Contacts of the helix formed by residues 1346 - 1367 (chain B) in PDB entry 4DM8
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 GLU1346 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1253B GLY 4.9 0.2 - - - +
1254B LEU* 4.7 0.8 - - + -
1255B THR* 3.6 29.8 + - + +
1258B ASP* 2.9 15.4 + - - +
1344B LEU* 4.6 0.2 - - - -
1345B GLU* 1.3 83.4 - - + +
1347B PRO* 1.3 66.5 - - - +
1348B THR 3.2 2.7 - - - -
1349B LYS* 2.8 58.8 + - + +
1350B VAL* 3.1 15.0 + - + +
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Residues in contact with PRO1347 (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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1339B GLY* 3.8 18.9 - - - +
1341B ARG 5.8 0.7 - - - +
1344B LEU* 3.6 32.0 - - + +
1345B GLU 3.2 11.4 - - - +
1346B GLU* 1.3 88.0 - - - +
1348B THR* 1.3 61.2 + - - +
1350B VAL* 3.3 3.1 + - - +
1351B ASP* 2.9 30.2 + - - +
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Residues in contact with THR1348 (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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1346B GLU 3.2 1.0 - - - -
1347B PRO* 1.3 83.3 - - - +
1349B LYS* 1.3 62.5 + - - +
1351B ASP* 3.4 6.7 + - - +
1352B LYS* 3.0 57.9 + - + +
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Residues in contact with LYS1349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1253B GLY 3.7 18.8 + - - +
1254B LEU* 3.6 23.8 - - + -
1346B GLU* 2.8 50.5 + - + +
1348B THR* 1.3 76.2 - - - +
1350B VAL* 1.3 66.4 - - - +
1352B LYS* 3.4 6.0 + - - +
1353B LEU* 3.0 22.6 + - + +
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Residues in contact with VAL1350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1254B LEU* 4.2 18.4 - - + -
1258B ASP* 4.5 6.3 - - + +
1262B LEU* 4.1 18.2 - - + -
1337B ILE* 3.4 11.5 - - + +
1338B CYS 3.5 19.7 - - - +
1339B GLY* 3.5 25.1 - - - +
1344B LEU* 4.1 17.3 - - + -
1346B GLU 3.1 14.4 + - - +
1347B PRO 3.6 6.1 - - - +
1349B LYS* 1.3 75.0 - - - +
1351B ASP* 1.3 65.1 + - - +
1353B LEU* 3.0 17.2 + - - +
1354B GLN* 3.1 10.9 + - - +
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Residues in contact with ASP1351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A LYS* 3.6 25.7 + - - +
382A LYS* 5.2 6.6 + - - -
1339B GLY* 4.0 17.2 + - - +
1340B ASP* 4.9 6.4 - - - +
1347B PRO 2.9 17.1 + - - +
1348B THR* 3.5 8.7 - - - +
1349B LYS 3.3 0.2 - - - -
1350B VAL* 1.3 77.2 - - - +
1352B LYS* 1.3 81.5 + - - +
1354B GLN* 3.2 26.5 + - - +
1355B GLU* 3.5 10.2 + - - +
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Residues in contact with LYS1352 (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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378A LYS* 4.5 7.4 - - - +
1348B THR* 3.0 39.9 + - + +
1349B LYS* 3.9 5.6 - - - +
1350B VAL 3.2 0.2 - - - -
1351B ASP* 1.3 96.1 - - - +
1353B LEU* 1.3 64.1 + - - +
1355B GLU* 3.5 24.2 + - - +
1356B PRO* 3.2 19.2 - - - +
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Residues in contact with LEU1353 (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 PRO 3.4 18.8 - - - +
1250B GLY* 3.7 32.5 - - - +
1251B PHE 4.0 0.4 - - - +
1254B LEU* 4.1 19.5 - - + -
1337B ILE* 3.7 29.2 - - + -
1349B LYS* 3.0 14.5 + - + +
1350B VAL 3.0 11.5 + - - +
1352B LYS* 1.3 77.5 - - - +
1354B GLN* 1.3 61.1 + - - +
1356B PRO* 3.3 14.6 - - + +
1357B LEU* 3.9 11.3 - - - +
