Contacts of the helix formed by residues 1366 - 1386 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1362A GLU 3.4 12.5 + - - +
1363A LEU 3.4 7.5 + - - +
1364A SER 3.5 0.6 - - - -
1365A SER* 1.3 82.5 - - - +
1367A ARG* 1.3 53.0 + - - +
1368A ALA* 3.4 17.9 + - - +
1369A LEU* 2.9 29.5 + - + +
1370A TYR* 2.7 32.2 + - - +
1372A ARG* 5.2 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1191A VAL* 2.7 51.8 + - + +
1192A SER* 4.1 11.8 + - - +
1194A ILE 3.0 13.5 + - - -
1196A MET* 3.0 38.3 - - - +
1363A LEU 4.4 0.8 + - - -
1364A SER 5.1 5.4 + - - +
1365A SER 5.8 0.7 - - - -
1366A ASP* 1.3 72.1 + - - +
1368A ALA* 1.3 57.5 + - - +
1370A TYR* 3.3 7.9 - - - +
1371A ASP* 2.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1366A ASP* 3.0 11.9 + - - +
1367A ARG* 1.3 76.2 - - - +
1369A LEU* 1.3 67.0 + - - +
1371A ASP* 3.3 5.9 + - - +
1372A ARG* 2.9 41.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1359A ARG* 4.0 14.8 - - - +
1362A GLU* 4.5 23.1 - - + +
1363A LEU* 3.5 19.1 - - + -
1366A ASP* 2.9 27.8 + - + +
1368A ALA* 1.3 77.5 - - - +
1370A TYR* 1.3 64.0 + - - +
1372A ARG* 3.3 29.7 + - - +
1373A GLU* 3.0 49.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1370 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1191A VAL* 3.5 22.9 - - + -
1194A ILE* 3.6 33.6 - - + +
1196A MET* 3.6 22.7 - - + -
1287A SER 3.6 2.4 + - - -
1288A GLY 2.7 29.0 + - - -
1289A PHE* 4.3 3.8 - + - -
1317A THR* 3.7 1.2 - - - -
1318A ILE* 3.2 37.1 + - + +
1363A LEU* 3.7 32.9 - - + +
1366A ASP 2.7 11.9 + - - +
1367A ARG* 3.3 13.0 - - - +
1368A ALA 3.2 0.2 - - - -
1369A LEU* 1.3 79.4 - - - +
1371A ASP* 1.3 63.7 + - - +
1373A GLU* 3.3 2.6 + - - +
1374A ARG* 3.1 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1371 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1188A TRP* 4.9 0.2 + - - -
1191A VAL* 3.2 21.4 - - + +
1367A ARG 2.8 20.1 + - - +
1368A ALA* 3.7 4.9 - - - +
1370A TYR* 1.3 71.4 - - - +
1372A ARG* 1.3 66.3 + - - +
1374A ARG* 2.9 30.1 + - - +
1375A GLU* 3.1 34.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1372 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1366A ASP* 5.2 2.0 + - - -
1368A ALA* 2.9 38.0 + - - +
1369A LEU* 3.3 34.1 + - - +
1371A ASP* 1.3 76.3 - - + +
1373A GLU* 1.3 66.7 + - - +
1375A GLU* 3.4 6.9 + - - +
1376A LYS* 2.9 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1373 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1318A ILE* 4.1 12.3 - - + -
1342A ASP* 4.6 1.6 - - - +
1344A GLY* 3.3 31.2 + - - +
1359A ARG* 3.7 23.5 + - - +
1363A LEU* 3.7 18.6 - - + +
1369A LEU* 3.0 35.3 + - + +
1370A TYR 3.6 3.4 - - - +
1372A ARG* 1.3 77.1 + - - +
1374A ARG* 1.3 60.4 + - - +
1376A LYS* 3.0 37.4 + - - +
1377A ALA* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1374 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1188A TRP* 3.2 39.4 - - + +
1189A LYS 2.8 30.3 + - - +
1190A ASP* 4.3 1.2 - - - +
1191A VAL* 2.9 32.5 - - - +
1194A ILE* 3.5 10.7 - - - +
1285A SER 5.3 0.2 + - - -
1313A GLY 5.1 1.3 - - - +
1315A CYS 5.1 0.2 + - - -
1316A GLY* 2.7 38.3 + - - -
1317A THR 4.1 10.8 - - - +
1318A ILE* 3.8 18.8 - - + +
1370A TYR* 3.1 19.6 + - - +
1371A ASP* 2.9 28.7 + - - +
1373A GLU* 1.3 73.1 - - - +
1375A GLU* 1.3 60.9 + - - +
1377A ALA* 3.1 7.9 + - + +
1378A TYR* 2.8 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1375 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1184A ARG* 2.8 45.3 + - - -
1188A TRP* 3.9 10.5 + - + -
1371A ASP* 3.1 30.5 + - - +
1372A ARG* 3.6 8.1 - - - +
1374A ARG* 1.3 77.5 - - - +
1376A LYS* 1.3 62.7 + - + +
1378A TYR* 3.6 5.3 + - - +
1379A GLU* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS1376 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1342A ASP* 2.7 55.7 + - - +
1343A SER* 3.1 10.6 - - - +
1344A GLY 4.3 3.1 - - - +
1372A ARG* 2.9 27.3 + - + +
1373A GLU* 3.0 36.1 + - - +
1374A ARG 3.1 0.4 - - - -
1375A GLU* 1.3 76.0 - - + +
1377A ALA* 1.3 59.7 + - - +
1379A GLU* 3.3 4.8 + - - +
1380A PHE* 2.8 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1377 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1313A GLY* 5.1 2.0 - - - -
