + - - +
1000A ALA* 3.3 6.1 - - - +
1001A GLU* 3.1 20.9 + - + +
1002A ARG* 2.8 41.9 + - - +
167E ARG* 4.7 5.5 + - - -
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Residues in contact with ASP 999 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
976A ARG* 3.1 19.7 + - - -
992A ALA* 5.7 1.2 - - - -
995A VAL* 3.5 23.7 - - + +
997A GLN 2.3 25.7 + - - +
998A TYR* 1.3 66.0 - - - +
1000A ALA* 1.3 62.1 + - - +
1001A GLU 3.1 0.9 - - - -
1002A ARG* 2.6 39.8 + - + +
1003A ASP* 2.9 42.9 + - - +
207E ARG* 4.3 30.7 + - - +
208E TYR* 5.8 1.3 - - - -
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Residues in contact with ALA1000 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918A GLY 3.3 25.8 - - - +
919A ASP* 4.2 15.7 - - - +
997A GLN 4.6 0.8 - - - -
998A TYR* 3.3 3.9 - - - +
999A ASP* 1.3 78.0 - - - +
1001A GLU* 1.3 56.2 + - - +
1003A ASP* 3.8 4.1 - - - +
1004A PHE* 2.9 26.5 + - - +
1078A TYR* 5.2 3.1 - - - +
205E SER* 4.1 25.6 + - - +
206E GLY* 5.8 0.4 - - - -
207E ARG 4.4 6.8 + - - +
208E TYR* 6.1 0.6 - - + +
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Residues in contact with GLU1001 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
970A LEU* 5.7 0.2 - - - +
974A LEU* 4.5 11.1 - - + +
998A TYR* 3.1 31.3 + - + +
1000A ALA* 1.3 77.9 - - - +
1002A ARG* 1.3 60.5 + - - +
1004A PHE* 3.1 6.5 + - + +
1005A TYR* 2.7 71.2 + - + -
1078A TYR* 3.9 28.4 + - + +
1082A ARG* 4.8 7.1 + - - -
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Residues in contact with ARG1002 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971A GLU* 5.3 14.6 + - + +
974A LEU* 3.5 25.6 + - + +
975A VAL 2.5 31.3 + - - -
976A ARG* 2.8 31.0 - - - +
995A VAL 4.7 1.2 + - - -
997A GLN 4.1 0.6 + - - -
998A TYR* 2.8 39.0 + - - +
999A ASP* 2.6 38.3 + - + +
1001A GLU* 1.3 71.8 - - - +
1003A ASP* 1.3 60.7 + - - +
1005A TYR* 4.2 6.5 - - + +
1006A HIS* 2.8 36.6 + - + +
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Residues in contact with ASP1003 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999A ASP* 2.9 30.6 + - - +
1000A ALA 4.0 3.1 - - - +
1002A ARG* 1.3 75.3 - - - +
1004A PHE* 1.3 60.3 + - - +
1006A HIS* 4.1 7.2 + - - +
1007A SER* 2.9 31.7 + - - -
205E SER 4.6 10.5 - - - +
206E GLY* 4.5 4.9 - - - -
207E ARG* 4.4 26.1 + - - +
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Residues in contact with PHE1004 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931A GLN* 5.9 2.2 - - - -
932A PRO* 4.8 10.3 - - + -
933A VAL* 3.3 35.4 - - + -
935A PHE* 4.5 15.4 - + - -
1000A ALA 2.9 16.8 + - - +
1001A GLU* 3.1 12.1 + - - +
1003A ASP* 1.3 73.3 - - - +
1005A TYR* 1.3 104.6 + + - +
1007A SER* 2.8 16.3 + - - -
1008A LEU* 2.8 22.5 + - + +
1074A ALA* 4.5 8.7 - - + -
1075A LEU* 4.8 4.7 - - - -
1078A TYR* 4.0 44.4 - + + -
205E SER* 5.9 0.7 - - - +
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Residues in contact with TYR1005 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967A LEU* 4.5 18.3 - - + +
970A LEU* 3.6 53.9 - - + +
971A GLU* 4.5 23.3 - - + +
