Contacts of the helix formed by residues 1366 - 1386 (chain B) in PDB entry 1Y8Z
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 ASP1366 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1362B GLU 3.4 9.9 + - - +
1363B LEU 3.4 8.2 + - - +
1365B SER* 1.3 79.3 - - - +
1367B ARG* 1.3 59.6 + - - +
1368B ALA* 2.8 25.3 + - - +
1369B LEU* 3.1 27.6 + - + +
1370B TYR 2.9 23.2 + - - -
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Residues in contact with ARG1367 (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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1191B VAL* 3.7 29.0 + - + +
1192B SER* 3.3 47.3 + - - +
1194B ILE 4.3 8.9 + - - -
1196B MET* 4.9 14.0 - - + +
1363B LEU 4.8 0.7 - - - -
1364B SER 5.3 3.6 + - - +
1365B SER 4.0 3.2 + - - +
1366B ASP* 1.3 72.0 + - - +
1368B ALA* 1.3 61.1 + - - +
1370B TYR* 3.5 8.1 - - - +
1371B ASP* 3.0 24.4 + - - +
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Residues in contact with ALA1368 (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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1366B ASP* 2.8 18.3 + - - +
1367B ARG* 1.3 74.6 - - - +
1369B LEU* 1.3 63.4 + - - +
1371B ASP* 3.5 5.9 + - - +
1372B ARG* 3.1 21.3 + - - +
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Residues in contact with LEU1369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1359B ARG* 4.4 8.3 - - - +
1362B GLU* 4.5 21.3 - - + +
1363B LEU* 3.3 21.5 - - + -
1366B ASP* 3.1 26.7 + - + +
1368B ALA* 1.3 76.6 - - - +
1370B TYR* 1.3 65.9 + - - +
1372B ARG* 3.1 47.3 + - - +
1373B GLU* 3.0 33.4 + - + +
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Residues in contact with TYR1370 (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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1191B VAL* 3.9 11.7 - - + -
1194B ILE* 3.6 27.4 - - + +
1196B MET* 3.3 35.4 - - + -
1287B SER 3.6 3.3 + - - -
1288B GLY 2.7 26.9 + - - -
1289B PHE* 4.0 4.5 - + - -
1317B THR* 3.8 1.6 - - - -
1318B ILE* 3.3 34.2 + - + +
1363B LEU* 3.6 27.3 - - + +
1366B ASP 2.9 12.4 + - - +
1367B ARG* 3.5 13.2 - - - +
1368B ALA 3.2 0.2 - - - -
1369B LEU* 1.3 77.3 - - - +
1371B ASP* 1.3 63.8 + - - +
1373B GLU* 3.2 1.8 + - - -
1374B ARG* 3.1 44.2 + - - +
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Residues in contact with ASP1371 (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 ASP* 6.2 0.2 - - - -
1191B VAL* 3.1 21.0 - - + +
1367B ARG 3.0 14.5 + - - +
1368B ALA* 3.7 6.5 - - - +
1370B TYR* 1.3 79.0 - - - +
1372B ARG* 1.3 62.5 + - - +
1374B ARG* 3.0 28.7 + - - +
1375B GLU* 3.1 44.1 + - - +
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Residues in contact with ARG1372 (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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1342B ASP* 4.3 5.5 + - - -
1359B ARG* 5.3 4.0 - - - +
1368B ALA 3.1 13.6 + - - +
1369B LEU* 3.1 36.5 + - - +
1371B ASP* 1.3 79.2 - - - +
1373B GLU* 1.3 78.2 + - - +
1375B GLU* 3.9 5.1 - - - +
1376B LYS* 2.9 51.5 + - + +
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Residues in contact with GLU1373 (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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1318B ILE* 3.8 15.3 - - + -
1342B ASP* 4.8 0.7 - - - +
1344B GLY* 3.3 31.9 - - - +
1359B ARG* 3.8 22.9 + - - +
1363B LEU* 3.7 19.7 - - + -
1369B LEU* 3.0 19.6 + - + +
1370B TYR 3.2 4.0 + - - +
1372B ARG* 1.3 111.2 + - - +
