Contacts of the helix formed by residues 1325 - 1346 (chain A) in PDB entry 5B2G
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 ALA1325 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190A LEU* 5.6 0.7 - - + -
1192A MET* 3.4 39.7 - - + -
1210A TRP* 4.6 4.9 - - + -
1324A GLY* 1.3 71.7 - - - +
1326A SER* 1.3 56.0 + - - +
1327A LEU 2.7 0.3 + - - -
1328A TYR* 2.7 47.1 + - - +
1329A VAL* 3.5 7.2 + - - +
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Residues in contact with SER1326 (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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1187A CYS* 3.5 30.0 - - - -
1190A LEU* 4.1 19.7 - - - +
1192A MET* 2.3 33.0 + - - +
1193A TRP* 3.3 14.6 - - - -
1324A GLY 3.2 1.4 + - - -
1325A ALA* 1.3 77.3 - - - +
1327A LEU* 1.3 50.5 + - - +
1328A TYR 3.2 0.4 - - - -
1329A VAL* 2.8 15.8 + - - +
1330A GLY 2.7 32.2 + - - -
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Residues in contact with LEU1327 (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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1187A CYS* 5.3 0.7 - - - -
1193A TRP* 3.1 68.0 - - + +
1299A VAL* 3.2 29.0 - - + +
1302A THR* 4.1 4.9 - - - +
1303A ALA* 3.7 25.8 - - + -
1306A ILE* 4.3 2.9 - - + -
1323A MET* 3.4 29.2 - - + -
1324A GLY 4.0 6.0 + - - +
1325A ALA 2.7 6.0 + - - +
1326A SER* 1.3 78.1 + - - +
1328A TYR* 1.3 57.1 + - + +
1331A TRP* 3.1 33.8 + - + -
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Residues in contact with TYR1328 (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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1323A MET* 4.0 43.5 + - + +
1324A GLY* 4.3 5.6 - - - -
1325A ALA* 2.7 26.3 + - - +
1327A LEU* 1.3 73.0 - - + +
1329A VAL* 1.3 62.1 + - + +
1331A TRP* 3.5 29.3 + + + +
1332A ALA* 3.0 26.7 + - - +
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Residues in contact with VAL1329 (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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1183A ALA* 3.2 29.1 - - + +
1186A LEU* 4.2 17.9 - - + -
1187A CYS* 3.8 11.7 - - + +
1190A LEU* 4.6 12.1 - - + -
1325A ALA* 4.0 4.9 - - - +
1326A SER* 2.8 29.7 + - - +
1328A TYR* 1.3 78.4 - - + +
1330A GLY* 1.3 51.4 + - - +
1332A ALA* 3.0 8.9 + - + +
1333A ALA* 2.7 33.4 + - - +
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Residues in contact with GLY1330 (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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1187A CYS* 3.5 23.9 - - - -
1295A VAL* 3.5 13.0 - - - +
1299A VAL* 4.1 11.4 - - - -
1326A SER 2.7 14.5 + - - -
1327A LEU 3.5 2.6 + - - -
1328A TYR 3.3 0.2 - - - -
1329A VAL* 1.3 73.4 - - - +
1331A TRP* 1.3 57.2 + - - +
1333A ALA* 4.2 2.2 - - - -
1334A SER* 2.9 31.7 + - - -
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Residues in contact with TRP1331 (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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1296A ILE* 5.1 8.6 - - + +
1299A VAL* 4.1 19.8 - - + +
1300A SER* 3.4 28.7 + - - -
1303A ALA* 3.9 11.2 - - + -
1323A MET* 3.9 34.1 - - + -
1327A LEU* 3.1 28.5 + - + +
1328A TYR* 3.7 32.1 - + + +
1329A VAL 3.3 0.2 - - - -
1330A GLY* 1.3 76.5 - - - +
1332A ALA* 1.3 59.3 + - - +
1334A SER* 3.3 17.9 + - - -
1335A GLY* 3.3 10.2 + - - -
