Contacts of the helix formed by residues 1307 - 1324 (chain A) in PDB entry 5IMX
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 THR1307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1246A ILE* 3.6 20.2 - - - +
1299A GLU* 4.9 0.9 + - - -
1305A ILE* 4.0 19.5 - - + -
1306A PHE* 1.3 78.9 - - - +
1308A SER* 1.3 65.9 + - - +
1309A LYS* 3.0 22.3 + - - +
1310A THR* 2.6 28.9 + - + +
1311A ASP 3.1 4.0 + - - -
1370A PRO* 5.1 1.6 - - - +
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Residues in contact with SER1308 (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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1241A GLU* 3.6 42.7 + - - +
1244A HIS* 5.6 2.8 - - - -
1245A PHE 4.8 4.7 + - - -
1246A ILE* 4.2 10.0 - - - +
1307A THR* 1.3 75.3 - - - +
1309A LYS* 1.3 62.4 + - - +
1311A ASP* 3.1 15.3 + - - +
1312A THR* 2.9 27.6 + - - -
1376A PHE* 4.1 3.9 - - - -
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Residues in contact with LYS1309 (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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1307A THR* 3.0 11.5 + - - +
1308A SER* 1.3 78.7 - - - +
1310A THR* 1.3 64.9 + - - +
1312A THR* 3.6 10.7 + - - +
1313A TRP 3.3 12.8 + - - -
1370A PRO* 3.1 45.7 + - + +
1371A GLU* 3.9 11.1 + - - +
1373A ARG* 2.7 55.6 + - + +
1375A ASN* 4.3 21.1 - - - +
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Residues in contact with THR1310 (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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1246A ILE* 4.4 1.7 - - - +
1297A PRO* 3.6 25.1 - - + +
1299A GLU* 3.1 26.5 - - + +
1300A ALA* 4.3 3.6 - - + -
1305A ILE 3.4 24.0 - - - +
1306A PHE* 3.3 15.1 - - - +
1307A THR* 2.6 38.3 + - + +
1309A LYS* 1.3 78.1 - - - +
1311A ASP* 1.3 62.5 + - - +
1313A TRP* 3.2 12.1 + - - +
1314A SER* 3.2 17.2 + - - -
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Residues in contact with ASP1311 (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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1237A CYS* 6.0 0.8 - - - -
1240A LEU* 5.5 1.9 - - - +
1245A PHE 4.1 4.2 - - - +
1246A ILE* 3.6 14.7 - - - +
1247A HIS* 2.9 33.1 + - - +
1248A ARG* 3.0 27.2 + - - -
1250A ILE* 4.2 10.7 - - + +
1307A THR 3.1 5.2 + - - -
1308A SER* 3.1 17.7 + - - +
1310A THR* 1.3 78.7 + - - +
1312A THR* 1.3 53.5 + - - +
1314A SER* 3.3 7.7 + - - -
1315A PHE* 2.9 29.3 + - - +
1376A PHE* 3.7 17.3 - - + -
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Residues in contact with THR1312 (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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1241A GLU* 5.2 0.2 + - - -
1308A SER 2.9 17.4 + - - -
1309A LYS* 3.6 16.9 - - - +
1311A ASP* 1.3 71.1 - - - +
1313A TRP* 1.3 64.0 + - - +
1315A PHE* 3.2 5.3 + - - +
1316A GLY 3.1 17.0 + - - -
1365A CYS* 3.4 32.9 - - - +
1373A ARG* 3.9 11.4 - - + -
1374A PRO* 2.9 30.4 + - + +
1375A ASN* 4.3 2.8 - - - -
1376A PHE* 3.7 20.0 - - - -
1379A ILE* 3.9 4.5 - - + +
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Residues in contact with TRP1313 (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 LYS 4.9 1.2 + - - -
1295A TRP 3.4 20.2 + - - -
1296A MET 3.4 12.0 + - - -
1297A PRO* 3.4 33.9 - - + -
1298A PRO* 3.8 11.7 - - + -
1309A LYS 3.3 7.3 + - - +
1310A THR 3.2 10.1 + - - +
1312A THR* 1.3 77.6 - - - +
1314A SER* 1.3 62.5 + - - +
1316A GLY* 2.9 13.5 + - - -
1317A VAL* 3.2 21.9 + - + +
1330A TYR* 4.3 12.6 + - - -
1342A VAL* 3.7 26.7 - - + -
1347A ARG* 3.5 30.1 - - - -
1365A CYS 3.5 10.1 + - - +
1366A TRP* 3.3 46.1 + + + -
1367A GLN 3.8 5.6 - - - -
1368A HIS* 4.9 0.2 - - - -
