Contacts of the helix formed by residues 1011 - 1039 (chain D) in PDB entry 5YWB
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 LEU1011 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1009D GLY* 3.1 1.4 - - - -
1010D ILE* 1.3 81.8 - - + +
1012D LEU* 1.3 70.0 + - + +
1014D SER* 3.0 17.5 + - - +
1015D LEU* 3.4 23.3 + - + +
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Residues in contact with LEU1012 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1008D ALA 3.6 18.2 - - - +
1009D GLY* 3.2 4.3 + - - -
1011D LEU* 1.3 91.5 - - + +
1013D LEU* 1.3 61.5 + - - +
1014D SER 3.2 0.9 - - - -
1015D LEU* 3.3 8.9 + - + +
1016D LEU* 2.9 26.3 + - - +
1085D THR* 3.5 13.3 - - + +
1088D TRP* 4.1 15.9 - - + -
1089D THR* 4.1 15.9 - - - +
1092D LYS* 3.5 39.9 - - + -
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Residues in contact with LEU1013 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1005D LEU* 3.2 52.5 - - + +
1008D ALA* 3.8 15.7 + - + -
1009D GLY 3.2 17.3 + - - +
1010D ILE* 4.6 7.2 - - + +
1012D LEU* 1.3 78.5 - - - +
1014D SER* 1.3 65.0 + - - +
1016D LEU* 3.2 14.7 + - + +
1017D VAL* 2.9 37.7 + - + +
1089D THR* 4.6 6.0 + - + -
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Residues in contact with SER1014 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1010D ILE 2.6 26.8 + - - -
1011D LEU* 3.0 19.4 + - - +
1013D LEU* 1.3 84.6 - - - +
1015D LEU* 1.3 56.8 + - - -
1017D VAL* 3.4 5.0 + - - +
1018D PHE* 2.9 30.8 + - - +
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Residues in contact with LEU1015 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1011D LEU* 3.4 23.5 + - + +
1012D LEU* 3.3 11.1 + - + +
1014D SER* 1.3 80.6 + - - +
1016D LEU* 1.3 58.7 + - - +
1018D PHE* 3.8 9.3 - - + +
1019D SER* 2.9 50.1 + - - +
1081D VAL* 4.3 8.7 - - + -
1085D THR* 3.5 24.9 - - + +
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Residues in contact with LEU1016 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012D LEU 2.9 13.4 + - - +
1013D LEU* 3.3 12.8 - - + +
1015D LEU* 1.3 76.1 - - - +
1017D VAL* 1.3 77.1 + - + +
1019D SER* 3.9 3.1 - - - -
1020D GLN* 3.0 38.2 + - + +
1082D THR* 4.9 1.6 - - - +
1085D THR* 3.7 13.2 - - + +
1086D VAL* 3.6 46.0 - - + +
1089D THR* 3.9 21.3 - - + +
1140D LEU* 5.6 11.0 - - + -
1144D SER* 5.0 11.0 - - - +
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Residues in contact with VAL1017 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1013D LEU* 2.9 25.5 + - + +
1014D SER* 3.9 5.4 - - - +
1016D LEU* 1.3 86.3 - - + +
1018D PHE* 1.3 63.3 + - - +
1020D GLN* 3.3 5.2 + - - +
1021D LEU* 3.0 44.8 + - + +
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Residues in contact with PHE1018 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1014D SER 2.9 18.6 + - - +
1015D LEU* 3.8 10.3 - - + +
1017D VAL* 1.3 78.9 - - - +
1019D SER* 1.3 66.1 + - - +
1021D LEU* 3.4 8.8 + - + +
1022D LEU* 2.9 58.0 + - + +
1078D LEU* 5.9 0.9 - - + -
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Residues in contact with SER1019 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1015D LEU* 2.9 35.4 + - - +
1016D LEU* 3.9 2.2 - - - -
1018D PHE* 1.3 85.2 - - - +
1020D GLN* 1.3 65.2 + - - +
1022D LEU* 3.4 5.0 + - - +
1023D LYS* 2.9 25.6 + - - +
1078D LEU* 4.6 11.1 - - - +
1081D VAL* 3.8 12.8 - - - +
1082D THR* 3.4 25.7 - - - +
1085D THR* 5.6 0.2 - - - -
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Residues in contact with GLN1020 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016D LEU* 3.0 32.5 + - + +
1017D VAL* 3.6 6.3 - - - +
1018D PHE 3.3 0.2 - - - -
1019D SER* 1.3 77.2 - - - +
1021D LEU* 1.3 62.4 + - + +
1023D LYS* 3.3 1.9 + - - +
1024D HIS* 3.0 39.5 + - - -
1082D THR* 3.6 25.3 - - + +
1086D VAL* 4.1 6.3 - - - +
1141D GLU* 2.8 39.9 + - - +
1144D SER* 4.6 10.5 - - - -
1145D ARG* 4.8 2.9 + - - +
1148D LEU* 3.4 28.7 - - + +
