Contacts of the helix formed by residues 1093 - 1122 (chain D) in PDB entry 3IKM
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 MET1093 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007D GLU* 3.6 36.8 - - + +
1011D PRO* 5.1 13.0 - - + -
1049D TRP* 6.2 0.4 - - - -
1092D PHE* 1.3 88.3 - - + +
1094D THR* 1.3 61.7 + - - +
1095D SER 2.6 16.6 + - - +
1096D ARG* 2.7 16.9 + - - +
1097D VAL* 2.8 23.2 + - + -
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Residues in contact with THR1094 (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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955D TYR 4.8 0.9 - - - -
956D GLY* 2.9 33.1 + - - -
957D ALA* 2.7 34.3 + - - +
961D PHE* 4.1 19.9 - - + -
1049D TRP* 5.2 9.6 - - + -
1056D GLU* 5.7 4.3 - - - +
1093D MET* 1.3 79.1 - - - +
1095D SER* 1.3 57.5 + - - +
1097D VAL* 3.8 7.1 - - - +
1098D ASN* 2.9 32.3 + - - +
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Residues in contact with SER1095 (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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305D SER* 3.6 6.4 + - - -
307D PHE* 4.1 22.4 - - - -
308D GLN* 4.8 0.3 + - - -
1027D LYS* 5.5 0.3 - - - +
1049D TRP* 6.1 2.8 - - - +
1090D GLU 4.3 12.4 + - - -
1091D GLU* 4.6 4.2 + - - -
1092D PHE* 4.6 9.0 - - - -
1093D MET 2.6 5.0 + - - +
1094D THR* 1.3 75.1 - - - +
1096D ARG* 1.3 68.4 + - - -
1098D ASN* 2.9 8.7 + - - +
1099D TRP* 2.8 50.1 + - - -
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Residues in contact with ARG1096 (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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1010D LEU* 4.4 13.4 - - + -
1011D PRO* 3.7 14.3 - - - +
1015D THR* 6.4 1.1 - - + -
1026D ARG* 4.6 5.4 - - + -
1027D LYS* 2.7 46.5 + - + +
1028D VAL* 2.6 35.1 - - - +
1031D GLU* 2.5 33.9 + - - +
1091D GLU 2.3 22.8 + - - -
1092D PHE* 2.4 27.8 + - - +
1093D MET* 2.7 13.2 + - - +
1095D SER* 1.3 74.9 + - - +
1097D VAL* 1.3 65.0 + - + +
1099D TRP* 2.9 14.7 + - + +
1100D VAL* 2.8 27.5 + - + +
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Residues in contact with VAL1097 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
955D TYR 4.4 3.6 - - - +
1003D TRP* 3.2 45.3 - - + +
1006D ARG* 5.0 10.8 - - + -
1007D GLU* 4.3 28.0 - - + +
1010D LEU* 5.9 4.9 - - + -
1093D MET* 2.8 33.5 + - + +
1094D THR* 3.8 7.9 - - - +
1096D ARG* 1.3 73.0 - - + +
1098D ASN* 1.3 68.0 + - - +
1100D VAL* 2.7 20.3 + - - +
1101D VAL* 2.9 12.2 + - + +
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Residues in contact with ASN1098 (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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955D TYR* 2.9 48.9 - - - +
956D GLY* 3.3 11.5 - - - +
1056D GLU* 4.1 17.8 + - - -
1074D VAL* 5.6 4.1 + - - +
1094D THR* 2.9 19.1 + - - +
1095D SER* 2.9 10.6 + - - +
1097D VAL* 1.3 74.8 - - - +
1099D TRP* 1.3 77.6 + - + +
1101D VAL* 2.9 14.1 + - - +
1102D GLN* 3.0 31.5 + - - +
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Residues in contact with TRP1099 (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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305D SER* 2.4 35.0 + - - -
