Contacts of the helix formed by residues 1008 - 1031 (chain A) in PDB entry 3KSS
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 VAL1008 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A ILE* 3.9 26.0 - - + -
391A MET* 4.5 14.4 - - + -
475A PHE* 4.9 1.1 - - + -
478A LEU* 4.4 20.6 - - + -
563A PRO* 4.9 6.1 - - + -
565A ILE* 4.5 15.0 - - + -
925A ALA* 4.1 17.0 - - + -
1005A GLY 4.4 8.5 - - - +
1006A SER 2.9 0.4 - - - -
1007A GLU* 1.3 81.3 - - - +
1009A MET* 1.3 82.2 + - + +
1010A SER 3.2 1.3 - - - -
1011A ARG* 3.1 12.1 + - - +
1012A ILE* 3.1 21.5 + - - +
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Residues in contact with MET1009 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ASN* 4.4 19.3 - - - +
338A LEU* 4.3 17.0 - - + -
341A LYS* 6.3 0.7 - - + -
390A ILE* 6.0 1.8 - - + -
394A GLY* 4.6 22.7 - - - +
397A ALA* 4.8 9.9 - - - -
398A ILE* 5.2 8.1 - - + +
478A LEU* 6.4 2.0 - - + -
998A ILE* 3.8 30.7 - - + -
1004A ALA 5.0 0.7 - - - +
1005A GLY 4.2 8.7 - - - +
1006A SER* 3.0 29.9 + - - +
1008A VAL* 1.3 91.1 - - + +
1010A SER* 1.3 57.2 + - - +
1012A ILE* 3.4 10.9 + - - +
1013A ALA* 2.9 29.1 + - - +
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Residues in contact with SER1010 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918A MET* 5.5 0.3 - - - -
920A PHE* 3.4 25.6 - - - -
998A ILE* 3.3 21.3 - - - +
999A LEU* 3.5 16.5 - - - +
1006A SER 3.4 17.4 + - - -
1007A GLU* 5.1 1.8 - - - -
1008A VAL 3.2 0.4 - - - -
1009A MET* 1.3 76.5 - - - +
1011A ARG* 1.3 57.6 + - - +
1013A ALA* 2.7 21.1 + - - -
1014A ALA* 2.8 18.2 + - - +
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Residues in contact with ARG1011 (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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561A PHE 2.7 28.7 + - - -
562A LEU* 3.7 0.8 - - - +
563A PRO* 3.3 23.9 - - + +
920A PHE* 4.0 16.2 - - + -
921A HIS* 2.9 41.5 + - - +
922A LEU 2.7 25.5 + - - +
923A SER* 3.3 28.8 + - - +
925A ALA* 3.7 3.1 - - + -
926A THR* 2.9 37.9 - - + +
1007A GLU* 2.9 29.4 + - - +
1008A VAL* 3.1 9.1 + - - +
1010A SER* 1.3 77.3 - - - +
1012A ILE* 1.3 57.4 + - - +
1014A ALA* 4.7 0.2 - - - +
1015A PRO* 3.2 12.7 - - - +
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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
----------------------------------------------------------
398A ILE* 3.4 52.3 - - + -
475A PHE* 4.7 2.2 - - + -
478A LEU* 4.7 6.3 - - + -
925A ALA* 3.0 36.3 - - + +
928A THR* 4.0 20.0 - - + +
929A GLY* 3.2 25.4 - - - +
932A ALA* 6.0 2.0 - - + -
1008A VAL* 3.1 21.5 - - + +
1009A MET* 3.8 7.9 - - - +
1010A SER 3.1 0.2 - - - -
1011A ARG* 1.3 75.6 - - - +
1013A ALA* 1.3 66.7 + - - +
1015A PRO* 3.9 3.6 - - - +
1016A MET* 4.1 9.9 - - + +
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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
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398A ILE* 5.8 3.4 - - + -
995A LEU* 3.3 29.9 - - + +
998A ILE* 4.1 17.3 - - + -
999A LEU* 4.7 3.8 - - + -
1009A MET 2.9 18.5 + - - +
1010A SER* 2.7 11.2 + - - +
1012A ILE* 1.3 81.9 - - + +
1014A ALA* 1.3 66.5 + - - +
1016A MET* 3.1 21.6 + - - +
1017A ILE* 4.4 0.5 - - - +
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Residues in contact with ALA1014 (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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911A GLY 4.6 0.4 - - - -
914A LEU* 2.8 42.2 - - + +
915A LEU* 5.0 5.2 - - + -
918A MET* 4.5 16.6 - - + -
920A PHE* 4.7 11.2 - - + -
926A THR* 6.4 0.2 - - + -
999A LEU* 5.2 6.8 - - + +
1010A SER* 2.8 17.7 + - - +
1011A ARG 4.7 0.9 - - - +
1013A ALA* 1.3 71.6 - - - +
1015A PRO* 1.3 74.6 - - + +
1016A MET 2.9 1.4 + - - -
1017A ILE* 2.9 10.6 + - - -
1018A GLY 3.4 0.2 + - - -
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Residues in contact with PRO1015 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911A GLY* 3.3 16.2 - - - +
