Contacts of the helix formed by residues 1252 - 1281 (chain D) in PDB entry 1P3F
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 SER1252 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877C ARG* 3.6 18.9 - - - +
878C ILE 2.9 20.1 + - - -
879C ILE* 3.9 14.3 - - - +
880C PRO* 4.2 1.0 - - - +
1251D ILE* 1.3 74.4 - - - +
1253D SER* 1.3 65.9 + - - +
1254D LYS* 3.5 8.6 + - - +
1255D ALA* 2.7 25.6 + - - +
1256D MET* 2.9 10.3 + - - +
19I A 3.4 17.5 - - - -
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Residues in contact with SER1253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1251D ILE 3.9 1.2 + - - -
1252D SER* 1.3 72.2 - - - +
1254D LYS* 1.3 58.2 + - - +
1256D MET* 3.6 9.3 - - - +
1257D SER* 2.5 38.2 + - - -
19I A 3.1 29.8 + - - -
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Residues in contact with LYS1254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880C PRO* 4.0 14.3 - - + +
904C GLN* 4.8 23.7 - - + +
1252D SER* 3.0 8.1 + - - +
1253D SER* 1.3 88.1 + - - +
1255D ALA* 1.4 54.7 + - - +
1257D SER* 3.3 7.4 - - - -
1258D ILE* 3.2 26.9 + - - +
299F GLY* 5.0 3.4 - - - +
19I A 4.6 0.2 + - - -
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Residues in contact with ALA1255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878C ILE* 4.0 8.7 - - + +
879C ILE 4.2 10.1 - - - -
880C PRO* 4.0 5.3 - - - +
883C LEU* 3.8 20.0 - - + +
1251D ILE* 3.5 21.5 - - + -
1252D SER* 2.7 22.4 + - - +
1254D LYS* 1.4 68.4 - - - +
1256D MET* 1.3 66.4 + - - +
1257D SER 2.9 1.3 - - - -
1258D ILE* 2.9 6.2 + - - +
1259D MET* 2.7 21.0 + - - +
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Residues in contact with MET1256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1235D ALA* 3.4 42.8 - - + +
1238D VAL* 3.3 43.3 - - + -
1239D TYR* 3.9 10.5 - - + +
1251D ILE* 3.6 31.4 - - + +
1252D SER 2.9 8.4 + - - +
1253D SER* 3.6 11.9 - - - +
1255D ALA* 1.3 78.0 - - - +
1257D SER* 1.3 59.3 + - - +
1259D MET* 3.3 2.7 - - - +
1260D ASN* 2.6 34.2 + - + +
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Residues in contact with SER1257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1253D SER 2.5 21.7 + - - -
1254D LYS* 3.3 9.9 - - - -
1255D ALA 2.9 0.2 - - - -
1256D MET* 1.3 74.2 - - - +
1258D ILE* 1.3 59.4 + - - +
1260D ASN* 2.8 23.0 + - - +
1261D SER* 2.9 13.4 + - - -
299F GLY 3.5 24.5 + - - -
301F GLY* 4.2 8.7 + - - -
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Residues in contact with ILE1258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862C ILE* 6.3 1.6 - - + -
880C PRO* 3.7 29.2 - - + -
883C LEU* 3.5 18.8 - - + -
902C ILE* 3.2 36.8 - - + -
903C ALA* 3.8 11.0 - - + +
1254D LYS 3.2 5.3 + - - +
1255D ALA 2.9 7.5 + - - +
1257D SER* 1.3 74.6 + - - +
1259D MET* 1.3 66.6 + - - +
1261D SER* 3.6 2.3 - - - -
1262D PHE* 2.9 22.0 + - + +
298F TYR* 3.9 19.5 - - + -
299F GLY* 3.7 26.9 - - - +
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Residues in contact with MET1259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
859C THR* 3.9 22.7 - - + -
862C ILE* 3.3 38.1 - - + -
863C LEU* 3.7 18.8 - - + -
883C LEU* 4.0 17.0 - - + -
1238D VAL* 4.2 12.3 - - + -
1251D ILE* 3.8 25.4 - - + -
1255D ALA 2.7 12.6 + - - +
1256D MET* 3.3 18.6 - - - +
1258D ILE* 1.3 72.9 - - - +
1260D ASN* 1.3 64.1 + - - +