1374B ARG* 1.3 61.6 + - - +
1376B LYS* 3.0 23.3 + - - +
1377B ALA* 2.8 23.6 + - - +
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Residues in contact with ARG1374 (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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1188B TRP* 3.3 35.9 - - + +
1189B LYS 2.7 30.1 + - - +
1190B ASP* 4.1 1.6 - - - +
1191B VAL* 3.1 32.3 - - - +
1194B ILE* 3.3 11.9 - - - +
1313B GLY 4.9 0.9 - - - +
1316B GLY* 2.6 40.8 + - - -
1317B THR 4.0 11.9 - - - +
1318B ILE* 3.6 16.2 - - + +
1370B TYR* 3.1 19.7 + - - +
1371B ASP* 3.0 25.0 + - - +
1373B GLU* 1.3 73.6 - - - +
1375B GLU* 1.3 64.0 + - - +
1377B ALA* 3.0 8.2 + - - +
1378B TYR* 2.8 32.4 + - - +
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Residues in contact with GLU1375 (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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1184B ARG* 2.8 45.5 + - - -
1188B TRP* 3.6 14.2 + - + -
1371B ASP* 3.1 37.0 + - - +
1372B ARG* 3.9 6.3 - - - +
1374B ARG* 1.3 75.9 - - - +
1376B LYS* 1.3 62.6 + - + +
1378B TYR* 3.8 3.2 - - - +
1379B GLU* 3.2 23.9 + - - +
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Residues in contact with LYS1376 (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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1342B ASP* 2.5 56.9 + - - +
1343B SER* 3.1 11.5 - - - +
1344B GLY 4.0 5.4 - - - +
1372B ARG* 2.9 42.1 + - + +
1373B GLU* 3.0 38.7 + - - +
1375B GLU* 1.3 76.6 - - + +
1377B ALA* 1.3 62.1 + - - +
1379B GLU* 3.4 5.1 + - - +
1380B PHE* 3.0 22.3 + - - +
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Residues in contact with ALA1377 (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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1313B GLY* 5.0 1.8 - - - -
1317B THR 5.3 0.2 - - - +
1319B PRO* 3.8 35.4 - - + -
1343B SER 2.9 14.2 + - - +
1344B GLY 4.5 1.8 - - - -
1345B ILE* 4.4 10.1 - - + -
1373B GLU 2.8 11.8 + - - +
1374B ARG* 3.0 8.0 + - - +
1376B LYS* 1.3 75.9 - - - +
1378B TYR* 1.3 58.0 + - - +
1380B PHE* 3.3 2.8 + - - +
1381B LEU* 2.9 39.1 + - + +
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Residues in contact with TYR1378 (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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1180B ILE* 3.5 26.9 - - + +
1181B VAL* 3.3 32.3 - - + +
1184B ARG* 3.4 54.3 - - + +
1188B TRP* 3.7 11.0 - + + -
1313B GLY 3.6 25.7 + - - +
1314B ALA* 4.2 1.1 - - - -
1374B ARG 2.8 19.7 + - - +
1375B GLU* 3.8 5.4 - - - +
1377B ALA* 1.3 73.4 - - - +
1379B GLU* 1.3 75.5 + - + +
1381B LEU* 3.4 2.1 + - - +
1382B TYR* 2.8 37.9 + + + +
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Residues in contact with GLU1379 (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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1375B GLU 3.2 15.9 + - - +
1376B LYS* 3.9 4.7 - - - +
1378B TYR* 1.3 94.1 - - + +
1380B PHE* 1.3 57.8 + - - +
1382B TYR* 3.5 11.1 - - - +
1383B GLN* 2.5 73.4 + - - +
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Residues in contact with PHE1380 (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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1331B PHE* 3.5 30.3 - + - -
1338B LEU* 3.7 54.7 - - + -
1341B HIS* 3.6 29.6 - + + -
1343B SER* 3.5 29.4 - - - -
1345B ILE* 4.0 17.3 - - + -
1376B LYS 3.0 17.7 + - - +
1377B ALA 3.6 2.9 - - - +
1379B GLU* 1.3 76.7 - - - +