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Residues in contact with GLN1354 (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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378A LYS* 5.9 1.7 - - - +
381A MET* 4.3 19.4 - - - +
1334B ILE* 3.0 36.5 + - - +
1337B ILE* 3.0 22.7 + - - +
1338B CYS* 3.8 14.3 - - - +
1339B GLY 5.0 2.6 + - - -
1340B ASP* 5.4 2.6 - - - +
1350B VAL 3.1 7.8 + - - +
1351B ASP* 3.5 20.2 - - - +
1352B LYS 3.2 0.4 - - - -
1353B LEU* 1.3 77.8 - - - +
1355B GLU* 1.3 63.7 + - - +
1356B PRO 3.4 0.2 - - - -
1357B LEU* 3.0 25.9 + - + +
1358B LEU* 3.1 32.2 + - + +
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Residues in contact with GLU1355 (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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374A HIS* 3.0 24.9 + - + +
378A LYS* 2.6 44.6 + - + -
1351B ASP 3.7 12.6 - - - +
1352B LYS* 3.5 21.6 + - - +
1354B GLN* 1.3 76.8 - - - +
1356B PRO* 1.3 71.6 - - + +
1358B LEU* 3.1 23.1 + - + +
1359B GLU* 3.1 19.4 + - + +
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Residues in contact with PRO1356 (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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1182B MET* 5.9 2.2 - - + -
1186B LEU* 4.3 13.8 - - + +
1189B LEU* 3.8 22.1 - - + +
1352B LYS 3.2 17.7 - - - +
1353B LEU* 3.3 14.6 - - + +
1355B GLU* 1.3 91.9 - - + +
1357B LEU* 1.3 54.3 + - - +
1359B GLU* 3.5 7.5 + - + +
1360B ALA* 2.9 30.0 + - - +
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Residues in contact with LEU1357 (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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1189B LEU* 4.1 20.9 - - + -
1193B ILE* 4.2 15.3 - - + -
1248B LEU* 5.8 0.9 - - + -
1249B PRO* 5.9 0.7 - - + -
1330B LEU* 3.9 11.2 - - + +
1333B ALA* 3.8 44.6 - - + +
1334B ILE* 3.9 17.3 - - + +
1337B ILE* 4.1 19.3 - - + -
1353B LEU 3.9 8.7 - - - +
1354B GLN* 3.0 23.0 + - - +
1356B PRO* 1.3 79.0 - - - +
1358B LEU* 1.3 60.5 + - - +
1360B ALA* 3.4 6.5 + - - +
1361B LEU* 3.1 22.5 + - - +
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Residues in contact with LEU1358 (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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377A PRO* 4.1 35.2 - - + +
378A LYS* 4.7 10.5 - - + +
381A MET* 4.3 7.6 - - + -
1334B ILE* 3.6 31.6 - - + -
1354B GLN* 3.1 33.3 + - + +
1355B GLU* 3.1 15.0 + - + +
1357B LEU* 1.3 74.3 - - - +
1359B GLU* 1.3 65.5 + - + +
1361B LEU* 3.2 4.2 + - - +
1362B LYS 3.0 18.5 + - - -
1376B PHE* 3.6 11.9 - - + -
1380B LEU* 3.8 27.1 - - + -
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Residues in contact with GLU1359 (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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373A PRO 5.2 0.5 - - - +
374A HIS* 4.0 25.2 - - + +
377A PRO* 4.5 12.5 - - - +
1182B MET* 5.6 4.0 - - + -
1186B LEU* 4.3 16.8 - - + -
1355B GLU* 3.1 19.5 + - + +
1356B PRO* 3.8 7.0 - - + +
1358B LEU* 1.3 77.8 - - + +
1360B ALA* 1.3 61.5 + - - +
1362B LYS* 3.1 36.7 + - - +
1363B ILE* 3.0 35.0 + - - +
1376B PHE* 6.4 0.4 - - - -
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Residues in contact with ALA1360 (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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1186B LEU* 4.5 15.9 - - + +
1189B LEU* 4.7 9.2 - - + -
1190B THR* 3.8 20.6 + - - +
1330B LEU* 4.0 16.9 - - + +
1356B PRO 2.9 18.8 + - - +
1357B LEU* 3.5 7.2 - - - +
1358B LEU 3.1 0.2 - - - -
1359B GLU* 1.3 74.6 - - - +