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Residues in contact with ALA1332 (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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1183A ALA* 4.7 5.8 - - + -
1328A TYR 3.0 13.3 + - - +
1329A VAL* 3.0 13.3 + - + +
1331A TRP* 1.3 77.5 - - - +
1333A ALA* 1.3 66.8 + - - +
1335A GLY* 2.9 10.5 + - - -
1336A LEU* 3.0 26.2 + - + +
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Residues in contact with ALA1333 (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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1180A GLY* 3.3 22.6 - - - +
1183A ALA* 3.5 14.8 - - + +
1184A VAL* 3.3 29.2 - - + +
1295A VAL* 4.6 2.5 - - + -
1329A VAL 2.7 15.7 + - - +
1330A GLY* 3.6 6.7 - - - +
1332A ALA* 1.3 72.8 - - - +
1334A SER* 1.3 55.0 + - - +
1335A GLY 2.9 0.5 + - - -
1336A LEU 3.3 0.3 + - - -
1337A LEU* 2.7 40.2 + - + +
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Residues in contact with SER1334 (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 GLY* 3.3 33.0 - - - -
1295A VAL* 3.9 4.9 - - - +
1296A ILE* 3.3 28.9 - - - +
1330A GLY 2.9 22.9 + - - -
1331A TRP* 3.3 13.7 + - - -
1333A ALA* 1.3 71.8 - - - +
1335A GLY* 1.3 59.8 + - - +
1337A LEU 4.0 1.1 - - - -
1338A LEU* 3.0 34.8 + - - +
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Residues in contact with GLY1335 (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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1331A TRP 3.3 8.9 + - - -
1332A ALA* 2.9 10.7 + - - -
1334A SER* 1.3 79.4 + - - +
1336A LEU* 1.3 65.6 + - - -
1337A LEU 3.1 1.1 - - - -
1338A LEU* 3.1 15.8 + - - +
1339A LEU* 3.1 14.3 + - - +
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Residues in contact with LEU1336 (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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1176A LEU* 3.3 47.6 - - + +
1179A LEU* 4.3 24.9 - - + -
1180A GLY* 4.4 5.4 - - - +
1183A ALA* 6.1 2.2 - - + -
1332A ALA* 3.0 19.7 + - + +
1333A ALA 4.4 1.1 - - - +
1335A GLY* 1.3 72.3 - - - -
1337A LEU* 1.3 57.5 + - - +
1338A LEU 3.3 0.2 - - - -
1339A LEU* 4.5 12.1 - - + -
1340A GLY* 3.0 24.8 + - - -
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Residues in contact with LEU1337 (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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1177A ALA* 3.2 27.1 - - - +
1180A GLY* 4.3 9.8 - - - +
1181A TRP* 3.9 10.1 - - - +
1184A VAL* 5.1 4.0 - - + -
1250A SER* 4.8 1.8 - - - +
1254A ALA* 4.5 6.1 - - + -
1288A PHE* 3.3 53.0 - - + +
1291A ALA* 3.7 14.1 - - + -
1292A GLY* 3.3 29.2 - - - +
1295A VAL* 4.7 9.2 - - + -
1333A ALA 2.7 20.6 + - - +
1334A SER* 4.2 0.2 - - - -
1336A LEU* 1.3 78.4 - - - +
1338A LEU* 1.3 60.9 + - - +
1340A GLY 4.2 0.4 - - - -
1341A GLY 3.6 11.1 + - - -
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Residues in contact with LEU1338 (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 LEU* 3.5 37.0 - - + +
1292A GLY 4.3 3.6 - - - -
1293A LEU* 3.9 19.5 - - + +
1296A ILE* 3.7 26.5 - - + -
1334A SER 3.0 22.4 + - - +
1335A GLY* 3.1 5.7 + - - +
1337A LEU* 1.3 77.9 - - - +
1339A LEU* 1.3 61.4 + - - +
1341A GLY* 2.9 17.3 + - - -
1342A GLY* 2.9 11.8 + - - -
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Residues in contact with LEU1339 (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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1176A LEU* 3.6 27.6 - - + -