306D SER* 4.7 7.4 - - - -
307D PHE* 4.7 8.3 - + - -
850D ILE* 3.1 47.7 - - + +
851D THR* 4.1 3.4 + - - +
1023D GLN* 2.6 29.3 + - + +
1027D LYS* 5.0 13.0 - - + +
1058D PHE* 6.1 1.8 - + - -
1074D VAL 6.0 1.8 - - - -
1095D SER* 2.8 38.0 + - - -
1096D ARG* 3.1 15.5 - - + +
1098D ASN* 1.3 82.7 - - + +
1100D VAL* 1.3 58.4 + - - +
1102D GLN* 3.2 31.8 + - - +
1103D SER* 3.1 7.8 + - - -
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Residues in contact with VAL1100 (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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902D LEU* 5.9 2.0 - - + -
1006D ARG* 4.0 34.5 - - + +
1010D LEU* 3.5 32.5 - - + -
1015D THR* 5.0 3.6 - - + -
1023D GLN* 2.6 24.0 - - + +
1096D ARG* 2.8 18.0 + - + +
1097D VAL* 2.7 16.6 + - - +
1099D TRP* 1.3 66.5 - - - +
1101D VAL* 1.3 68.2 + - + +
1103D SER* 3.2 14.8 + - - -
1104D SER* 3.0 11.4 + - - +
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Residues in contact with VAL1101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853D ARG* 6.2 1.1 - - - +
895D GLU* 5.6 5.6 - - + +
898D ILE* 4.6 9.7 - - + +
899D ALA* 5.4 6.3 - - + -
902D LEU* 6.4 1.3 - - - -
954D ILE* 4.8 1.1 - - + -
955D TYR* 3.6 32.1 - - + -
1003D TRP* 3.0 40.8 - - + -
1006D ARG* 5.9 0.9 - - + -
1097D VAL* 2.9 15.0 + - + +
1098D ASN 2.9 6.7 + - - +
1100D VAL* 1.3 78.4 - - + +
1102D GLN* 1.3 65.6 + - - +
1104D SER* 2.5 22.7 + - - +
1105D ALA* 3.3 9.0 + - + +
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Residues in contact with GLN1102 (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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851D THR* 2.9 39.0 - - + +
853D ARG* 2.9 29.7 + - + +
955D TYR* 4.4 14.1 - - - -
1074D VAL* 5.3 11.3 - - - +
1098D ASN* 3.0 33.7 + - - +
1099D TRP* 3.3 30.2 - - - +
1100D VAL 3.2 0.2 - - - -
1101D VAL* 1.3 77.1 - - - +
1103D SER* 1.3 70.1 + - - +
1105D ALA 2.8 9.9 + - - -
1106D VAL* 2.8 14.4 + - - +
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Residues in contact with SER1103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851D THR* 4.4 1.6 - - - +
852D ARG* 4.3 16.4 + - - +
1019D TRP 5.8 4.0 - - - -
1020D ILE 5.9 1.6 - - - -
1021D SER* 5.7 2.7 - - - -
1023D GLN* 2.7 42.9 + - - +
1099D TRP 3.1 0.2 + - - -
1100D VAL* 3.2 6.7 + - - -
1102D GLN* 1.3 74.2 - - - +
1104D SER* 1.3 57.2 + - - +
1106D VAL* 2.5 44.6 + - - +
1107D ASP* 2.9 12.6 + - - -
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Residues in contact with SER1104 (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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898D ILE* 4.0 16.7 - - - +
902D LEU* 5.0 11.2 - - - +
1019D TRP* 5.8 1.1 - - - -
1100D VAL* 3.0 11.4 + - - +
1101D VAL* 2.5 24.9 + - - +
1103D SER* 1.3 75.2 - - - +
1105D ALA* 1.3 59.7 + - - -
1107D ASP* 3.3 10.3 + - - +
1108D TYR 2.9 17.7 + - - -
1164D PHE* 3.2 13.7 - - - -
1168D LEU* 4.7 21.1 - - - -
