Contacts of the helix formed by residues 1145 - 1168 (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 ASP1145 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124D ALA 4.3 3.1 - - - +
1125D ILE 4.3 9.0 - - - +
1126D ASP* 2.8 42.1 - - + +
1141D VAL* 3.3 3.6 - - - +
1142D ARG* 4.1 6.0 - - + +
1144D GLU* 1.3 93.4 - - - +
1146D ARG* 1.3 58.6 + - - +
1147D TYR 3.1 7.7 + - - +
1148D ARG* 3.0 47.3 + - - +
1149D ALA 3.2 11.6 + - - -
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Residues in contact with ARG1146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885D THR* 2.6 36.2 + - - +
886D LEU 2.5 16.6 + - - +
887D VAL* 2.4 39.9 - - - +
1139D TYR 2.7 21.8 + - - -
1141D VAL* 2.6 52.2 + - - +
1142D ARG 3.5 3.6 - - - +
1143D GLU* 2.5 33.0 - - + +
1144D GLU 2.9 3.0 + - - -
1145D ASP* 1.3 79.0 - - - +
1147D TYR* 1.3 75.4 + - + +
1149D ALA* 3.7 3.8 - - - +
1150D ALA* 3.3 21.0 + - - +
1185D ILE* 3.5 17.7 - - + +
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Residues in contact with TYR1147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1143D GLU 5.6 0.4 - - - -
1145D ASP* 3.1 1.4 - - - +
1146D ARG* 1.3 95.5 - - + +
1148D ARG* 1.3 62.8 + - - +
1149D ALA 3.0 1.8 - - - -
1150D ALA* 3.1 7.1 + - + +
1151D LEU* 2.8 26.5 + - - +
1185D ILE* 5.3 16.0 - - + +
1218D LEU* 5.3 13.7 - - + -
1223D ILE* 3.5 9.3 - - + +
1226D LEU* 3.3 42.6 - - + -
1227D THR* 3.2 20.4 - - + +
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Residues in contact with ARG1148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124D ALA* 2.6 64.8 + - + +
1126D ASP* 4.4 2.0 - - - +
1145D ASP* 3.0 57.8 + - - +
1147D TYR* 1.3 79.6 - - - +
1149D ALA* 1.3 57.6 + - - +
1151D LEU* 3.3 8.7 + - - +
1152D ALA* 2.8 30.4 + - - +
1227D THR* 4.2 9.1 - - - +
1230D SER* 4.8 8.2 + - - +
1231D LEU* 3.0 44.4 - - + +
1232D GLU 4.8 0.8 + - - -
1236D GLN* 5.1 2.0 + - - +
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Residues in contact with ALA1149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887D VAL* 3.9 4.5 - - + -
1120D PHE* 4.1 21.5 - - + -
1126D ASP* 4.4 1.9 + - - +
1141D VAL* 3.0 37.2 - - + -
1145D ASP 3.2 11.4 + - - +
1146D ARG 3.7 6.1 - - - +
1148D ARG* 1.3 75.2 - - - +
1150D ALA* 1.3 67.6 + - - +
1152D ALA* 2.9 4.2 + - - +
1153D LEU* 2.7 31.2 + - + +
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Residues in contact with ALA1150 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887D VAL* 4.0 7.1 - - + +
1146D ARG 3.3 12.3 + - - +
1147D TYR* 3.1 11.8 + - + +
1149D ALA* 1.3 78.2 - - - +
1151D LEU* 1.3 64.1 + - - +
1153D LEU* 2.9 12.8 + - - +
1154D GLN* 2.8 23.4 + - - +
1183D VAL* 4.1 21.0 - - + +
1185D ILE* 5.1 2.9 - - + -
1218D LEU* 6.3 1.8 - - + -
1223D ILE* 3.5 20.0 - - + -
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Residues in contact with LEU1151 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D LEU* 4.9 11.0 - - + -