1262D PHE* 3.3 15.1 + - + +
1263D VAL* 3.1 29.2 + - - +
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Residues in contact with ASN1260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1232D GLU 5.1 2.0 + - - -
1233D SER* 3.8 19.6 + - - +
1234D TYR* 2.9 40.2 + - - +
1235D ALA 4.3 1.6 + - - +
1238D VAL* 5.8 0.7 - - - -
1256D MET* 2.6 20.1 + - + +
1257D SER* 3.2 11.7 - - - +
1259D MET* 1.3 77.9 - - - +
1261D SER* 1.3 62.6 + - - +
1263D VAL* 3.5 3.5 + - - +
1264D ASN* 3.1 39.0 + - - +
301F GLY* 6.0 4.8 - - - -
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Residues in contact with SER1261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1257D SER 2.9 9.4 + - - -
1258D ILE 3.6 3.8 - - - -
1260D ASN* 1.3 75.8 - - - +
1262D PHE* 1.3 64.0 + - - +
1264D ASN* 3.3 7.8 + - - +
1265D ASP* 2.9 22.9 + - - +
298F TYR* 3.5 31.4 - - - -
299F GLY* 3.3 15.2 + - - -
301F GLY* 4.4 1.2 + - - -
302F GLY* 3.2 34.5 + - - +
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Residues in contact with PHE1262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858C LEU* 3.9 41.7 - - + -
859C THR* 4.2 8.7 - - + -
862C ILE* 4.3 12.6 - - + -
893C LEU* 4.7 12.1 - - + -
896C LEU* 4.6 7.6 - - + -
897C LEU* 4.0 21.3 - - + -
1258D ILE* 2.9 18.7 + - + +
1259D MET* 3.5 24.2 - - + +
1261D SER* 1.3 76.4 - - - +
1263D VAL* 1.3 74.9 + - + +
1265D ASP* 2.9 13.7 + - - +
1266D VAL* 3.1 36.4 + - + +
298F TYR* 3.4 32.5 - + + -
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Residues in contact with VAL1263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825C PHE* 4.0 9.4 - - + -
855C LEU* 3.8 19.1 - - + +
859C THR* 3.7 29.2 - - + -
1234D TYR* 3.6 46.2 - - + -
1238D VAL* 4.6 5.4 - - + -
1259D MET* 3.1 13.5 + - + +
1260D ASN 3.7 6.5 - - - +
1262D PHE* 1.3 82.2 - - + +
1264D ASN* 1.3 58.1 + - - +
1266D VAL* 3.4 6.2 + - - +
1267D PHE* 2.9 26.9 + - - +
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Residues in contact with ASN1264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833C LEU* 5.3 3.5 - - - +
1234D TYR* 3.5 28.3 + - - -
1260D ASN* 3.1 35.8 + - - +
1261D SER* 3.6 8.6 - - - +
1263D VAL* 1.3 74.8 - - - +
1265D ASP* 1.3 69.4 + - - +
1267D PHE* 3.4 10.2 - - - +
1268D GLU* 3.0 36.6 + - - +
302F GLY* 6.2 2.0 - - - -
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Residues in contact with ASP1265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900C VAL* 4.3 3.3 - - - +
1261D SER 2.9 12.4 + - - +
1262D PHE 2.9 9.4 + - - +
1264D ASN* 1.3 76.1 - - - +
1266D VAL* 1.3 65.0 + - - +
1268D GLU* 2.9 17.2 + - - +
1269D ARG* 2.9 59.2 + - - +
291F LYS* 5.9 2.4 - - - +
296F THR* 5.0 8.1 + - - +
298F TYR* 2.7 33.4 + - + +
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Residues in contact with VAL1266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855C LEU* 3.3 26.5 - - + -
858C LEU* 3.5 21.8 - - + -
896C LEU* 5.0 10.1 - - + -
1262D PHE* 3.1 45.2 + - + +
1263D VAL 3.7 3.1 - - - +
1265D ASP* 1.3 78.5 - - + +
1267D PHE* 1.3 57.0 + - - +
1269D ARG* 3.2 11.6 + - - +
1270D ILE* 2.9 42.9 + - + +
1298D LEU* 5.8 1.6 - - + -
1299D LEU* 5.4 3.6 - - + -
298F TYR* 5.4 0.2 - - - +
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Residues in contact with PHE1267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830C VAL* 3.7 17.7 - - + -
