Contacts of the helix formed by residues 1314 - 1335 (chain A) in PDB entry 3B13
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 ASP1314 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1308A TYR* 3.0 12.3 + - + +
1312A ILE* 3.4 15.7 - - + +
1313A PHE* 1.3 76.2 - - - +
1315A TYR* 1.3 59.4 + - - +
1316A GLU* 3.0 12.7 + - - +
1317A LEU* 3.0 47.2 + - + +
1318A LEU* 3.1 24.9 + - - +
1333C MET* 5.7 0.2 - - - -
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Residues in contact with TYR1315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1308A TYR 4.6 1.6 - - - -
1309A GLU* 4.5 20.9 + - + +
1313A PHE* 3.8 19.6 + + - -
1314A ASP* 1.3 75.3 + - - +
1316A GLU* 1.3 59.9 + - - +
1318A LEU* 3.8 8.6 - - + +
1319A SER* 2.8 30.0 + - - -
1329C TYR* 3.7 45.7 - + + +
1330C GLU* 6.1 0.2 - - - -
1332C ILE* 4.3 21.8 - - + -
1333C MET* 3.5 39.2 - - + +
1420C ARG* 4.7 12.8 + - - -
1421C PHE* 5.4 0.2 - - - -
1430C ILE* 3.3 39.5 - - + +
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Residues in contact with GLU1316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1314A ASP* 3.0 8.1 + - - +
1315A TYR* 1.3 77.1 - - - +
1317A LEU* 1.3 60.8 + - + +
1319A SER* 3.2 6.5 + - - -
1320A GLN* 2.9 65.3 + - - +
1330C GLU* 2.6 29.8 - - - +
1333C MET* 4.8 7.6 - - + +
1334C LYS* 4.0 14.8 + - - -
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Residues in contact with LEU1317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1278A GLU* 3.7 12.6 - - - +
1282A GLU* 5.5 3.4 - - - +
1308A TYR* 3.6 42.4 - - + +
1312A ILE* 5.7 1.1 - - + -
1314A ASP* 3.0 33.5 + - + +
1316A GLU* 1.3 77.7 - - + +
1318A LEU* 1.3 59.8 + - - +
1320A GLN* 3.4 20.4 + - + +
1321A ASN* 2.9 29.3 + - - +
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Residues in contact with LEU1318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1305A ALA* 3.3 43.7 - - + +
1308A TYR* 3.7 9.2 - - + -
1309A GLU* 3.5 25.1 - - + +
1314A ASP 3.1 18.3 + - - +
1315A TYR* 3.8 8.7 - - + +
1316A GLU 3.2 0.2 - - - -
1317A LEU* 1.3 73.8 - - - +
1319A SER* 1.3 67.8 + - - +
1321A ASN* 3.2 2.1 + - - +
1322A LEU* 2.9 43.7 + - + +
1329C TYR* 3.4 42.2 - - + +
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Residues in contact with SER1319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1315A TYR 2.8 20.2 + - - -
1316A GLU* 3.4 10.1 - - - -
1318A LEU* 1.3 77.7 - - - +
1320A GLN* 1.3 62.6 + - - +
1322A LEU* 3.4 1.5 + - - -
1323A ILE* 3.0 33.2 + - - +
1326C ALA* 3.0 39.7 + - - +
1329C TYR* 4.6 4.7 - - - +
1330C GLU* 3.4 21.1 - - - +
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Residues in contact with GLN1320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1316A GLU* 2.9 48.6 + - - +
1317A LEU* 3.8 18.8 - - + +
1319A SER* 1.3 75.2 - - - +
1321A ASN* 1.3 64.2 + - - +
1323A ILE* 3.1 12.9 + - + +
1324A GLN* 2.9 23.8 + - - +
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Residues in contact with ASN1321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1301A CYS* 3.1 30.7 + - - +
1304A LEU* 3.6 22.6 - - - +
1305A ALA* 3.4 11.7 - - + +
1308A TYR* 4.0 8.3 - - + -