1001A GLU* 2.7 58.0 + - + +
1002A ARG* 4.2 4.0 - - + +
1004A PHE* 1.3 94.7 - + - +
1006A HIS* 1.3 57.0 + - - +
1008A LEU* 2.8 29.0 + - + +
1009A ARG* 2.9 14.0 + - - +
1075A LEU* 4.6 13.7 - - + +
1078A TYR* 4.8 9.2 - + - -
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Residues in contact with HIS1006 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
971A GLU* 4.5 10.2 + - - +
1002A ARG* 2.8 27.0 + - + +
1003A ASP* 4.1 6.8 + - - +
1005A TYR* 1.3 72.8 - - - +
1007A SER* 1.3 62.1 + - - +
1009A ARG* 3.2 34.0 + - - +
1010A GLU* 2.9 44.6 + - + +
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Residues in contact with SER1007 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935A PHE* 4.3 16.5 - - - -
1003A ASP 2.9 22.0 + - - -
1004A PHE* 2.8 10.4 + - - -
1006A HIS* 1.3 74.5 + - - +
1008A LEU* 1.3 57.2 + - - +
1010A GLU* 3.3 9.4 + - - +
1011A TYR* 2.9 28.2 + - - +
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Residues in contact with LEU1008 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935A PHE* 3.4 32.7 - - + -
967A LEU* 4.4 13.0 - - + -
1004A PHE* 2.8 23.0 + - + +
1005A TYR* 2.8 18.1 + - + +
1007A SER* 1.3 69.5 - - - +
1009A ARG* 1.3 67.7 + - - +
1011A TYR* 2.9 15.1 + - + +
1012A ILE* 2.9 12.7 + - + +
1070A PHE* 3.5 30.7 - - + -
1071A LEU* 3.5 28.0 - - + +
1074A ALA* 4.0 17.5 - - + -
1075A LEU* 5.3 4.0 - - + +
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Residues in contact with ARG1009 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
960A MET* 4.8 13.6 - - - +
963A ALA* 4.9 4.7 - - + -
964A ASN* 3.1 31.6 + - - +
967A LEU* 3.6 23.6 - - + +
971A GLU* 3.5 28.3 + - - +
1005A TYR 2.9 8.9 + - - +
1006A HIS* 3.2 40.5 + - - +
1008A LEU* 1.3 75.8 - - - +
1010A GLU* 1.3 60.5 + - - +
1012A ILE* 3.1 7.9 + - - +
1013A ASN* 2.9 29.5 + - + +
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Residues in contact with GLU1010 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1006A HIS* 2.9 40.4 + - + +
1007A SER* 3.7 8.5 - - - +
1008A LEU 3.2 0.2 - - - -
1009A ARG* 1.3 78.9 - - - +
1011A TYR* 1.3 57.3 + - - +
1013A ASN* 3.9 6.6 - - + +
1014A GLY* 2.9 22.7 + - - -
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Residues in contact with TYR1011 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935A PHE* 4.1 35.9 - + + -
936A ASN* 3.8 24.2 + - + +
939A TRP* 4.0 9.0 - + + +
1007A SER* 2.9 13.8 + - - +
1008A LEU* 2.9 11.0 + - - +
1010A GLU* 1.3 74.3 - - - +
1012A ILE* 1.3 73.3 + - + +
1014A GLY* 2.9 13.0 + - - -
1015A LYS* 2.9 45.7 + - + +
1070A PHE* 4.1 24.7 - + - -
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Residues in contact with ILE1012 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939A TRP* 5.2 10.5 - - + -
959A ILE* 3.5 30.5 - - + -
960A MET* 3.6 7.0 - - + -
963A ALA* 4.6 12.3 - - + -
967A LEU* 5.7 0.4 - - + -
1008A LEU* 2.9 17.5 + - + +
1009A ARG* 3.8 8.1 - - - +
1011A TYR* 1.3 78.4 - - + +
1013A ASN* 1.3 63.8 + - - +
1015A LYS* 2.9 8.5 + - + +
1016A ALA* 2.8 21.5 + - - +
1067A VAL* 4.5 11.7 - - + -
