Contacts of the helix formed by residues 1284 - 1307 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1283D VAL* 1.3 81.7 - - - +
1285D TRP* 1.3 63.6 + - - +
1286D LYS* 3.0 4.9 - - - +
1287D GLU* 2.7 47.5 + - + +
1288D LEU* 3.3 8.2 + - - +
1328D PRO* 3.0 31.7 + - - +
1331D ARG* 3.9 26.1 - - - +
1332D PHE* 3.1 32.1 - - - +
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Residues in contact with TRP1285 (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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1255D ASP 4.6 0.7 - - - -
1256D LEU* 2.8 47.6 + - + +
1259D VAL* 3.6 31.4 - - + +
1260D THR* 3.4 21.2 + - - -
1264D GLN* 4.2 15.7 - - - +
1282D PHE* 2.9 20.6 + + + +
1283D VAL 3.4 1.6 + - - -
1284D ASN* 1.3 74.6 + - - +
1286D LYS* 1.3 62.9 + - - +
1288D LEU* 3.1 13.4 + - + +
1289D ILE* 3.1 23.6 + - + +
1332D PHE* 3.5 37.8 - + - -
1374D PHE* 3.5 25.4 - - + -
1375D ILE* 3.9 19.1 - - + -
1377D LYS* 5.3 1.8 - - + -
1378D PRO* 3.9 17.3 - - + -
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Residues in contact with LYS1286 (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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1260D THR* 5.9 0.7 - - - -
1264D GLN* 5.3 5.1 + - - +
1283D VAL 5.3 0.2 + - - -
1284D ASN* 2.9 2.4 + - - -
1285D TRP* 1.3 79.8 - - - +
1287D GLU* 1.3 61.0 + - + +
1289D ILE* 3.3 13.0 + - + +
1290D MET* 3.1 43.1 + - + +
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Residues in contact with GLU1287 (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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1284D ASN* 2.7 48.5 + - + +
1286D LYS* 1.3 72.8 - - + +
1288D LEU* 1.3 59.9 + - - +
1290D MET* 3.4 22.9 + - + +
1291D CYS* 2.9 32.5 + - - +
1328D PRO* 3.7 24.6 - - + +
1331D ARG* 5.2 3.6 - - - -
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Residues in contact with LEU1288 (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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1256D LEU* 4.2 12.8 - - + -
1284D ASN* 3.8 13.0 - - - +
1285D TRP* 3.1 15.9 + - + +
1287D GLU* 1.3 77.3 - - - +
1289D ILE* 1.3 61.3 + - - +
1291D CYS* 3.4 3.8 + - - -
1292D ASN* 3.0 31.8 + - - +
1328D PRO* 4.0 26.0 - - + +
1329D TYR* 3.9 34.3 - - + +
1332D PHE* 3.7 24.9 - - + -
1378D PRO* 3.7 33.7 - - + -
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Residues in contact with ILE1289 (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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1253D VAL* 5.6 1.5 - - + +
1256D LEU* 3.8 39.7 - - + +
1257D GLN* 4.1 19.1 - - + +
1260D THR* 3.5 27.8 - - + +
1285D TRP* 3.1 15.6 + - + +
1286D LYS* 3.5 12.3 - - + +
1288D LEU* 1.3 77.2 - - - +
1290D MET* 1.3 68.1 + - + +
1292D ASN* 3.9 0.7 - - - +
1293D ILE* 2.9 46.2 + - + +
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Residues in contact with MET1290 (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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1286D LYS* 3.1 33.5 + - + +
1287D GLU* 3.4 28.5 + - + +
1289D ILE* 1.3 80.7 - - + +
1291D CYS* 1.3 64.0 + - - +
1293D ILE* 3.4 6.3 + - - +
1294D LYS* 3.2 21.5 + - - +
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Residues in contact with CYS1291 (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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1287D GLU 2.9 19.4 + - - +
1288D LEU* 3.7 4.7 - - - +
1290D MET* 1.3 78.9 - - - +
1292D ASN* 1.3 66.7 + - - +
1294D LYS* 3.5 7.7 + - - +
1295D LEU* 3.5 15.9 + - - +
1322D GLN* 4.7 3.1 + - - -
1325D HIS* 3.5 26.2 - - - +
1326D MET* 3.2 38.6 - - - +
1328D PRO* 5.0 8.1 - - + -
1329D TYR* 4.2 6.5 - - - -