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Residues in contact with ALA1105 (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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853D ARG* 2.9 43.1 - - - +
895D GLU* 5.1 8.3 - - + +
898D ILE* 3.9 12.9 - - + +
1101D VAL* 3.3 7.4 + - + +
1102D GLN 2.8 3.6 + - - +
1103D SER 2.7 3.4 + - - -
1104D SER* 1.3 71.4 - - - +
1106D VAL* 1.3 67.0 + - - +
1108D TYR* 2.9 19.3 + - - +
1109D LEU* 3.0 14.7 + - - +
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Residues in contact with VAL1106 (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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851D THR* 3.4 31.9 - - + +
852D ARG* 4.2 24.2 - - + +
853D ARG* 4.1 9.3 - - - +
1102D GLN 2.8 23.8 + - - +
1103D SER* 2.5 20.3 + - - +
1105D ALA* 1.3 72.0 - - - +
1107D ASP* 1.3 68.9 + - - +
1109D LEU* 3.2 5.7 + - - +
1110D HIS* 2.8 44.2 + - + +
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Residues in contact with ASP1107 (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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420D HIS* 6.5 0.4 - - - -
423D THR* 4.8 5.4 + - - -
852D ARG* 4.2 9.0 + - - -
1019D TRP* 3.7 29.7 + - + +
1020D ILE* 3.5 22.7 - - - +
1021D SER* 4.7 2.6 + - - -
1103D SER* 2.9 18.8 + - - +
1104D SER* 3.3 11.3 + - - +
1106D VAL* 1.3 73.3 - - - +
1108D TYR* 1.3 68.8 + - - +
1110D HIS* 2.6 21.0 + - - +
1111D LEU* 2.7 29.1 + - + +
1164D PHE* 4.0 7.9 - - + -
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Residues in contact with TYR1108 (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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891D VAL* 5.4 4.3 - - + -
894D GLN* 3.4 36.1 - - + +
895D GLU* 5.0 4.3 - - + -
898D ILE* 4.9 12.6 - - + -
1104D SER 2.9 3.8 + - - +
1105D ALA* 2.9 16.2 + - - +
1107D ASP* 1.3 79.9 - - - +
1109D LEU* 1.3 73.7 + - + +
1111D LEU* 2.9 2.9 + - - +
1112D MET* 2.8 31.5 + - + +
1157D ASN* 3.6 5.9 + - - -
1160D THR* 3.0 32.8 - - + -
1161D ARG* 2.5 50.3 + - + +
1164D PHE* 3.0 32.6 - + + -
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Residues in contact with LEU1109 (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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430D MET* 5.6 4.3 - - + -
891D VAL* 5.0 12.6 - - + -
1105D ALA 3.0 8.9 + - - +
1106D VAL* 3.7 7.4 - - - +
1108D TYR* 1.3 81.6 - - + +
1110D HIS* 1.3 55.2 + - - +
1112D MET* 2.9 23.4 - - - +
1113D LEU* 2.7 59.2 + - + +
1132D SER* 3.9 29.6 - - - +
1133D ILE 6.0 0.7 - - - +
1135D ASP* 6.3 1.6 - - - +
1136D GLU 4.9 1.1 - - - +
1137D VAL* 3.3 30.1 - - + -
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Residues in contact with HIS1110 (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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422D VAL* 3.8 18.4 - - + +
423D THR* 3.7 36.6 + - + +
426D GLY* 3.7 12.1 + - - -
427D MET* 3.5 31.9 - - + +
430D MET* 5.2 9.6 - - + +
852D ARG* 5.8 1.8 - - - +
1106D VAL* 2.8 38.7 + - + +
1107D ASP* 2.6 20.1 + - - +
1109D LEU* 1.3 70.9 - - - +
1111D LEU* 1.3 68.7 + - + +
1113D LEU* 3.2 7.8 + - - +
1114D VAL* 3.0 23.8 + - - +