1070A PHE* 3.9 25.1 - - + -
1071A LEU* 3.7 34.8 - - + -
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Residues in contact with ASN1013 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
960A MET* 3.4 33.7 - - - +
1009A ARG* 2.9 18.3 + - + +
1010A GLU* 3.9 8.5 - - + +
1012A ILE* 1.3 74.9 - - - +
1014A GLY* 1.3 62.7 + - - +
1016A ALA* 4.4 1.3 - - - +
1017A THR* 2.9 32.4 + - - +
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Residues in contact with GLY1014 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010A GLU 2.9 14.1 + - - -
1011A TYR* 2.9 11.3 + - - -
1013A ASN* 1.3 76.2 - - - +
1015A LYS* 1.3 56.4 + - - +
1017A THR* 3.1 21.6 - - - +
1018A ALA* 4.1 4.2 + - - +
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Residues in contact with LYS1015 (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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936A ASN* 5.8 1.2 + - - -
939A TRP* 3.3 61.7 - - + +
1011A TYR* 2.9 37.7 + - + +
1012A ILE* 2.9 10.3 + - + +
1014A GLY* 1.3 76.2 - - - +
1016A ALA* 1.3 65.9 + - - +
1018A ALA* 2.9 23.6 + - + +
1019A LEU* 3.5 4.0 + - - +
1060A TYR* 6.0 6.8 - - + -
1062A ILE* 4.4 11.9 - - + -
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Residues in contact with ALA1016 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956A PRO* 3.8 15.9 - - - +
959A ILE* 3.8 38.4 - - + -
960A MET* 4.3 8.1 - - + -
1012A ILE 2.8 17.9 + - - +
1013A ASN* 4.1 2.9 - - - +
1015A LYS* 1.3 73.7 - - - +
1017A THR* 1.3 63.5 + - - +
1019A LEU* 3.0 9.9 + - - +
1020A ALA* 2.9 21.0 + - - +
1032A LEU* 5.9 0.7 - - - -
1062A ILE* 5.3 2.0 - - - -
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Residues in contact with THR1017 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013A ASN* 2.9 23.4 + - - +
1014A GLY* 3.1 26.2 - - - +
1016A ALA* 1.3 76.9 - - - +
1018A ALA* 1.3 58.4 + - - +
1020A ALA* 3.4 8.5 + - - +
1021A ASN* 2.9 38.2 + - - +
1032A LEU* 4.1 20.4 - - - +
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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
----------------------------------------------------------
1014A GLY 4.6 4.9 - - - +
1015A LYS* 2.9 15.4 + - + +
1017A THR* 1.3 79.7 - - + +
1019A LEU* 1.3 59.0 + - - +
1021A ASN* 2.7 32.1 + - - +
1022A LEU* 2.9 20.6 + - + +
1060A TYR* 4.4 18.2 - - + +
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Residues in contact with LEU1019 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
953A GLY 4.9 11.9 - - - +
954A LEU* 5.1 9.0 - - + -
956A PRO* 4.4 27.6 - - + -
959A ILE* 4.7 12.1 - - + -
1015A LYS 3.5 2.5 + - - +
1016A ALA* 3.0 12.8 + - - +
1018A ALA* 1.3 77.0 - - - +
1020A ALA* 1.3 58.3 + - - +
1022A LEU* 3.6 1.5 + - + +
1023A ARG* 2.9 36.5 + - + +
1056A VAL* 4.5 19.3 - - + -
1060A TYR* 3.5 45.9 - - + +
1061A ARG* 5.7 0.4 - - - -
1062A ILE* 4.7 15.0 - - + +
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Residues in contact with ALA1020 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
956A PRO* 4.5 10.0 - - + +
1016A ALA 2.9 11.5 + - - +