1381B LEU* 1.3 64.4 + - + +
1383B GLN* 3.2 7.0 + - - +
1384B HIS* 2.9 30.6 + + + +
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Residues in contact with LEU1381 (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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1180B ILE* 3.2 19.3 - - + +
1305B LEU* 3.6 31.4 - - + -
1309B HIS 4.1 11.2 - - - +
1310B LEU* 4.4 10.9 - - + +
1313B GLY* 3.5 35.4 - - - +
1319B PRO* 4.5 5.2 - - + -
1321B PHE* 4.4 10.1 - - + -
1345B ILE* 4.3 19.1 - - + -
1377B ALA* 2.9 20.7 + - + +
1378B TYR* 3.9 3.4 - - - +
1380B PHE* 1.3 82.1 - - + +
1382B TYR* 1.3 63.5 + - - +
1384B HIS* 3.8 3.4 - - - +
1385B GLN* 3.0 23.2 + - - +
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Residues in contact with TYR1382 (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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1180B ILE* 3.6 17.0 - - + +
1181B VAL* 3.2 33.3 - - + +
1378B TYR* 2.8 26.8 + + + +
1379B GLU* 3.5 15.7 - - - +
1381B LEU* 1.3 76.5 - - - +
1383B GLN* 1.3 96.0 + - - +
1386B ASP* 3.0 58.4 + - + +
1388B SER* 4.0 6.2 + - - -
1389B PHE* 3.5 23.6 - + - -
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Residues in contact with GLN1383 (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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1331B PHE* 3.9 16.4 - - + -
1332B ARG* 2.7 34.9 + - - +
1333B VAL* 4.1 14.1 - - + +
1379B GLU* 2.5 63.0 + - - +
1380B PHE* 3.6 5.4 - - - +
1382B TYR* 1.3 101.9 - - - +
1384B HIS* 1.3 57.4 + - - +
1389B PHE* 3.8 14.3 - - + -
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Residues in contact with HIS1384 (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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1175B GLN* 2.9 24.2 + - - +
1303B ARG* 2.7 31.2 + - - -
1305B LEU* 3.8 24.4 - - + +
1329B LEU* 5.7 0.2 - - - +
1330B LYS 3.4 12.3 + - - -
1331B PHE* 3.4 22.4 - + + -
1332B ARG* 3.0 47.1 + - + +
1338B LEU* 3.8 11.7 - - + +
1380B PHE* 2.9 19.2 + + + +
1381B LEU* 3.8 6.9 + - + +
1382B TYR 3.2 0.2 - - - -
1383B GLN* 1.3 80.0 - - - +
1385B GLN* 1.3 78.2 + - - +
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Residues in contact with GLN1385 (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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1175B GLN* 3.2 23.6 - - + +
1176B PRO* 2.7 31.8 + - - +
1177B PRO* 3.5 12.9 - - + +
1178B MET 3.5 4.9 + - - +
1180B ILE* 4.2 2.2 - - - +
1303B ARG 3.4 0.3 - - - +
1305B LEU* 2.9 46.0 + - - +
1306B GLU 5.0 0.2 - - - -
1310B LEU* 3.6 28.4 - - + +
1381B LEU 3.0 7.6 + - - -
1384B HIS* 1.3 96.1 + - - +
1386B ASP* 1.3 68.0 + - - +
1390B CYS* 3.6 9.0 - - - -
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Residues in contact with ASP1386 (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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1177B PRO* 4.0 0.2 - - - -
1178B MET 3.5 3.9 - - - +
1179B ASP* 3.9 4.3 - - - +
1180B ILE* 3.0 37.4 + - + +
1181B VAL* 3.7 7.0 + - - +
1381B LEU 4.0 0.6 + - - -
1382B TYR* 3.0 47.4 + - + +
1384B HIS 4.0 0.2 - - - -
1385B GLN* 1.3 78.6 - - - +
1387B SER* 1.3 66.4 + - - +
1388B SER* 2.6 34.8 + - - -
1389B PHE* 3.0 20.7 + - + +
1390B CYS* 3.1 10.8 + - - -
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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
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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