Contacts of the helix formed by residues 1284 - 1307 (chain B) in PDB entry 1KI1
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 ASN1284 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1283B VAL* 1.3 81.3 - - - +
1285B TRP* 1.3 53.4 + - - +
1286B LYS* 3.0 4.7 - - - +
1287B GLU* 2.7 57.7 + - + +
1288B LEU* 3.3 8.4 + - - +
1328B PRO* 3.1 31.5 + - - +
1331B ARG* 3.9 26.1 - - - +
1332B PHE* 3.1 32.5 - - - +
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Residues in contact with TRP1285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1255B ASP 4.6 0.7 - - - -
1256B LEU* 2.8 47.4 + - + +
1259B VAL* 3.6 31.2 - - + +
1260B THR* 3.4 21.2 + - - -
1264B GLN* 4.2 15.7 - - - +
1282B PHE* 2.9 21.0 + + + +
1283B VAL 3.4 1.4 + - - -
1284B ASN* 1.3 74.6 + - - +
1286B LYS* 1.3 62.9 + - - +
1288B LEU* 3.1 13.2 + - + +
1289B ILE* 3.1 23.4 + - + +
1332B PHE* 3.5 38.3 - + - -
1374B PHE 3.5 25.4 - - - -
1375B ILE* 3.9 19.1 - - + -
1377B LYS* 5.4 1.6 - - + -
1378B PRO* 3.9 17.0 - - + -
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Residues in contact with LYS1286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1260B THR* 5.9 0.7 - - - -
1264B GLN* 5.3 5.1 + - - +
1283B VAL 5.3 0.2 + - - -
1284B ASN* 2.9 2.4 + - - -
1285B TRP* 1.3 80.0 - - - +
1287B GLU* 1.3 61.2 + - + +
1289B ILE* 3.3 13.0 + - + +
1290B MET* 3.1 42.5 + - + +
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Residues in contact with GLU1287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1284B ASN* 2.7 48.8 + - + +
1286B LYS* 1.3 72.6 - - + +
1288B LEU* 1.3 60.2 + - - +
1290B MET* 3.4 22.6 + - + +
1291B CYS* 2.9 32.3 + - - +
1328B PRO* 3.7 24.6 - - + +
1331B ARG* 5.2 3.6 - - - -
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Residues in contact with LEU1288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1256B LEU* 4.2 12.8 - - + -
1284B ASN* 3.8 12.8 - - - +
1285B TRP* 3.1 15.7 + - + +
1287B GLU* 1.3 77.0 - - - +
1289B ILE* 1.3 61.2 + - - +
1291B CYS* 3.4 3.5 + - - -
1292B ASN* 3.0 31.8 + - - +
1328B PRO* 4.0 26.0 - - + +
1329B TYR* 3.9 34.3 - - + +
1332B PHE* 3.7 25.1 - - + -
1378B PRO* 3.7 33.9 - - + -
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Residues in contact with ILE1289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1253B VAL* 5.6 1.5 - - + +
1256B LEU* 3.8 39.7 - - + +
1257B GLN* 4.1 19.1 - - + +
1260B THR* 3.5 28.0 - - + +
1285B TRP* 3.1 15.8 + - + +
1286B LYS* 3.5 12.3 - - + +
1288B LEU* 1.3 77.6 - - - +
1290B MET* 1.3 68.1 + - + +
1292B ASN* 3.9 0.7 - - - +
1293B ILE* 2.9 45.8 + - + +
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Residues in contact with MET1290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1286B LYS* 3.1 33.5 + - + +
1287B GLU* 3.4 28.9 + - + +
1289B ILE* 1.3 80.7 - - + +
1291B CYS* 1.3 63.7 + - - +
1293B ILE* 3.4 6.6 + - - +
1294B LYS* 3.2 21.3 + - - +
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Residues in contact with CYS1291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1287B GLU 2.9 19.4 + - - +
1288B LEU* 3.7 4.7 - - - +
1290B MET* 1.3 78.7 - - - +
1292B ASN* 1.3 66.7 + - - +
1294B LYS* 3.5 7.9 + - - +
1295B LEU* 3.5 15.8 + - - +
1322B GLN* 4.7 3.1 + - - -
1325B HIS* 3.5 26.0 - - - +
1326B MET* 3.3 38.6 - - - +
1328B PRO* 5.0 8.1 - - + -
1329B TYR* 4.2 6.7 - - - -