915A LEU* 4.9 6.5 - - + -
926A THR* 3.5 17.0 - - - +
929A GLY* 4.1 2.9 - - - -
930A PHE* 3.1 48.2 - - + +
933A LEU* 3.0 10.8 - - + +
1011A ARG 3.2 17.7 - - - +
1012A ILE 3.9 2.5 - - - +
1013A ALA 3.7 2.0 - - - -
1014A ALA* 1.3 96.3 - - + +
1016A MET* 1.3 61.4 + - - +
1019A GLY 2.9 21.0 + - - -
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Residues in contact with MET1016 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ILE* 5.6 14.1 - - - +
401A GLY 6.3 1.6 - - - -
402A ALA* 5.6 7.0 - - - -
929A GLY* 2.8 41.1 - - - +
932A ALA* 3.5 16.8 - - + -
933A LEU* 3.2 22.9 - - - +
936A VAL* 6.0 4.3 - - + -
991A ILE* 4.3 12.8 - - + -
995A LEU* 3.1 33.7 - - + -
1012A ILE* 4.1 4.5 + - - +
1013A ALA* 3.1 8.9 + - - +
1014A ALA 3.0 0.4 - - - -
1015A PRO* 1.3 80.5 - - - +
1017A ILE* 1.3 54.2 + - - +
1019A GLY* 3.6 1.2 - - - -
1020A MET* 2.8 32.3 + - - +
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Residues in contact with ILE1017 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914A LEU* 3.9 16.8 - - + -
992A ILE* 3.6 44.7 - - + +
995A LEU* 3.2 39.5 - - + +
996A LEU* 4.2 3.4 - - + +
999A LEU* 4.0 20.6 - - + -
1013A ALA 4.4 1.3 - - - +
1014A ALA* 2.9 9.6 + - - +
1016A MET* 1.3 76.5 - - - +
1018A GLY* 1.3 61.4 + - - +
1020A MET* 2.7 21.5 + - - +
1021A ILE* 2.9 14.8 + - + +
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Residues in contact with GLY1018 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910A GLY* 3.0 36.0 - - - -
911A GLY* 3.1 8.5 - - - -
914A LEU* 3.7 6.2 - - - +
1014A ALA 3.4 7.1 + - - -
1017A ILE* 1.3 81.1 - - - +
1019A GLY* 1.3 62.5 + - - +
1021A ILE* 3.1 22.6 + - - +
1022A THR 3.2 2.3 + - - -
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Residues in contact with GLY1019 (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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907A ALA 3.1 23.7 - - - +
911A GLY 3.1 4.3 - - - +
933A LEU* 3.3 21.3 - - - -
1015A PRO 2.9 10.7 + - - -
1016A MET 3.6 1.1 - - - -
1018A GLY* 1.3 75.3 - - - +
1020A MET* 1.3 49.5 + - - +
1021A ILE 3.2 0.4 - - - -
1023A ALA* 2.5 43.6 + - - +
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Residues in contact with MET1020 (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 VAL* 4.0 22.9 - - + -
940A PHE* 3.5 39.3 - - + -
987A THR* 4.2 5.6 - - - +
988A VAL* 3.3 23.6 - - + +
991A ILE* 3.2 50.0 - - + -
992A ILE* 3.6 11.4 - - + +
1016A MET* 2.8 19.3 + - - +
1017A ILE 2.7 13.8 + - - +
1019A GLY* 1.3 72.0 - - - +
1021A ILE* 1.3 56.4 + - - -
1023A ALA* 4.4 5.2 - - - -
1024A PRO* 3.0 22.5 - - - +
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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
----------------------------------------------------------
910A GLY* 4.6 4.3 - - - -
988A VAL* 5.4 3.8 - - + -
992A ILE* 4.7 15.7 - - + -
1017A ILE* 2.9 10.8 + - + +
1018A GLY* 3.1 18.1 + - - +
1020A MET* 1.3 82.3 - - - +
1022A THR* 1.3 72.7 + - - +
1024A PRO* 3.6 7.2 - - - +
1025A LEU* 4.0 13.7 + - - +
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Residues in contact with THR1022 (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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906A PHE* 3.0 31.0 - - + +
907A ALA* 3.5 17.0 - - - -
909A VAL* 4.4 4.6 - - + +
910A GLY* 3.3 21.4 + - - +
1018A GLY 3.2 6.9 + - - -
1021A ILE* 1.3 85.3 - - - +
1023A ALA* 1.3 53.1 + - - +
1024A PRO* 3.4 0.9 - - - -
1025A LEU* 3.4 13.3 + - + +
1026A LEU* 2.8 35.8 + - + +
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Residues in contact with ALA1023 (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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907A ALA* 4.5 3.4 - - + -
933A LEU* 5.5 0.9 - - + -
936A VAL* 5.2 2.0 - - + -
937A ALA* 4.2 17.7 - - + +
940A PHE* 4.4 7.4 - - + -
1019A GLY 2.5 24.5 + - - +
1020A MET* 4.2 13.2 - - - -
1022A THR* 1.3 70.5 - - - +