1147D TYR 2.8 12.2 + - - +
1148D ARG* 3.3 9.9 - - - +
1150D ALA* 1.3 73.6 - - - +
1152D ALA* 1.3 58.0 + - - +
1153D LEU 3.1 0.3 + - - -
1154D GLN* 3.1 7.3 + - + +
1155D ILE* 2.6 48.5 + - + +
1220D ILE* 6.0 1.8 - - + -
1223D ILE* 3.2 28.0 - - + +
1224D ILE* 3.9 16.6 - - + -
1227D THR* 2.5 33.4 - - - +
1230D SER* 3.3 35.9 - - - +
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Residues in contact with ALA1152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116D MET* 3.0 8.9 - - + +
1119D LEU* 4.3 25.0 - - + +
1120D PHE* 4.0 23.3 - - + +
1148D ARG 2.8 16.8 + - - +
1149D ALA* 3.3 8.1 - - - +
1151D LEU* 1.3 72.2 - - - +
1153D LEU* 1.3 57.9 - - - +
1155D ILE* 3.1 8.4 - - - +
1156D THR* 2.8 27.5 + - - -
1230D SER* 5.3 0.6 + - - -
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Residues in contact with LEU1153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887D VAL* 3.3 29.6 - - + +
888D GLY* 4.5 2.7 - - - +
1112D MET* 5.3 0.5 - - - +
1116D MET* 2.9 25.4 - - - +
1120D PHE* 3.3 26.5 - - + -
1139D TYR* 3.2 33.4 - - + -
1149D ALA 2.7 35.6 + - - +
1150D ALA* 2.9 8.5 + - - +
1152D ALA* 1.3 70.4 - - - +
1154D GLN* 1.3 69.8 + - - +
1156D THR* 3.2 10.9 + - - +
1157D ASN* 3.2 16.1 + - - +
1180D PHE* 5.6 2.9 - - + -
1183D VAL* 4.2 10.1 - - + -
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Residues in contact with GLN1154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1150D ALA 2.8 13.6 + - - +
1151D LEU* 3.7 10.4 - - + +
1153D LEU* 1.3 72.5 - - - +
1155D ILE* 1.3 70.0 + - + +
1157D ASN* 2.7 23.0 + - - +
1158D LEU* 2.7 13.7 - - - +
1178D ALA 5.3 0.2 - - - +
1179D PHE* 3.2 30.4 - - + -
1180D PHE* 3.6 27.6 + - + +
1181D SER 5.2 0.4 + - - -
1182D ALA* 4.7 1.2 - - - +
1183D VAL* 4.4 14.3 - - + +
1218D LEU 4.3 6.4 + - - -
1220D ILE* 2.8 52.9 + - - +
1223D ILE* 4.4 10.1 - - - +
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Residues in contact with ILE1155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127D LEU* 3.3 33.2 - - + -
129D PRO* 4.4 13.7 - - + -
1119D LEU* 3.9 20.2 - - + -
1151D LEU* 2.6 39.3 + - + +
1152D ALA* 3.1 10.5 - - - +
1154D GLN* 1.3 79.8 - - + +
1156D THR* 1.3 57.9 + - - +
1157D ASN 2.5 14.2 + - - -
1158D LEU* 2.7 36.4 + - + +
1159D LEU* 3.3 24.0 + - + -
1179D PHE* 5.5 4.0 - - + -
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Residues in contact with THR1156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1112D MET* 3.0 50.3 - - + +
1115D ALA* 3.0 15.6 - - + +
1116D MET* 2.8 49.4 + - + +
1119D LEU* 5.0 3.6 - - - +
1152D ALA 2.8 9.6 + - - -
1153D LEU 3.5 1.8 - - - +
1155D ILE* 1.3 73.2 - - - +
1157D ASN* 1.3 65.6 + - - +
1159D LEU* 4.1 4.2 - - - +
1160D THR* 2.9 26.9 + - - -
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Residues in contact with ASN1157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894D GLN* 4.5 0.2 + - - -