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Residues in contact with LEU1021 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1017D VAL* 3.0 38.9 + - + +
1018D PHE* 3.8 6.5 - - + +
1020D GLN* 1.3 77.3 - - + +
1022D LEU* 1.3 58.3 + - - +
1024D HIS* 3.3 3.2 + - - +
1025D MET* 2.9 30.0 + - - +
1148D LEU* 3.5 28.9 - - + -
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Residues in contact with LEU1022 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1018D PHE* 2.9 48.6 + - + +
1019D SER 3.8 3.8 - - - +
1020D GLN 3.3 0.2 - - - -
1021D LEU* 1.3 74.5 - - - +
1023D LYS* 1.3 65.1 + - - +
1025D MET* 3.3 16.6 + - + +
1026D VAL* 3.0 36.3 + - + +
1078D LEU* 3.6 32.1 - - + -
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Residues in contact with LYS1023 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548D THR* 4.8 8.3 - - - +
552D ILE* 5.2 5.9 - - - +
1019D SER 2.9 18.4 + - - +
1020D GLN* 3.7 5.2 - - - +
1022D LEU* 1.3 76.8 - - - +
1024D HIS* 1.3 75.4 + - + +
1026D VAL* 3.2 6.1 + - - +
1027D LEU* 2.9 58.1 + - - +
1075D GLY* 4.0 15.2 - - - +
1078D LEU* 3.8 16.1 - - + +
1079D CYS* 3.7 45.1 - - + +
1082D THR* 4.5 4.9 - - + -
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Residues in contact with HIS1024 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020D GLN* 3.0 35.6 + - - +
1021D LEU* 4.0 4.7 - - - +
1023D LYS* 1.3 89.8 + - + +
1025D MET* 1.3 66.1 + - - +
1027D LEU* 3.2 15.0 + - + +
1028D VAL* 3.0 27.2 + - - +
1145D ARG* 3.8 22.1 + - + +
1148D LEU* 3.4 56.7 - - + +
1149D LEU* 3.9 18.8 - - + +
1152D SER* 4.9 8.0 + - - -
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Residues in contact with MET1025 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1021D LEU 2.9 17.1 + - - +
1022D LEU* 3.6 17.3 - - + +
1024D HIS* 1.3 77.0 - - - +
1026D VAL* 1.3 64.3 + - + +
1028D VAL* 3.1 11.5 - - + +
1029D ALA* 3.0 30.9 + - + +
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Residues in contact with VAL1026 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022D LEU* 3.0 29.9 + - + +
1023D LYS* 3.5 9.4 - - - +
1025D MET* 1.3 74.8 - - + +
1027D LEU* 1.3 64.0 + - - +
1029D ALA* 3.3 5.3 + - - +
1030D ILE* 3.0 28.8 + - + +
1071D LEU* 4.1 28.7 - - + +
1074D LEU* 4.3 14.8 - - + -
1075D GLY* 4.1 28.0 - - - +
1078D LEU* 5.0 7.2 - - + -
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Residues in contact with LEU1027 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552D ILE* 6.3 3.1 - - + -
580D LEU* 6.4 1.6 - - + -
584D HIS* 6.2 2.7 - - + -
1023D LYS* 2.9 43.0 + - - +
1024D HIS* 3.2 13.0 + - + +
1026D VAL* 1.3 78.1 - - - +
1028D VAL* 1.3 63.0 + - - +
1030D ILE* 3.1 22.1 - - + +
1031D ASP* 3.2 31.4 - - - +
1149D LEU* 4.7 20.6 - - + -
1152D SER* 5.9 3.4 - - - +
1287D TYR* 5.1 2.9 - - + +
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Residues in contact with VAL1028 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1024D HIS 3.0 13.7 + - - +
1025D MET* 3.1 26.2 - - + +
1027D LEU* 1.3 78.5 - - - +
1029D ALA* 1.3 63.5 + - + +
1031D ASP* 3.4 3.3 + - - +
1032D TYR* 3.0 25.5 + - + +
1152D SER* 3.4 22.7 - - - +
1155D THR* 6.0 5.2 - - + -
1156D VAL* 3.6 31.4 - - + -
1287D TYR* 3.4 10.0 - - - +
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Residues in contact with ALA1029 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025D MET* 3.0 23.1 + - + +
1026D VAL* 3.8 5.8 - - - +
1028D VAL* 1.3 80.2 - - + +
1030D ILE* 1.3 58.4 + - - +
1032D TYR* 3.8 5.9 - - - +
1033D TRP* 2.9 37.3 + - + +
1071D LEU* 4.9 7.6 - - + -
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Residues in contact with ILE1030 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552D ILE* 5.8 2.9 - - + -
1026D VAL* 3.0 16.4 + - + +
1027D LEU* 3.1 29.2 - - + +
1029D ALA* 1.3 76.1 - - - +
1031D ASP* 1.3 66.7 + - - +
1033D TRP* 3.5 2.5 + - - +
1034D LEU* 2.9 29.4 + - + +
1068D PHE* 3.4 39.9 - - + -
1071D LEU* 3.7 37.8 - - + +