1024A PRO* 1.3 69.4 - - + +
1026A LEU* 2.6 33.8 - - + +
1027A SER* 2.7 13.9 + - - -
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Residues in contact with PRO1024 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
940A PHE* 4.9 4.7 - - + -
980A ARG* 4.1 5.0 + - - +
984A LYS* 5.3 7.2 - - + -
988A VAL* 3.3 32.5 - - + -
1020A MET* 3.0 30.1 - - - +
1021A ILE* 3.6 6.1 - - - +
1022A THR 3.4 4.5 - - - -
1023A ALA* 1.3 93.6 - - + +
1025A LEU* 1.3 62.7 + - - +
1027A SER* 3.3 7.6 + - - +
1028A LEU* 3.0 32.5 + - + +
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Residues in contact with LEU1025 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021A ILE 4.0 12.6 - - - +
1022A THR* 3.4 15.9 + - + +
1024A PRO* 1.3 81.2 - - - +
1026A LEU* 1.3 70.6 + - + +
1028A LEU* 3.1 26.9 - - - +
1029A PHE* 3.1 32.7 + - + -
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Residues in contact with LEU1026 (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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903A SER* 3.8 3.1 - - - +
906A PHE* 3.2 42.0 - - + -
907A ALA* 3.7 13.5 - - + -
937A ALA* 4.3 10.3 - - + +
1022A THR* 2.8 18.6 + - + +
1023A ALA* 2.6 48.5 - - + +
1024A PRO 3.2 0.2 - - - -
1025A LEU* 1.3 77.9 - - + +
1027A SER* 1.3 74.4 + - - +
1028A LEU 2.9 2.3 + - - -
1029A PHE* 2.9 2.0 + - - +
1030A ILE* 2.8 55.9 + - + +
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Residues in contact with SER1027 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937A ALA 4.3 0.3 + - - -
940A PHE* 3.0 37.7 - - - +
941A GLY* 4.1 1.7 + - - -
944A MET* 5.2 0.2 - - - -
980A ARG* 3.4 26.1 + - - -
1023A ALA 2.7 21.8 + - - -
1024A PRO* 3.6 1.6 - - - -
1026A LEU* 1.3 89.6 - - - +
1028A LEU* 1.3 57.4 + - - +
1030A ILE* 3.9 5.6 - - - -
1031A ILE* 3.1 31.6 + - - +
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Residues in contact with LEU1028 (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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525A TYR* 3.0 54.2 + - + +
944A MET* 6.2 0.2 - - - +
980A ARG* 3.0 42.4 - - - +
981A VAL* 4.7 2.9 - - + -
1024A PRO* 3.0 21.2 + - + +
1025A LEU* 3.1 19.5 - - - +
1026A LEU 2.9 0.2 - - - -
1027A SER* 1.3 79.7 - - - +
1029A PHE* 1.3 76.9 + - + +
1030A ILE 3.6 0.2 - - - -
1031A ILE* 4.1 2.1 - - - +
1032A PRO* 3.0 23.4 - - - +
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Residues in contact with PHE1029 (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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525A TYR* 4.1 18.6 - + - -
528A LEU* 4.8 13.2 - - + -
529A LEU* 5.0 5.4 - - - -
532A VAL* 4.5 38.6 - - + -
539A THR* 4.8 12.9 + - + -
1025A LEU* 3.1 35.8 + - + +
1026A LEU* 2.9 4.8 + - - +
1028A LEU* 1.3 105.0 - - + +
1030A ILE* 1.3 63.5 + - - +
1031A ILE 3.4 1.1 - - - -
1032A PRO* 3.5 9.0 - - + -
1033A ALA* 3.8 18.8 - - + +
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Residues in contact with ILE1030 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899A LEU* 3.4 39.4 - - + +
900A ILE* 5.7 0.7 - - + -
903A SER* 3.9 6.7 - - - +
906A PHE* 3.3 37.5 - - + -
941A GLY* 4.6 16.6 - - - -
945A LEU* 5.8 0.5 - - - +
1026A LEU* 2.8 41.6 + - + +
1027A SER* 3.8 9.2 - - - +
1029A PHE* 1.3 80.4 - - - +
1031A ILE* 1.3 69.8 + - + +
1032A PRO 3.6 0.4 - - - -
1034A ALA* 3.0 31.3 - - + +
1035A TYR 4.2 0.3 + - - -
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Residues in contact with ILE1031 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
899A LEU* 6.1 0.2 - - + -
941A GLY* 3.9 5.6 - - - +
944A MET* 3.2 31.6 - - + -
945A LEU* 3.3 54.5 - - + +
948A LEU* 3.2 24.3 - - + +
973A LEU* 5.9 1.6 - - + -
1027A SER 3.1 22.0 - - - +
1028A LEU 4.1 2.2 - - - +
1030A ILE* 1.3 90.7 - - + +
1032A PRO* 1.3 70.5 - - + +
1035A TYR* 3.1 26.0 - - - +
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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