1317A LEU 2.9 18.7 + - - +
1318A LEU* 3.3 9.2 - - - +
1320A GLN* 1.3 76.0 - - - +
1322A LEU* 1.3 58.6 + - - +
1324A GLN* 3.0 8.9 + - - +
1325A GLN* 2.9 57.0 + - - +
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Residues in contact with LEU1322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1305A ALA* 5.1 2.2 - - + -
1318A LEU* 2.9 36.5 + - + +
1319A SER 3.7 2.9 - - - +
1321A ASN* 1.3 72.0 + - - +
1323A ILE* 1.3 64.3 + - - +
1325A GLN* 3.2 18.0 + - - +
1326A ALA* 2.9 22.7 + - - +
1322C LEU* 3.8 40.4 - - + +
1325C GLN* 3.8 19.7 - - + +
1326C ALA* 3.9 8.1 - - + +
1329C TYR* 3.8 35.4 - - + -
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Residues in contact with ILE1323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1319A SER* 3.0 24.2 + - - +
1320A GLN* 3.1 13.0 + - + +
1322A LEU* 1.3 76.7 - - - +
1324A GLN* 1.3 59.9 + - - +
1326A ALA* 3.1 9.1 + - + +
1327A LYS* 3.0 26.9 + - + +
1323C ILE* 5.0 17.0 - - + +
1326C ALA* 3.5 19.3 - - + -
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Residues in contact with GLN1324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1285A ILE* 5.6 1.8 - - + -
1289A ASP* 5.1 0.3 - - - +
1301A CYS* 4.8 7.0 - - - -
1320A GLN 2.9 13.6 + - - +
1321A ASN* 3.3 12.8 - - - +
1323A ILE* 1.3 77.8 + - - +
1325A GLN* 1.3 65.2 + - - +
1326A ALA 3.0 1.3 - - - -
1327A LYS* 3.1 41.6 + - - +
1328A PHE* 2.9 58.7 + - + -
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Residues in contact with GLN1325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1298A ILE* 4.1 10.9 - - + +
1301A CYS* 3.5 36.1 + - + -
1302A LYS* 3.6 32.2 + - - +
1305A ALA* 3.9 7.1 - - - +
1321A ASN* 2.9 36.7 + - - +
1322A LEU* 3.2 15.8 + - - +
1324A GLN* 1.3 76.3 - - - +
1326A ALA* 1.3 57.4 + - - +
1328A PHE* 3.2 9.1 + - - +
1329A TYR* 2.9 42.0 + - + -
1322C LEU* 3.6 15.9 - - + +
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Residues in contact with ALA1326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1322A LEU 2.9 14.7 + - - +
1323A ILE 3.3 10.3 - - - +
1324A GLN 3.0 0.2 - - - -
1325A GLN* 1.3 77.4 - - - +
1327A LYS* 1.3 56.7 + - - +
1329A TYR* 3.7 0.4 + - - -
1330A GLU* 3.0 19.6 + - - +
1319C SER* 2.9 45.4 + - - +
1322C LEU* 3.9 11.6 - - + +
1323C ILE* 3.6 19.3 - - + -
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Residues in contact with LYS1327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1289A ASP* 4.2 17.7 + - - -
1323A ILE* 3.0 14.0 + - + +
1324A GLN* 3.1 36.9 + - - +
1326A ALA* 1.3 75.4 - - - +
1328A PHE* 1.3 64.7 + - + +
1330A GLU* 3.4 6.9 + - - +
1331A SER* 2.9 39.5 + - - +
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Residues in contact with PHE1328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1285A ILE* 3.9 11.2 - - + -
1289A ASP* 3.6 30.7 - - + -
1294A TRP* 3.7 24.0 - + + +
1297A ALA* 3.5 27.8 - - + -
1298A ILE* 3.5 29.8 - - + -
1301A CYS* 3.8 17.0 - - - -
1324A GLN* 2.9 54.6 + - + -
1325A GLN* 3.2 2.7 + - - +
1327A LYS* 1.3 79.6 - - + +
1329A TYR* 1.3 61.4 + - - +
1331A SER* 2.8 22.2 + - - -
1332A ILE* 2.9 16.3 + - - +