1319A PRO* 4.0 33.9 - - + -
1343A SER 2.8 17.2 + - - +
1344A GLY 4.5 1.8 - - - -
1345A ILE* 4.3 9.9 - - + -
1373A GLU 3.0 9.1 + - - +
1374A ARG* 3.1 9.4 + - + +
1376A LYS* 1.3 76.6 - - - +
1378A TYR* 1.3 57.2 + - - +
1380A PHE* 3.6 2.4 - - - +
1381A LEU* 2.9 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1378 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1180A ILE* 3.5 26.5 - - + +
1181A VAL* 3.6 31.0 - - - +
1184A ARG* 3.4 57.4 - - + +
1188A TRP* 3.8 21.8 - + + -
1313A GLY 3.9 14.5 + - - +
1314A ALA* 4.1 2.0 - - - -
1374A ARG 2.8 19.8 + - - +
1375A GLU* 3.8 5.6 - - - +
1377A ALA* 1.3 73.7 - - - +
1379A GLU* 1.3 73.3 + - + +
1381A LEU* 3.8 2.6 - - - +
1382A TYR* 2.9 38.1 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1379 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1375A GLU 3.1 15.7 + - - +
1376A LYS* 3.9 4.0 - - - +
1378A TYR* 1.3 89.0 - - + +
1380A PHE* 1.3 66.1 + - - +
1382A TYR* 3.9 16.6 - - - -
1383A GLN* 3.0 56.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1380 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1331A PHE* 3.4 40.9 - + - -
1338A LEU* 3.8 44.6 - - + -
1341A HIS* 3.6 27.1 - + + -
1343A SER* 3.5 29.6 - - - -
1345A ILE* 3.9 19.1 - - + -
1376A LYS 2.8 18.6 + - - +
1377A ALA 3.6 3.4 - - - +
1379A GLU* 1.3 78.8 - - - +
1381A LEU* 1.3 65.2 + - + +
1383A GLN* 3.3 5.0 + - - +
1384A HIS* 2.9 32.9 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1381 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1180A ILE* 3.4 18.7 - - + +
1305A LEU* 3.5 32.1 - - + -
1309A HIS 4.2 8.7 - - - +
1310A LEU* 4.4 9.4 - - + +
1313A GLY* 3.4 37.2 - - - +
1319A PRO* 4.7 8.5 - - + -
1321A PHE* 4.4 6.1 - - + -
1345A ILE* 4.3 10.5 - - + -
1377A ALA* 2.9 21.2 + - + +
1378A TYR* 3.9 3.1 - - - +
1380A PHE* 1.3 86.6 - - + +
1382A TYR* 1.3 60.8 + - - +
1384A HIS* 3.7 4.4 - - + +
1385A GLN* 2.8 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1382 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1180A ILE* 3.8 17.4 - - + +
1181A VAL* 3.5 25.3 - - + +
1378A TYR* 2.9 28.9 + + + +
1379A GLU* 3.6 21.1 - - - +
1381A LEU* 1.3 75.8 - - - +
1383A GLN* 1.3 80.5 + - - +
1386A ASP* 3.0 61.6 + - + +
1388A SER* 4.0 5.5 + - - -
1389A PHE* 3.6 29.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1383 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1331A PHE* 3.9 18.4 - - + -
1332A ARG* 2.8 40.4 + - - +
1333A VAL* 4.2 10.6 - - + +
1379A GLU* 3.0 45.0 + - + +
1380A PHE* 3.6 4.9 - - - +
1382A TYR* 1.3 90.7 - - - +
1384A HIS* 1.3 58.7 + - - +
1389A PHE* 3.9 17.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1384 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1175A GLN* 3.0 22.0 + - - +
1303A ARG* 2.8 29.7 + - - +
1305A LEU* 3.8 24.3 - - + +
1329A LEU* 5.7 0.2 - - - +
1330A LYS 3.3 14.6 + - - -
1331A PHE* 3.6 20.8 - + + -
1332A ARG* 3.0 49.3 + - + +
1338A LEU* 4.0 13.6 - - + +
1380A PHE* 2.9 21.4 + + + +
1381A LEU* 3.7 8.1 - - + +
1382A TYR 3.2 0.4 - - - -
1383A GLN* 1.3 77.9 - - - +
1385A GLN* 1.3 77.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1385 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1175A GLN* 3.2 32.1 - - + +
1176A PRO* 2.7 32.3 + - - +
1177A PRO* 3.4 2.1 - - - +
1178A MET 3.4 15.1 + - - +
1180A ILE* 4.2 2.5 - - - -
1303A ARG 3.5 0.3 - - - +
1305A LEU* 2.9 48.5 + - - +
1306A GLU 5.0 0.2 - - - -
1310A LEU* 3.7 29.6 - - + +
1381A LEU 2.8 12.5 + - - -
1384A HIS* 1.3 83.7 + - - +
1386A ASP* 1.3 64.7 - - - +
1390A CYS* 3.6 7.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1386 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177A PRO* 4.1 0.2 - - - -
1178A MET 3.2 4.0 - - - +
1179A ASP* 3.7 4.0 - - - +
1180A ILE* 2.9 37.9 + - - +
1181A VAL* 3.7 6.7 + - - +
1381A LEU 3.9 0.8 + - - -
1382A TYR* 3.0 46.8 + - + +
1384A HIS 4.0 0.2 - - - -
1385A GLN* 1.3 78.9 - - - +
1387A SER* 1.3 65.8 - - - +
1388A SER* 2.7 33.8 + - - -
1389A PHE* 3.0 20.0 + - + +
1390A CYS* 3.1 12.0 + - - -
----------------------------------------------------------
Back to top of page
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