1108D TYR* 3.6 1.6 + - - -
1112D MET* 3.2 22.7 - - - +
1153D LEU 3.2 16.6 + - - -
1154D GLN* 2.7 16.2 + - - +
1155D ILE 2.5 4.4 + - - -
1156D THR* 1.3 75.4 - - - +
1158D LEU* 1.3 69.1 + - - +
1160D THR* 3.5 1.9 - - - -
1161D ARG* 2.4 69.0 + - - +
1178D ALA 3.9 0.9 - - - +
1180D PHE* 3.0 40.2 - - + -
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Residues in contact with LEU1158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D LEU* 6.1 4.7 - - + -
127D LEU* 6.6 0.2 - - + -
1154D GLN 2.7 32.5 - - - +
1155D ILE* 2.7 33.0 - - + +
1157D ASN* 1.3 78.1 - - - +
1159D LEU* 1.3 86.6 + - + +
1161D ARG* 2.9 2.9 + - - +
1162D CYS* 2.8 27.7 + - - +
1178D ALA* 3.5 34.0 + - + +
1179D PHE* 3.6 28.7 - - + -
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Residues in contact with LEU1159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86D GLN* 4.6 25.6 - - + +
87D ILE* 5.5 3.8 - - + -
129D PRO* 6.0 4.7 - - + -
130D LEU* 6.3 1.6 - - - +
135D LEU* 3.9 13.3 - - + +
139D PHE* 4.6 12.3 - - + -
1115D ALA* 5.8 5.2 - - + -
1119D LEU* 5.6 4.9 - - + -
1155D ILE* 3.3 26.2 + - + +
1156D THR* 4.1 5.2 - - - +
1158D LEU* 1.3 98.4 - - + +
1160D THR* 1.3 63.5 + - - +
1162D CYS* 2.9 25.4 + - + +
1163D MET* 3.0 7.8 + - - +
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Residues in contact with THR1160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D PHE* 3.6 20.5 - - - -
1108D TYR* 3.0 38.1 - - + -
1111D LEU* 3.8 16.8 - - + -
1112D MET* 3.3 26.1 + - + +
1156D THR* 2.9 29.2 + - - +
1157D ASN* 3.0 3.3 + - - -
1159D LEU* 1.3 72.8 - - - +
1161D ARG* 1.3 62.9 + - - +
1163D MET* 3.4 3.7 + - - +
1164D PHE* 2.9 24.1 + - + +
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Residues in contact with ARG1161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893D SER* 5.6 0.6 + - - -
894D GLN* 3.9 13.5 - - + +
897D TRP* 4.6 9.4 - - + -
1108D TYR* 2.5 32.3 + - + +
1157D ASN* 2.4 65.2 + - - +
1158D LEU* 3.4 4.3 - - - +
1160D THR* 1.3 72.9 - - - +
1162D CYS* 1.3 66.9 + - - +
1164D PHE* 3.0 19.7 - - - +
1165D ALA* 3.0 7.6 + - - +
1173D LEU* 4.5 4.2 - - - +
1176D SER 5.7 0.2 - - - -
1177D VAL* 2.9 36.7 + - + +
1178D ALA* 2.4 33.1 + - - -
1179D PHE* 4.0 4.0 - - - +
1180D PHE* 3.0 28.9 - - - +
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Residues in contact with CYS1162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D LEU* 4.8 16.2 - - - -
87D ILE* 3.5 31.2 - - + -
135D LEU* 3.7 1.1 - - + -
1158D LEU* 2.8 17.3 + - - +
1159D LEU* 2.9 15.9 + - - +
1161D ARG* 1.3 74.2 - - - +
1163D MET* 1.3 55.5 + - - +
1165D ALA* 2.5 30.9 + - - +
1166D TYR* 2.7 25.2 - - - -
1173D LEU* 5.6 8.3 - - - -
1178D ALA* 6.5 0.9 - - - -
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Residues in contact with MET1163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D LEU* 3.0 29.9 - - + +