1072D CYS* 3.8 17.0 - - - +
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Residues in contact with ASP1031 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577D PHE* 5.0 1.5 - - + -
580D LEU* 3.7 29.4 - - + +
1027D LEU* 3.2 28.1 - - - +
1028D VAL 3.4 1.7 + - - +
1029D ALA 3.3 0.4 - - - -
1030D ILE* 1.3 88.9 - - - +
1032D TYR* 1.3 56.5 + - - +
1034D LEU* 3.4 9.8 + - - +
1035D ALA* 2.9 23.7 + - - +
1283D LEU* 3.5 21.3 - - + +
1287D TYR* 3.4 26.4 + - + +
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Residues in contact with TYR1032 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1028D VAL* 3.0 20.7 + - + +
1029D ALA* 3.3 6.7 + - - +
1031D ASP* 1.3 76.9 - - - +
1033D TRP* 1.3 61.9 + - - +
1035D ALA* 3.2 3.3 + - - +
1036D LYS* 3.0 23.9 + - - +
1156D VAL* 6.3 1.3 - - + -
1159D TYR* 6.6 0.4 - - + -
1283D LEU* 3.6 23.6 - - + +
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Residues in contact with TRP1033 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1029D ALA* 2.9 23.8 + - + +
1030D ILE* 3.7 6.3 - - - +
1032D TYR* 1.3 77.0 - - - +
1034D LEU* 1.3 57.9 + - - +
1036D LYS* 3.3 7.9 + - + +
1037D TRP* 2.9 26.0 + - + +
1064D TYR* 4.0 26.3 - + + +
1067D VAL* 4.1 36.4 - - + +
1071D LEU* 5.0 8.7 - - + -
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Residues in contact with LEU1034 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555D VAL* 5.9 2.0 - - + -
559D PHE* 5.2 18.2 - - + -
576D ALA* 4.5 14.8 - - + -
577D PHE* 5.1 8.1 - - + -
1030D ILE* 2.9 19.9 + - + +
1031D ASP* 3.7 8.7 - - - +
1033D TRP* 1.3 76.5 - - - +
1035D ALA* 1.3 55.1 + - - +
1037D TRP* 3.2 1.0 + - - +
1038D THR* 2.6 57.1 + - + +
1064D TYR* 3.5 25.5 - - + +
1068D PHE* 3.8 33.2 - - + -
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Residues in contact with ALA1035 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577D PHE* 3.4 29.4 - - + -
1031D ASP 2.9 16.4 + - - +
1032D TYR 3.5 4.9 - - - +
1034D LEU* 1.3 76.5 - - - +
1036D LYS* 1.3 60.7 + - - +
1038D THR* 2.9 20.6 + - - -
1039D ASP* 3.5 12.8 + - - +
1279D GLY* 3.7 16.3 - - - +
1280D LEU* 6.2 0.2 - - + -
1283D LEU* 3.5 19.3 - - + -
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Residues in contact with LYS1036 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032D TYR 3.0 15.1 + - - +
1033D TRP* 3.3 8.5 + - + +
1035D ALA* 1.3 77.5 - - - +
1037D TRP* 1.3 58.2 + - - +
1039D ASP* 2.8 20.1 - - - +
1040D SER* 4.6 3.6 + - - -
1279D GLY* 5.3 1.1 - - - -
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Residues in contact with TRP1037 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563D VAL* 4.0 31.9 - - + -
571D LEU* 4.8 3.8 - - + -
1033D TRP* 2.9 18.6 + + + +
1034D LEU 3.7 1.6 - - - +
1035D ALA 3.1 0.4 - - - -
1036D LYS* 1.3 79.2 - - - +
1038D THR* 1.3 88.9 + - + +
1040D SER* 3.2 23.8 + - - -
1060D ASP* 5.5 3.8 + - - -
1061D GLN* 4.6 25.5 - - + +
1064D TYR* 3.2 70.4 - + + +
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Residues in contact with THR1038 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559D PHE* 5.9 0.4 - - + -
571D LEU* 3.9 29.3 - - + +
573D PRO* 3.9 27.4 - - - +
576D ALA* 4.4 7.6 - - + -
577D PHE* 4.4 2.8 - - - -
1034D LEU* 2.6 38.8 + - + +
1035D ALA* 2.9 16.6 + - - -
1037D TRP* 1.3 96.1 - - + +
1039D ASP* 1.3 56.7 + - - +
1040D SER 3.0 10.4 + - - -
----------------------------------------------------------
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Residues in contact with ASP1039 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573D PRO* 3.8 17.2 - - + +
1035D ALA 3.6 8.2 - - - +
1036D LYS* 2.8 26.3 - - - +
1038D THR* 1.3 75.5 + - - +
1040D SER* 1.3 60.8 + - - -
1278D ALA* 4.1 22.5 + - + +
1279D GLY* 3.0 27.3 + - - +
----------------------------------------------------------
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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