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Residues in contact with TYR1329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1298A ILE* 3.6 41.6 - - + +
1302A LYS* 3.6 4.2 - - - -
1325A GLN* 2.9 32.2 + - - +
1326A ALA 4.0 3.6 - - - +
1328A PHE* 1.3 73.9 - - - +
1330A GLU* 1.3 63.0 - - - +
1332A ILE* 3.6 9.7 + - + +
1333A MET* 3.6 20.1 + - - +
1420A ARG* 5.4 1.1 + - - -
1309C GLU* 3.5 27.6 + - + +
1315C TYR* 3.5 55.1 - + + +
1318C LEU* 3.4 26.5 - - + -
1319C SER* 4.5 3.6 - - - -
1322C LEU* 3.7 22.4 - - + -
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Residues in contact with GLU1330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1326A ALA 3.0 19.8 + - - +
1327A LYS* 3.5 8.5 - - - +
1328A PHE 3.2 0.2 - - - -
1329A TYR* 1.3 75.4 - - - +
1331A SER* 1.3 58.1 + - - +
1333A MET* 3.3 8.4 + - - +
1334A LYS* 2.9 64.6 + - + +
1315C TYR 4.7 0.8 - - - +
1316C GLU* 2.9 33.5 - - - +
1319C SER* 3.6 16.2 + - - +
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Residues in contact with SER1331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1294A TRP* 3.5 32.0 + - - -
1327A LYS* 2.9 26.5 + - - +
1328A PHE* 2.8 12.6 + - - -
1330A GLU* 1.3 74.4 - - - +
1332A ILE* 1.3 62.7 + - - +
1334A LYS* 4.4 1.3 - - - +
1335A ILE* 2.8 49.6 + - - +
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Residues in contact with ILE1332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1294A TRP* 3.6 28.5 - - + -
1295A GLU* 3.8 21.3 - - + +
1298A ILE* 3.7 29.2 - - + -
1328A PHE 2.9 13.2 + - - +
1329A TYR* 3.7 11.2 - - + +
1330A GLU 3.4 0.2 - - - -
1331A SER* 1.3 77.9 - - - +
1333A MET* 1.3 73.7 + - + +
1335A ILE 4.0 4.9 - - - +
1337A ARG* 3.6 23.1 + - - +
1429A GLN* 3.5 23.5 + - - +
1430A ILE* 4.8 4.7 - - + +
1315C TYR* 4.6 17.7 - - + -
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Residues in contact with MET1333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1329A TYR 3.6 13.7 - - - +
1330A GLU* 3.3 10.5 + - - +
1331A SER 3.1 0.4 - - - -
1332A ILE* 1.3 82.9 - - + +
1334A LYS* 1.3 67.2 + - + +
1427A PRO* 5.6 1.3 - - + -
1429A GLN* 3.1 45.6 + - + +
1430A ILE* 3.2 44.9 - - + +
1315C TYR* 3.8 24.7 - - + -
1316C GLU* 5.0 4.9 - - + +
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Residues in contact with LYS1334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1330A GLU* 2.9 46.9 + - + +
1331A SER* 5.1 0.4 - - - -
1333A MET* 1.3 82.9 - - + +
1335A ILE* 1.3 67.2 + - + +
1336A LEU 4.3 0.2 + - - -
1316C GLU* 4.7 7.4 + - - +
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Residues in contact with ILE1335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1292A LYS* 4.2 10.1 - - - +
1294A TRP* 3.8 22.4 - - + -
1331A SER* 2.8 42.7 + - - +
1332A ILE 4.0 8.3 - - - +
1333A MET 3.6 0.6 - - - -
1334A LYS* 1.3 81.8 - - + +
1336A LEU* 1.3 75.5 + - - +
1337A ARG* 3.5 9.7 + - - +
1429A GLN* 4.3 6.9 + - - -
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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
------------------------------------------------------------
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