1017A THR 3.5 9.4 - - - +
1019A LEU* 1.3 78.5 - - - +
1021A ASN* 1.3 62.4 + - - +
1023A ARG* 3.1 7.1 + - - +
1024A LYS* 2.9 28.0 + - - +
1030A GLY* 4.4 2.4 - - - -
1031A LEU 4.6 3.6 - - - +
1032A LEU* 3.5 46.2 - - + +
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Residues in contact with ASN1021 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017A THR* 2.9 30.5 + - - +
1018A ALA* 2.7 21.2 + - - +
1020A ALA* 1.3 71.6 - - - +
1022A LEU* 1.3 64.2 + - + +
1024A LYS* 3.0 23.7 + - - +
1025A SER* 2.7 29.3 + - - -
1032A LEU* 5.0 4.3 - - - +
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Residues in contact with LEU1022 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018A ALA* 2.9 22.8 + - + +
1019A LEU* 4.3 3.1 - - + +
1021A ASN* 1.3 80.6 - - + +
1023A ARG* 1.3 58.0 + - - +
1025A SER* 3.6 11.2 - - - +
1026A ARG* 2.9 41.0 + - + +
1056A VAL* 5.9 1.1 - - - -
1059A LEU* 3.5 32.1 - - + -
1060A TYR* 3.5 21.8 - - + +
106H GLU* 3.3 32.3 - - + +
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Residues in contact with ARG1023 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
954A LEU* 4.0 39.1 - - - +
956A PRO* 3.9 26.3 - - - +
1019A LEU* 2.9 26.4 + - + +
1020A ALA 3.1 6.5 + - - +
1022A LEU* 1.3 79.3 - - - +
1024A LYS* 1.3 60.1 + - - +
1025A SER 3.4 0.2 + - - -
1026A ARG* 3.5 4.9 + - - +
1028A MET* 3.0 54.3 + - + +
1029A LEU* 4.2 11.6 + - - +
1031A LEU* 4.1 26.4 - - - +
1044A PRO* 5.6 3.2 - - - +
1045A ASP* 4.3 24.9 - - - +
1056A VAL* 4.7 17.0 - - + +
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Residues in contact with LYS1024 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020A ALA 2.9 14.1 + - - +
1021A ASN* 3.0 31.5 + - - +
1023A ARG* 1.3 76.5 - - - +
1025A SER* 1.3 62.3 + - - +
1027A GLY* 3.3 10.0 + - - -
1028A MET 3.2 17.9 - - - +
1029A LEU 4.5 1.0 + - - -
1030A GLY* 3.6 33.9 - - - +
1032A LEU* 4.7 15.7 - - - +
----------------------------------------------------------
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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
----------------------------------------------------------
1021A ASN 2.7 23.0 + - - -
1022A LEU* 3.6 16.4 - - - +
1023A ARG 3.2 0.6 - - - -
1024A LYS* 1.3 75.6 - - - +
1026A ARG* 1.3 64.8 + - - +
1027A GLY 3.2 1.1 + - - -
108H SER 5.8 0.3 + - - -
109H LYS* 5.7 7.4 - - - +
----------------------------------------------------------
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Residues in contact with ARG1026 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022A LEU* 2.9 27.0 + - + +
1023A ARG 3.5 4.0 + - - +
1024A LYS 3.3 0.4 - - - -
1025A SER* 1.3 81.5 - - - +
1027A GLY* 1.3 57.2 + - - +
1028A MET* 3.6 2.4 - - + +
1052A VAL* 3.8 31.6 - - + +
1055A SER* 3.5 23.2 + - - +
1056A VAL* 4.7 15.7 - - + -
1059A LEU* 5.7 8.7 - - + +
106H GLU* 6.5 1.1 - - - -
109H LYS* 4.2 13.7 - - - +
110H ASP* 3.2 40.6 - - - +
112H ILE* 5.3 6.2 - - - +
129H TYR* 2.5 44.4 + - - -
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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