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Residues in contact with ASN1292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1249B GLU* 2.7 25.2 - - - +
1252B TYR* 3.3 13.1 - - + -
1253B VAL* 3.7 16.2 - - + +
1256B LEU* 4.4 2.5 - - + -
1288B LEU 3.0 27.0 + - - +
1289B ILE 4.2 0.9 - - - +
1291B CYS* 1.3 75.1 - - - +
1293B ILE* 1.3 61.1 + - - +
1294B LYS 3.1 2.2 - - - -
1295B LEU* 3.1 8.7 + - - +
1296B LEU* 2.8 29.6 + - - +
1326B MET* 4.5 3.9 - - - +
1329B TYR* 2.5 37.4 + - - -
1385B TYR* 3.1 16.1 + - - -
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Residues in contact with ILE1293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1253B VAL* 3.9 20.0 - - + -
1257B GLN* 3.6 27.8 - - - +
1289B ILE* 2.9 31.4 + - + +
1290B MET* 3.8 7.0 - - - +
1292B ASN* 1.3 77.5 - - - +
1294B LYS* 1.3 63.7 + - - +
1296B LEU* 3.8 6.6 - - + +
1297B LYS* 3.0 53.5 + - + +
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Residues in contact with LYS1294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1290B MET 3.2 11.9 + - - +
1291B CYS* 3.6 11.2 - - - +
1292B ASN 3.1 0.4 - - - -
1293B ILE* 1.3 81.6 - - - +
1295B LEU* 1.3 60.8 + - - +
1297B LYS* 3.7 7.4 + - - +
1298B ALA* 3.3 20.4 + - - +
1322B GLN* 3.2 25.9 - - - +
1325B HIS* 3.7 26.4 + - + -
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Residues in contact with LEU1295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1249B GLU* 3.8 18.2 - - + +
1291B CYS 3.5 7.8 + - - +
1292B ASN* 3.1 9.5 + - - +
1294B LYS* 1.3 77.8 - - - +
1296B LEU* 1.3 64.6 + - - +
1298B ALA* 3.2 3.3 + - - +
1299B LEU* 3.0 44.7 + - + +
1318B ILE* 4.1 10.1 - - + -
1319B LEU* 4.4 12.8 - - + -
1322B GLN* 3.5 32.9 - - + +
1326B MET* 4.3 11.2 - - + -
1385B TYR* 3.6 33.0 - - + +
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Residues in contact with LEU1296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1246B ILE* 4.5 4.3 - - + +
1249B GLU* 4.1 20.8 - - + +
1250B GLU* 3.1 55.9 - - + +
1253B VAL* 4.3 22.7 - - + -
1292B ASN 2.8 19.8 + - - +
1293B ILE* 3.8 7.6 - - + +
1295B LEU* 1.3 72.2 - - - +
1297B LYS* 1.3 58.4 + - + +
1299B LEU* 3.1 13.1 + - + -
1300B ARG* 2.8 56.7 + - + +
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Residues in contact with LYS1297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1293B ILE* 3.0 41.8 + - + +
1294B LYS* 4.0 7.6 - - - +
1296B LEU* 1.3 78.0 - - + +
1298B ALA* 1.3 57.1 + - - +
1300B ARG* 3.4 18.9 + - - +
1301B VAL* 2.9 35.3 + - + +
161C THR* 5.0 11.5 + - - +
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Residues in contact with ALA1298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1294B LYS 3.3 10.9 + - - +
1295B LEU 3.2 8.0 + - - +
1296B LEU 3.2 0.8 - - - -
1297B LYS* 1.3 75.5 - - - +
1299B LEU* 1.3 64.1 - - - +
1301B VAL* 3.4 7.2 + - - +
1302B ARG* 3.0 23.7 + - - +
1318B ILE* 3.7 27.0 - - + +
1322B GLN* 4.3 8.1 - - - +
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Residues in contact with LEU1299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1245B LEU* 4.2 23.8 - - + -
1246B ILE* 4.5 22.2 - - + +
1249B GLU* 4.0 29.8 - - + -
1295B LEU* 3.0 39.9 + - + +
1296B LEU* 3.1 10.7 + - + +
1298B ALA* 1.3 75.9 - - - +
1300B ARG* 1.3 57.4 + - - +
1302B ARG* 3.4 3.0 + - - +
1303B LYS* 2.9 28.8 + - - +
1315B ILE* 3.7 30.1 - - + +