1335A GLY 3.1 11.6 + - - +
1336A LEU* 4.3 9.6 - - + +
1338A LEU* 1.3 77.0 - - - +
1340A GLY* 1.3 58.6 + - - +
1341A GLY 3.1 0.3 + - - -
1342A GLY* 3.1 2.0 + - - +
1343A LEU* 2.9 59.3 + - + +
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Residues in contact with GLY1340 (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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1173A GLY* 3.3 26.3 - - - +
1176A LEU* 4.0 6.4 - - - +
1177A ALA* 4.0 11.2 - - - -
1336A LEU 3.0 20.1 + - - -
1339A LEU* 1.3 77.0 - - - +
1341A GLY* 1.3 57.2 + - - +
1343A LEU 4.2 0.2 - - - -
1344A LEU* 3.1 32.1 + - - +
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Residues in contact with GLY1341 (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 GLY* 3.6 22.0 - - - -
1288A PHE* 4.0 13.2 - - - +
1289A LEU* 4.5 5.8 - - - -
1337A LEU 3.6 5.2 + - - -
1338A LEU 2.9 10.1 + - - -
1340A GLY* 1.3 76.7 - - - +
1342A GLY* 1.3 63.8 + - - +
1344A LEU* 3.0 13.9 + - - +
1345A CYS* 3.3 18.2 + - - -
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Residues in contact with GLY1342 (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 LEU* 5.3 3.4 - - - +
1338A LEU 2.9 12.5 + - - -
1339A LEU* 3.7 2.5 - - - -
1341A GLY* 1.3 74.6 - - - +
1343A LEU* 1.3 64.8 - - - +
1345A CYS* 3.1 19.7 + - - +
1346A CYS* 3.4 12.3 + - - +
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Residues in contact with LEU1343 (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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1169A LEU* 3.5 51.1 - - + +
1170A GLN* 5.0 2.9 - - - -
1172A MET* 5.0 8.3 - - + -
1173A GLY* 3.8 23.3 - - - +
1176A LEU* 5.2 3.6 - - + -
1339A LEU* 2.9 55.3 + - + +
1340A GLY* 5.0 0.2 - - - -
1342A GLY* 1.3 78.2 - - - +
1344A LEU* 1.3 60.5 + - - +
1345A CYS 3.4 0.2 - - - -
1346A CYS* 3.7 19.5 + - - +
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Residues in contact with LEU1344 (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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1170A GLN* 4.0 24.2 - - + +
1173A GLY* 4.2 6.5 - - - -
1174A ILE* 3.6 31.0 - - + +
1261A SER* 5.0 0.2 - - - +
1281A MET* 3.5 43.0 - - + +
1282A ILE* 3.6 9.4 + - - +
1284A ALA* 4.5 3.4 - - + -
1285A GLY* 3.8 9.9 - - - +
1288A PHE* 3.6 32.3 - - + -
1340A GLY 3.1 21.9 + - - +
1341A GLY 3.0 9.8 + - - +
1342A GLY 3.0 1.0 - - - -
1343A LEU* 1.3 77.2 - - - +
1345A CYS* 1.3 61.6 + - - +
1346A CYS* 3.4 1.6 - - - -
1347A SER* 4.3 6.2 + - - -
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Residues in contact with CYS1345 (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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1282A ILE* 4.0 46.5 - - + +
1285A GLY 4.1 10.8 - - - -
1286A VAL* 4.2 4.9 - - - -
1289A LEU* 4.2 14.4 - - - -
1341A GLY 3.5 14.6 - - - -
1342A GLY* 3.1 10.1 + - - +
1344A LEU* 1.3 76.4 - - - +
1346A CYS* 1.3 59.8 + - - +
1347A SER* 3.3 6.3 + - - -
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Residues in contact with CYS1346 (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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1169A LEU* 4.5 22.4 - - + +
1342A GLY 3.4 11.1 + - - +
1343A LEU* 3.7 15.2 + - - +
1344A LEU 3.4 0.8 - - - -
1345A CYS* 1.3 75.2 - - - +
1347A SER* 1.3 63.3 + - - +
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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