1117D LYS* 4.4 0.3 + - - -
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Residues in contact with LEU1111 (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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139D PHE* 3.6 14.8 - - + -
422D VAL* 3.2 32.3 - - + -
1019D TRP* 3.7 16.8 - - + -
1107D ASP* 2.7 43.8 + - + +
1108D TYR 3.4 3.8 - - - +
1110D HIS* 1.3 72.2 - - - +
1112D MET* 1.3 69.9 + - - +
1114D VAL* 2.9 9.7 + - - +
1115D ALA 3.1 9.2 + - - -
1160D THR* 3.7 13.7 - - + +
1163D MET* 4.0 22.0 - - + -
1164D PHE* 3.1 36.1 - - + -
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Residues in contact with MET1112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890D ASP 5.4 0.7 - - - +
891D VAL* 6.3 1.8 - - + -
894D GLN* 4.9 5.6 - - - +
1108D TYR* 2.8 20.9 + - + +
1109D LEU* 2.9 33.4 - - - +
1111D LEU* 1.3 79.6 - - - +
1113D LEU* 1.3 71.5 + - + +
1114D VAL 3.0 0.2 + - - -
1115D ALA 3.0 5.4 + - - -
1116D MET* 3.1 3.6 + - - +
1137D VAL* 4.4 11.0 - - + -
1139D TYR* 4.4 12.3 - - + +
1153D LEU 5.3 0.7 - - - +
1156D THR* 3.0 31.3 - - + +
1157D ASN* 3.2 40.6 - - - +
1160D THR* 3.3 19.6 + - + +
1180D PHE* 3.9 13.9 - - + -
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Residues in contact with LEU1113 (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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426D GLY 5.4 1.6 - - - +
429D GLU* 5.1 7.9 - - + +
430D MET* 5.4 13.7 - - + +
1109D LEU* 2.7 50.9 + - + +
1110D HIS* 3.7 6.7 - - - +
1112D MET* 1.3 75.5 - - + +
1114D VAL* 1.3 56.2 + - - +
1116D MET* 2.9 10.9 - - - +
1117D LYS* 2.9 57.8 + - - +
1129D PHE* 3.8 24.5 - - + -
1132D SER* 5.7 3.1 - - - -
1137D VAL* 4.1 4.9 - - + -
1139D TYR* 3.5 16.4 - - - +
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Residues in contact with VAL1114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D PHE* 4.1 12.3 - - + -
142D LEU* 3.7 27.4 - - + -
143D ALA* 3.9 16.4 - - + +
146D GLN* 3.6 12.7 - - - +
422D VAL* 4.0 24.5 - - + +
425D ALA 5.0 1.6 - - - -
426D GLY* 4.2 5.6 - - - +
1110D HIS 3.0 17.6 + - - +
1111D LEU* 2.9 10.2 + - - +
1113D LEU* 1.3 73.8 - - - +
1115D ALA* 1.3 68.6 + - - +
1117D LYS* 3.3 18.3 + - + +
1118D TRP* 2.9 22.2 + - - +
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Residues in contact with ALA1115 (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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139D PHE* 3.8 23.6 - - + -
142D LEU* 4.4 6.5 - - + -
1111D LEU 3.1 1.0 + - - -
1112D MET 3.0 6.6 + - - +
1114D VAL* 1.3 81.0 - - - +
1116D MET* 1.3 68.1 + - - +
1118D TRP* 2.9 16.2 + - - +
1119D LEU* 2.9 19.4 + - + +
1156D THR* 3.0 27.1 - - + +
1159D LEU* 5.8 5.4 - - + -
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Residues in contact with MET1116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1112D MET* 3.1 14.5 + - - +
1113D LEU 2.9 8.3 + - - +
1115D ALA* 1.3 77.1 - - - +
1117D LYS* 1.3 67.2 + - + +
1119D LEU* 3.3 2.0 + - - +
1120D PHE* 2.8 29.4 + - + -
1129D PHE* 4.9 0.4 - - + -
1139D TYR* 3.0 49.8 - - + +
1152D ALA* 3.0 12.1 - - + +