833C LEU* 3.6 31.6 - - + -
834C LEU* 3.9 19.1 - - + -
839C TYR* 4.1 20.0 - + - -
851C LEU* 3.6 28.5 - - + +
855C LEU* 3.8 22.2 - - + +
1234D TYR* 4.2 13.0 - - - +
1263D VAL 2.9 18.5 + - - +
1264D ASN* 3.4 13.0 - - - +
1266D VAL* 1.3 77.2 - - - +
1268D GLU* 1.3 67.7 + - + +
1270D ILE* 3.8 0.7 - - - +
1271D ALA* 2.8 36.5 + - + +
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Residues in contact with GLU1268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839C TYR* 4.3 19.2 - - + +
1264D ASN* 3.0 29.8 + - - +
1265D ASP* 2.9 16.3 + - - +
1267D PHE* 1.3 87.7 - - + +
1269D ARG* 1.3 60.2 + - + +
1271D ALA* 3.9 0.2 - - - +
1272D GLY* 2.8 26.3 + - - -
291F LYS* 4.1 25.9 + - - +
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Residues in contact with ARG1269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
896C LEU* 2.9 36.4 + - - +
897C LEU* 4.2 10.9 - - - +
900C VAL* 4.3 7.9 - - - +
1265D ASP* 2.9 47.8 + - - +
1266D VAL* 3.5 9.3 - - - +
1268D GLU* 1.3 78.7 - - + +
1270D ILE* 1.3 62.0 + - - +
1272D GLY* 3.1 2.4 + - - -
1273D GLU* 2.9 27.9 + - - +
1276D ARG* 5.4 0.7 + - - -
1298D LEU* 3.2 42.1 - - + +
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Residues in contact with ILE1270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851C LEU* 3.6 27.8 - - + -
854C VAL* 3.5 32.3 - - + -
858C LEU* 5.4 0.7 - - + -
1266D VAL* 2.9 31.5 + - + +
1267D PHE 3.9 0.4 - - - +
1269D ARG* 1.3 77.5 - - - +
1271D ALA* 1.3 53.5 + - - +
1273D GLU 3.2 0.5 + - - -
1274D ALA* 2.8 32.7 + - - +
1291D ILE* 3.9 26.9 - - + +
1294D ALA* 3.6 16.5 - - + +
1295D VAL* 3.7 14.1 - - + -
1298D LEU* 4.2 14.6 - - + -
1299D LEU* 5.5 4.0 - - + -
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Residues in contact with ALA1271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834C LEU* 4.0 19.1 - - + -
839C TYR* 3.4 41.5 - - + +
851C LEU* 5.3 1.5 - - + +
1267D PHE* 2.8 21.7 + - + +
1268D GLU 3.9 0.9 - - - +
1270D ILE* 1.3 80.3 - - - +
1272D GLY* 1.3 52.0 + - - +
1274D ALA* 3.1 7.8 + - - +
1275D SER* 2.7 35.7 + - - -
1286D ILE* 6.1 0.4 - - - -
1291D ILE* 5.2 1.3 - - - -
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Residues in contact with GLY1272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839C TYR* 4.3 6.0 - - - -
1268D GLU 2.8 17.5 + - - -
1269D ARG* 3.5 1.8 - - - -
1270D ILE 3.1 0.2 - - - -
1271D ALA* 1.3 73.8 - - - +
1273D GLU* 1.3 65.9 + - - +
1274D ALA 3.0 1.3 - - - -
1275D SER* 3.2 8.7 + - - -
1276D ARG* 3.1 44.7 + - - -
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Residues in contact with GLU1273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 3.1 21.1 + - - -
92B ARG* 2.8 40.6 + - - +
1269D ARG 2.9 16.3 + - - +
1270D ILE* 4.8 0.2 - - - -
1272D GLY* 1.3 75.1 - - - +
1274D ALA* 1.3 63.4 + - - +
1276D ARG* 3.1 24.7 + - - +
1277D LEU* 2.9 27.5 + - - +
1294D ALA* 3.6 28.9 - - + +
1297D LEU* 3.5 12.8 - - + +
1298D LEU* 4.8 6.3 - - + -
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Residues in contact with ALA1274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1270D ILE 2.8 14.5 + - - +
1271D ALA* 3.3 12.1 - - - +
1273D GLU* 1.3 77.5 - - - +
1275D SER* 1.3 73.4 + - - +
1277D LEU* 3.4 5.9 - - - +
1278D ALA* 2.9 24.3 + - - +
1286D ILE* 3.9 27.8 - - + -
1290D GLU* 4.3 9.2 - - + +
1291D ILE* 4.2 12.1 - - + +