1318B ILE* 3.9 13.5 - - + -
1319B LEU* 4.8 2.0 - - + -
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Residues in contact with ARG1300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1246B ILE* 5.6 4.5 - - + -
1250B GLU* 2.7 44.2 + - - +
1296B LEU* 2.8 38.5 + - + +
1297B LYS* 3.6 17.0 - - - +
1299B LEU* 1.3 74.1 - - - +
1301B VAL* 1.3 65.9 + - + +
1303B LYS* 3.2 6.9 + - - +
1304B LYS* 2.9 38.9 + - + +
118C ASP 5.3 4.4 + - - -
121C ASP* 3.6 45.3 + - + +
122C ASP* 4.6 2.8 + - - +
123C PRO* 3.9 5.1 - - - +
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Residues in contact with VAL1301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1297B LYS* 2.9 23.8 + - + +
1298B ALA* 3.8 7.6 - - - +
1299B LEU 3.3 0.2 - - - -
1300B ARG* 1.3 76.3 - - + +
1302B ARG* 1.3 65.7 + - - +
1304B LYS* 3.3 12.5 + - + +
1305B MET* 2.9 33.3 + - + +
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Residues in contact with ARG1302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1298B ALA 3.0 8.8 + - - +
1299B LEU 3.7 3.8 - - - +
1301B VAL* 1.3 77.6 - - - +
1303B LYS* 1.3 57.9 + - - +
1305B MET* 3.3 25.9 + - - +
1306B SER* 2.8 37.5 + - - -
1312B VAL* 4.1 11.0 - - + -
1313B LYS 6.2 0.2 - - - +
1314B MET* 2.8 43.4 + - - +
1315B ILE* 4.2 4.3 - - + -
1317B ASP* 2.9 38.6 + - - -
1318B ILE* 3.5 38.0 - - + +
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Residues in contact with LYS1303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1243B HIS* 6.1 5.1 - - - -
1246B ILE* 4.3 26.2 - - + -
1299B LEU 2.9 17.7 + - - +
1300B ARG* 3.2 8.7 + - - +
1302B ARG* 1.3 77.4 - - - +
1304B LYS* 1.3 62.0 + - + +
1306B SER* 3.3 21.9 - - - -
1307B GLY* 3.4 16.0 + - - +
1308B GLU 4.3 9.8 + - - -
1309B LYS* 5.9 0.2 - - - +
1310B MET 4.0 18.0 + - - -
1312B VAL* 5.5 13.0 - - + +
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Residues in contact with LYS1304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1300B ARG* 2.9 29.2 + - - +
1301B VAL* 3.6 11.2 - - + +
1303B LYS* 1.3 73.6 - - + +
1305B MET* 1.3 67.1 + - - +
1307B GLY* 3.3 14.2 + - - -
120C ARG* 5.7 2.8 - - - +
121C ASP* 2.8 41.4 + - - -
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Residues in contact with MET1305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1301B VAL* 2.9 27.2 + - + +
1302B ARG* 3.5 30.3 - - - +
1304B LYS* 1.3 77.7 - - - +
1306B SER* 1.3 65.5 + - - +
1307B GLY* 3.3 1.4 + - - -
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Residues in contact with SER1306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1302B ARG* 2.8 25.0 + - - +
1303B LYS* 3.3 14.8 - - - -
1305B MET* 1.3 78.5 - - - +
1307B GLY* 1.3 60.9 + - - +
1310B MET* 3.3 18.9 - - - +
1311B PRO 4.3 7.3 - - - +
1312B VAL* 3.5 40.1 - - - +
1313B LYS* 4.6 2.9 + - - -
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Residues in contact with GLY1307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1303B LYS* 3.4 13.6 + - - +
1304B LYS* 3.3 12.3 + - - -
1305B MET 3.3 4.3 - - - -
1306B SER* 1.3 79.6 - - - +
1308B GLU* 1.3 69.4 + - - +
1309B LYS 3.5 2.0 - - - -
1310B MET* 3.2 24.4 + - - +
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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
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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