1361B LEU* 1.3 64.2 + - - +
1363B ILE* 4.0 3.5 - - - +
1364B TYR* 3.1 26.3 + - - +
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Residues in contact with LEU1361 (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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1327B GLU* 4.4 19.3 - - + +
1330B LEU* 3.8 29.1 - - + +
1331B LEU* 3.9 19.1 - - + -
1334B ILE* 3.9 22.9 - - + -
1357B LEU 3.1 13.4 + - - +
1358B LEU 3.2 7.2 + - - +
1360B ALA* 1.3 77.4 - - - +
1362B LYS* 1.3 57.6 + - - +
1364B TYR* 3.8 0.7 - - + +
1365B ILE* 2.9 64.5 + - + +
1376B PHE* 3.9 15.3 - - + -
1379B ILE* 4.6 7.9 - - + -
1380B LEU* 4.1 7.6 - - + -
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Residues in contact with LYS1362 (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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376A PHE* 6.3 0.9 - - + -
377A PRO* 6.0 4.1 - - + +
1358B LEU 3.0 16.1 + - - +
1359B GLU* 3.1 34.2 + - - +
1361B LEU* 1.3 77.3 - - - +
1363B ILE* 1.3 58.2 + - - +
1365B ILE* 3.6 2.2 - - - +
1366B ARG* 2.9 61.8 + - + +
1376B PHE* 3.7 46.3 - - + +
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Residues in contact with ILE1363 (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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1183B THR* 5.6 7.9 - - + +
1186B LEU* 3.4 38.6 - - + -
1187B ASP* 5.1 9.2 - - - +
1359B GLU* 3.0 18.5 + - + +
1360B ALA* 4.0 3.1 - - - +
1362B LYS* 1.3 77.7 - - + +
1364B TYR* 1.3 60.0 + - - +
1366B ARG* 3.3 27.1 + - - +
1367B LYS* 2.9 65.5 + - + +
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Residues in contact with TYR1364 (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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1190B THR* 4.2 12.3 - - + +
1324B ASP* 2.5 32.0 + - - -
1326B THR* 3.7 36.0 + - + -
1327B GLU* 3.6 31.0 - - + -
1330B LEU* 4.7 2.0 - - + -
1360B ALA 3.1 19.5 + - - +
1361B LEU* 3.8 4.0 - - + +
1363B ILE* 1.3 76.4 - - - +
1365B ILE* 1.3 68.8 + - + +
1367B LYS* 3.4 5.5 + - + +
1368B ARG* 3.2 40.1 + - + +
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Residues in contact with ILE1365 (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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1327B GLU* 4.3 9.6 - - + +
1361B LEU* 2.9 53.5 + - + +
1362B LYS* 3.6 4.7 - - - +
1364B TYR* 1.3 76.8 - - - +
1366B ARG* 1.3 59.8 + - - +
1368B ARG 3.1 1.4 + - - -
1369B ARG* 2.8 54.9 + - + +
1372B LYS 5.1 2.2 - - - +
1375B MET* 3.7 20.4 - - + +
1376B PHE* 3.9 27.1 - - + +
1379B ILE* 3.6 27.4 - - + -
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Residues in contact with ARG1366 (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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1362B LYS* 2.9 44.6 + - + +
1363B ILE* 3.5 31.7 + - - +
1365B ILE* 1.3 74.5 - - - +
1367B LYS* 1.3 68.6 + - + +
1368B ARG 2.9 10.3 + - - -
1369B ARG 3.7 4.9 + - - -
1370B PRO* 3.5 22.7 - - + +
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Residues in contact with LYS1367 (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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1183B THR* 5.3 15.3 + - - +
1187B ASP* 5.6 4.7 - - - +
1363B ILE* 2.9 50.1 + - + +
1364B TYR* 3.7 5.6 - - + +
1365B ILE 3.4 0.2 - - - -
1366B ARG* 1.3 82.1 - - + +
1368B ARG* 1.3 58.1 + - - +
1370B PRO* 4.7 6.1 - - - +
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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