136D ASP* 4.0 16.4 - - + -
139D PHE* 3.4 39.0 - - + -
140D ARG* 5.8 0.4 - - - -
422D VAL* 6.1 1.1 - - - -
1019D TRP* 4.1 3.4 - - + -
1111D LEU* 4.0 16.4 - - + -
1159D LEU 3.0 4.8 + - - +
1160D THR 3.6 7.4 - - - +
1162D CYS* 1.3 77.0 - - - +
1164D PHE* 1.3 69.6 + - - +
1166D TYR* 3.0 18.0 + - - +
1167D LYS* 3.0 66.0 + - + +
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Residues in contact with PHE1164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897D TRP* 6.2 1.3 - - + -
898D ILE* 4.7 19.1 - - + -
901D VAL* 6.2 2.9 - - + -
1019D TRP* 3.4 29.2 - + - -
1104D SER* 3.2 17.7 - - - -
1107D ASP* 4.0 0.7 - - + -
1108D TYR* 3.0 61.7 - + + -
1111D LEU* 3.1 32.3 - - + -
1160D THR 2.9 7.3 + - - +
1161D ARG* 3.0 14.8 - - - +
1162D CYS 2.7 3.4 + - - -
1163D MET* 1.3 82.0 - - - +
1165D ALA* 1.3 52.9 + - - +
1166D TYR 2.8 11.4 + - - -
1167D LYS* 3.2 1.4 + - - +
1168D LEU* 3.2 39.9 + - + +
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Residues in contact with ALA1165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901D VAL* 5.8 4.7 - - - -
1161D ARG 3.0 2.6 + - - +
1162D CYS 2.5 19.8 + - - +
1164D PHE* 1.3 72.8 - - - +
1166D TYR* 1.3 63.3 + - + -
1168D LEU 5.2 0.7 - - - -
1169D GLY* 2.7 26.8 - - - -
1170D LEU* 2.7 11.3 + - - -
1172D ASP 3.9 3.1 - - - +
1173D LEU* 2.7 44.7 - - + +
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Residues in contact with TYR1166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D ILE* 2.8 52.5 - - + +
134D ASN* 5.5 4.9 - - - +
135D LEU* 4.2 15.3 - - + -
1162D CYS* 2.7 32.3 - - - -
1163D MET* 3.5 7.2 - - - +
1164D PHE 2.8 2.2 + - - -
1165D ALA* 1.3 95.4 - - + +
1167D LYS* 1.3 64.1 + - + +
1169D GLY 2.4 34.1 + - - +
1171D ASN* 3.4 26.0 - - + +
1172D ASP* 3.3 22.9 + - - -
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Residues in contact with LYS1167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D ASP* 2.5 32.1 - - - +
140D ARG* 3.4 25.1 - - - +
420D HIS* 4.6 4.6 - - - -
422D VAL* 6.3 0.4 - - - +
1018D GLY 5.6 2.3 - - - -
1019D TRP* 3.3 58.2 + - + +
1020D ILE* 4.6 4.9 - - - +
1163D MET* 3.0 32.2 + - + +
1164D PHE 3.2 0.9 + - - +
1166D TYR* 1.3 81.7 - - + +
1168D LEU* 1.3 60.9 + - - +
1169D GLY 3.2 0.9 + - - -
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Residues in contact with LEU1168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898D ILE* 5.6 4.3 - - + +
901D VAL* 5.7 6.5 - - + +
902D LEU* 3.4 39.0 - - + +
905D ALA* 3.6 18.4 - - - +
1006D ARG* 6.2 1.1 - - - +
1016D GLU 5.8 0.2 - - - +
1017D GLY 5.4 3.8 - - - +
1019D TRP* 2.7 62.8 - - + +
1104D SER* 4.7 13.9 - - - -
1164D PHE* 3.2 25.0 + - + +
1165D ALA* 4.2 1.8 - - - -
1167D LYS* 1.3 78.3 - - - +
1169D GLY* 1.3 56.5 + - - +
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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