1153D LEU* 2.9 54.1 - - + +
1156D THR* 2.8 41.2 + - + +
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Residues in contact with LYS1117 (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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146D GLN* 3.8 22.7 - - - +
425D ALA 4.6 1.4 + - - +
426D GLY* 3.7 20.4 + - - -
429D GLU* 3.3 38.9 - - + +
1113D LEU* 2.9 45.2 + - - +
1114D VAL* 3.3 16.5 - - - +
1116D MET* 1.3 72.0 - - + +
1118D TRP* 1.3 66.6 + - - +
1120D PHE* 2.9 12.4 + - - +
1121D GLU* 2.7 30.0 + - - +
1128D ARG* 4.1 17.3 - - - +
1129D PHE* 4.7 3.8 - - + -
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Residues in contact with TRP1118 (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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131D TYR* 5.7 8.1 - + - -
141D LEU* 4.9 0.9 - - + -
142D LEU* 3.3 51.7 - - + +
145D LYS* 2.9 46.9 - - + -
146D GLN* 2.9 30.1 - - + +
1114D VAL 2.9 13.1 + - - +
1115D ALA* 2.9 13.8 + - - +
1117D LYS* 1.3 73.8 - - - +
1119D LEU* 1.3 72.6 + - + +
1121D GLU* 2.6 54.3 + - - +
1122D GLU* 2.5 41.6 + - + +
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Residues in contact with LEU1119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129D PRO* 4.3 23.8 - - + -
131D TYR* 5.8 6.5 - - + -
142D LEU* 6.2 1.3 - - + -
1115D ALA* 2.9 21.2 + - + +
1116D MET 3.9 2.5 - - - +
1118D TRP* 1.3 87.1 - - + +
1120D PHE* 1.3 63.0 + - - +
1122D GLU* 2.9 37.1 + - + +
1123D PHE 3.5 3.1 - - - +
1152D ALA* 4.3 23.6 - - + +
1155D ILE* 3.9 33.2 - - + -
1156D THR* 5.0 3.1 - - - +
1159D LEU* 5.6 3.8 - - + -
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Residues in contact with PHE1120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116D MET* 2.8 37.6 + - + -
1117D LYS* 2.9 12.9 + - - +
1118D TRP 2.9 0.2 + - - -
1119D LEU* 1.3 76.7 - - - +
1121D GLU* 1.3 59.2 + - - +
1123D PHE 2.8 20.1 - - - +
1125D ILE* 3.3 24.2 - - + +
1126D ASP* 3.5 31.4 - - - -
1127D GLY* 4.6 11.7 - - - -
1128D ARG* 5.6 2.5 - - - -
1129D PHE* 5.8 2.2 - + - -
1139D TYR* 4.4 15.0 - + + -
1140D LEU 4.9 3.6 - - - -
1141D VAL* 4.7 5.4 - - + -
1149D ALA* 4.1 22.7 - - + -
1152D ALA* 4.0 11.4 - - + +
1153D LEU* 3.3 35.2 - - + -
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Residues in contact with GLU1121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D GLN* 3.8 9.9 + - - +
1117D LYS* 2.7 18.0 + - - +
1118D TRP* 2.6 62.8 + - - +
1120D PHE* 1.3 75.4 - - - +
1122D GLU* 1.3 58.6 + - - +
1123D PHE* 2.4 18.9 + - - -
1125D ILE* 4.2 16.9 - - + +
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Residues in contact with GLU1122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D TYR* 5.7 8.3 - - + +
1118D TRP* 2.5 74.6 + - + +
1119D LEU* 2.9 24.1 + - + +
1121D GLU* 1.3 85.5 - - - +
1123D PHE* 1.3 88.7 + - + +
1231D LEU 5.2 0.3 - - - +
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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) + - + + + + + -
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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