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Residues in contact with ASN1292 (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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1249D GLU* 2.7 25.2 - - - +
1252D TYR* 3.3 13.1 - - + -
1253D VAL* 3.7 16.4 - - + +
1256D LEU* 4.4 2.2 - - + -
1288D LEU 3.0 27.0 + - - +
1289D ILE 4.2 0.9 - - - +
1291D CYS* 1.3 75.3 - - - +
1293D ILE* 1.3 61.1 + - - +
1294D LYS 3.1 2.2 - - - -
1295D LEU* 3.1 9.2 + - - +
1296D LEU* 2.8 29.8 + - - +
1326D MET* 4.5 3.9 - - - +
1329D TYR* 2.5 37.2 + - - -
1385D TYR* 3.1 16.1 + - - -
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Residues in contact with ILE1293 (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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1253D VAL* 3.9 20.2 - - + -
1257D GLN* 3.6 27.8 - - - +
1289D ILE* 2.9 30.5 + - + +
1290D MET* 3.8 7.0 - - - +
1292D ASN* 1.3 77.5 - - - +
1294D LYS* 1.3 63.7 + - - +
1296D LEU* 3.8 6.6 - - + +
1297D LYS* 3.0 53.9 + - + +
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Residues in contact with LYS1294 (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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1290D MET 3.2 11.9 + - - +
1291D CYS* 3.6 11.0 - - - +
1292D ASN 3.1 0.4 - - - -
1293D ILE* 1.3 81.8 - - - +
1295D LEU* 1.3 60.6 + - - +
1297D LYS* 3.7 7.4 + - - +
1298D ALA* 3.3 20.6 + - - +
1322D GLN* 3.2 25.9 - - - +
1325D HIS* 3.7 26.4 + - + -
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Residues in contact with LEU1295 (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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1249D GLU* 3.8 18.2 - - + +
1291D CYS 3.5 7.8 + - - +
1292D ASN* 3.1 9.7 + - - +
1294D LYS* 1.3 78.0 - - - +
1296D LEU* 1.3 64.6 + - - +
1298D ALA* 3.2 3.3 + - - +
1299D LEU* 3.0 44.8 + - + +
1318D ILE* 4.1 10.1 - - + -
1319D LEU* 4.4 12.8 - - + -
1322D GLN* 3.5 32.9 - - + +
1326D MET* 4.3 11.2 - - + -
1385D TYR* 3.6 32.8 - - + +
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Residues in contact with LEU1296 (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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1246D ILE* 4.5 4.3 - - + +
1249D GLU* 4.1 19.2 - - + +
1250D GLU* 3.2 57.2 - - + +
1253D VAL* 4.3 22.2 - - + -
1292D ASN 2.8 19.6 + - - +
1293D ILE* 3.8 7.4 - - + +
1295D LEU* 1.3 72.4 - - - +
1297D LYS* 1.3 58.6 + - + +
1299D LEU* 3.1 13.1 + - + -
1300D ARG* 2.8 57.1 + - + +
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Residues in contact with LYS1297 (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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1293D ILE* 3.0 40.9 + - + +
1294D LYS* 4.0 7.6 - - - +
1296D LEU* 1.3 77.8 - - + +
1298D ALA* 1.3 56.9 + - - +
1300D ARG* 3.4 18.7 + - - +
1301D VAL* 2.9 35.4 + - + +
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Residues in contact with ALA1298 (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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1294D LYS 3.3 10.9 + - - +
1295D LEU 3.2 7.7 + - - +
1296D LEU 3.2 0.8 - - - -
1297D LYS* 1.3 75.5 - - - +
1299D LEU* 1.3 63.7 - - - +
1301D VAL* 3.4 7.2 + - - +
1302D ARG* 3.0 23.9 + - - +
1318D ILE* 3.7 27.0 - - + +
1322D GLN* 4.3 8.1 - - - +
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Residues in contact with LEU1299 (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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1245D LEU* 4.2 24.0 - - + -
1246D ILE* 4.5 22.2 - - + +
1249D GLU* 4.0 29.6 - - + -
1295D LEU* 3.0 40.2 + - + +
1296D LEU* 3.1 10.7 + - + +
1298D ALA* 1.3 77.5 - - - +
1300D ARG* 1.3 56.3 + - - +