1294D ALA* 3.9 4.9 - - + +
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Residues in contact with SER1275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838C ASN 5.0 0.2 + - - -
839C TYR* 2.7 44.9 + - - -
1271D ALA 2.7 17.3 + - - -
1272D GLY* 3.3 11.4 - - - -
1274D ALA* 1.3 76.0 - - - +
1276D ARG* 1.3 64.0 + - - +
1278D ALA* 3.2 2.1 + - - +
1279D HIS* 2.9 33.1 + - - -
1286D ILE* 4.5 2.6 - - - +
1038G ASN* 5.1 2.9 + - - +
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Residues in contact with ARG1276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 5.4 1.0 + - - +
91B LYS* 6.4 1.3 - - - +
92B ARG* 5.5 2.0 - - - +
1269D ARG 5.4 0.6 + - - -
1272D GLY* 3.1 32.2 + - - +
1273D GLU* 3.1 39.7 + - - +
1275D SER* 1.3 76.0 - - - +
1277D LEU* 1.3 57.4 + - - +
1279D HIS* 2.9 5.8 + - - +
1280D TYR* 2.6 75.2 + - + +
----------------------------------------------------------
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Residues in contact with LEU1277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 3.2 38.1 - - + -
75B HIS* 3.7 28.7 - - + +
1273D GLU* 2.9 19.5 + - - +
1274D ALA* 3.4 5.4 - - - +
1276D ARG* 1.3 78.0 - - - +
1278D ALA* 1.3 63.5 + - - +
1280D TYR* 3.0 8.6 + - + -
1281D ASN* 2.8 28.0 + - - +
1290D GLU* 3.9 15.0 - - + +
1293D THR* 3.0 42.2 - - + +
1294D ALA* 4.0 5.8 - - - +
1297D LEU* 4.7 4.0 - - + -
----------------------------------------------------------
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Residues in contact with ALA1278 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840C ALA* 5.0 2.0 - - + -
1274D ALA 2.9 11.1 + - - +
1275D SER* 3.3 9.6 - - - +
1277D LEU* 1.3 74.3 - - - +
1279D HIS* 1.3 70.4 + - + +
1281D ASN* 3.2 5.4 + - - +
1283D ARG* 3.1 37.9 + - - +
1285D THR 4.0 21.1 - - - +
1286D ILE* 4.3 13.5 - - + -
1290D GLU* 4.3 11.5 + - + +
----------------------------------------------------------
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Residues in contact with HIS1279 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839C TYR 3.6 14.5 + - - -
840C ALA* 5.1 1.8 - - + -
1275D SER* 2.9 33.0 + - - -
1276D ARG* 2.9 8.2 + - - -
1278D ALA* 1.3 83.4 - - + +
1280D TYR* 1.3 63.3 + - - +
1281D ASN 2.7 4.9 + - - -
1282D LYS* 3.2 14.3 + - - +
1283D ARG 3.9 11.2 - - - +
1036G LYS 3.7 18.4 + - - -
1037G GLY* 3.7 24.7 - - - -
1038G ASN* 3.5 21.1 + - + +
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Residues in contact with TYR1280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 3.7 33.5 + + - -
88B TYR* 3.2 70.4 + + + +
91B LYS* 4.9 9.5 - - - +
1276D ARG* 2.6 65.7 + - + -
1277D LEU* 3.0 6.2 + - + +
1279D HIS* 1.3 73.9 - - - +
1281D ASN* 1.3 65.7 + - - +
1282D LYS* 3.5 4.2 + - - +
1468H GLU* 6.2 0.2 - - - -
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Residues in contact with ASN1281 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B TYR* 6.0 0.2 - - - -
75B HIS* 3.9 19.7 - - + +
76B ALA* 3.3 30.2 - - - +
1277D LEU* 2.8 30.4 + - - +
1278D ALA* 3.2 4.6 + - - +
1279D HIS 2.7 2.8 - - - -
1280D TYR* 1.3 92.0 - - - +
1282D LYS* 1.3 73.0 + - - +
1283D ARG* 3.0 30.4 + - + +
1290D GLU* 6.0 0.2 - - - +
----------------------------------------------------------
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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