1302D ARG* 3.4 3.0 + - - +
1303D LYS* 2.9 29.0 + - - +
1315D ILE* 3.7 30.1 - - + +
1318D ILE* 3.9 13.5 - - + -
1319D LEU* 4.8 2.0 - - + -
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Residues in contact with ARG1300 (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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1246D ILE* 5.6 4.5 - - + -
1250D GLU* 2.6 44.0 + - - +
1296D LEU* 2.8 38.7 + - + +
1297D LYS* 3.6 17.0 - - - +
1299D LEU* 1.3 73.9 - - - +
1301D VAL* 1.3 66.3 + - + +
1303D LYS* 3.2 6.9 + - - +
1304D LYS* 2.9 42.2 + - + +
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Residues in contact with VAL1301 (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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1297D LYS* 2.9 23.6 + - + +
1298D ALA* 3.8 7.6 - - - +
1299D LEU 3.3 0.2 - - - -
1300D ARG* 1.3 76.1 - - + +
1302D ARG* 1.3 65.3 + - - +
1304D LYS* 3.3 12.5 + - + +
1305D MET* 2.9 33.4 + - + +
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Residues in contact with ARG1302 (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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1298D ALA 3.0 8.8 + - - +
1299D LEU 3.7 3.8 - - - +
1301D VAL* 1.3 77.6 - - - +
1303D LYS* 1.3 57.9 + - - +
1305D MET* 3.3 26.1 + - - +
1306D SER* 2.8 37.7 + - - -
1312D VAL* 4.1 11.0 - - + -
1313D LYS 6.2 0.2 - - - +
1314D MET* 2.8 43.1 + - - +
1315D ILE* 4.2 4.3 - - + -
1317D ASP* 2.9 38.2 + - - -
1318D ILE* 3.5 37.6 - - + +
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Residues in contact with LYS1303 (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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1243D HIS* 6.1 5.1 - - - -
1246D ILE* 4.3 25.4 - - + -
1299D LEU 2.9 17.5 + - - +
1300D ARG* 3.2 8.7 + - - +
1302D ARG* 1.3 77.6 - - - +
1304D LYS* 1.3 62.5 + - + +
1306D SER* 3.3 21.9 - - - -
1307D GLY* 3.4 16.3 + - - +
1308D GLU 4.3 9.8 + - - -
1309D LYS* 5.9 0.2 - - - +
1310D MET 4.0 18.2 + - - -
1312D VAL* 5.5 13.0 - - + +
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Residues in contact with LYS1304 (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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1300D ARG* 2.9 33.6 + - - +
1301D VAL* 3.6 11.2 - - + +
1303D LYS* 1.3 73.2 - - + +
1305D MET* 1.3 67.1 + - - +
1307D GLY* 3.3 14.2 + - - -
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Residues in contact with MET1305 (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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1301D VAL* 2.9 27.2 + - + +
1302D ARG* 3.5 29.8 - - - +
1304D LYS* 1.3 77.7 - - - +
1306D SER* 1.3 65.2 + - - +
1307D GLY* 3.3 1.4 + - - -
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Residues in contact with SER1306 (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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1302D ARG* 2.8 25.0 + - - +
1303D LYS* 3.3 14.8 - - - -
1305D MET* 1.3 78.9 - - - +
1307D GLY* 1.3 60.9 + - - +
1310D MET* 3.3 18.9 - - - +
1311D PRO 4.3 7.3 - - - +
1312D VAL* 3.5 39.9 - - - +
1313D LYS* 4.6 2.9 + - - -
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Residues in contact with GLY1307 (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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1303D LYS* 3.4 13.4 + - - +
1304D LYS* 3.3 12.3 + - - -
1305D MET 3.3 4.3 - - - -
1306D SER* 1.3 79.4 - - - +
1308D GLU* 1.3 69.6 + - - +
1309D LYS 3.5 2.0 - - - -
1310D 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
------------------------------------------------------------
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