1373A ARG* 3.8 11.2 - - - +
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Residues in contact with SER1314 (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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1248A ARG 5.2 5.2 + - - -
1249A ASP* 5.5 0.3 - - - -
1250A ILE* 3.6 36.6 + - - +
1295A TRP* 2.8 28.3 + - - +
1296A MET* 4.8 2.1 - - - +
1297A PRO* 4.9 0.9 - - - +
1310A THR 3.2 10.9 + - - -
1311A ASP* 3.3 11.7 + - - -
1313A TRP* 1.3 77.1 - - - +
1315A PHE* 1.3 58.1 + - - +
1317A VAL* 3.1 6.9 + - - +
1318A LEU* 2.9 27.0 + - - +
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Residues in contact with PHE1315 (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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1230A ALA* 3.6 21.1 - - - -
1233A ILE* 4.1 6.3 - - + -
1234A ALA* 3.7 27.8 - - + -
1237A CYS* 4.5 1.3 - - - -
1250A ILE* 4.1 10.7 - - + +
1311A ASP 2.9 13.8 + - - +
1312A THR* 3.5 9.2 - - - +
1313A TRP 3.2 0.2 - - - -
1314A SER* 1.3 73.5 - - - +
1316A GLY* 1.3 60.3 - - - +
1318A LEU* 3.2 25.9 + - + +
1319A LEU* 2.8 51.3 + - + +
1365A CYS* 4.3 9.2 - - - -
1376A PHE* 3.7 21.8 - + + -
1379A ILE* 3.5 27.8 - - + -
1383A ILE* 4.0 5.8 - - + -
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Residues in contact with GLY1316 (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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1312A THR 3.1 6.9 + - - -
1313A TRP 2.9 9.5 + - - -
1315A PHE* 1.3 77.0 - - - +
1317A VAL* 1.3 56.4 + - - +
1319A LEU* 3.2 9.7 - - - +
1320A TRP 3.0 22.5 + - - -
1362A MET* 3.7 6.1 - - - +
1365A CYS* 3.6 24.0 - - - -
1366A TRP* 3.6 18.4 - - - -
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Residues in contact with VAL1317 (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 LYS 3.7 19.5 - - - +
1295A TRP* 3.5 27.8 - - + +
1313A TRP* 3.2 21.3 + - + +
1314A SER 3.1 8.4 + - - +
1316A GLY* 1.3 73.6 - - - +
1318A LEU* 1.3 57.9 + - - +
1320A TRP* 3.2 4.9 + - - +
1321A GLU* 2.8 26.4 + - - +
1329A PRO* 3.6 24.5 - - + -
1330A TYR* 4.8 2.7 - - - +
1348A MET* 4.4 7.6 - - + -
1366A TRP* 3.5 25.1 - - + +
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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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1204A LEU* 4.0 14.6 - - + -
1233A ILE* 3.6 33.9 - - + -
1250A ILE* 4.1 12.1 - - + -
1251A ALA* 4.0 3.6 - - - -
1252A ALA* 3.5 39.3 - - + +
1255A CYS* 4.3 5.2 - - - -
1295A TRP* 4.6 0.6 - - - -
1314A SER 2.9 12.8 + - - +
1315A PHE* 3.3 25.6 - - + +
1317A VAL* 1.3 75.0 - - - +
1319A LEU* 1.3 53.4 + - - +
1321A GLU* 3.0 13.3 + - - +
1322A ILE* 2.6 44.7 + - + +
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Residues in contact with LEU1319 (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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1227A LEU* 6.1 0.9 - - + -
1230A ALA* 3.9 28.5 - - + -
1315A PHE* 2.8 31.1 + - + +
1316A GLY* 3.2 10.3 - - - +
1318A LEU* 1.3 77.0 - - - +
1320A TRP* 1.3 57.8 + - - +
1322A ILE* 3.2 5.1 + - + -
1323A PHE* 2.9 50.1 + - + +
1358A VAL* 4.3 11.2 - - + +
1361A ILE* 3.5 39.9 - - + -
1362A MET* 3.9 21.1 - - + +
1383A ILE* 5.2 4.7 - - + -
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Residues in contact with TRP1320 (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 GLY 3.0 12.6 + - - +
1317A VAL 3.4 7.6 - - - +
1319A LEU* 1.3 76.0 - - - +
1321A GLU* 1.3 68.5 + - + +
1323A PHE 3.7 0.3 - - - -
1324A SER* 2.9 47.3 + - - -
1327A TYR* 3.6 30.7 - + + -
1328A MET 3.7 18.4 - - - -
1329A PRO* 3.9 7.9 - - + -
1331A PRO* 4.4 16.4 - - + -
1348A MET* 3.5 44.5 - - + -
1349A ASP 2.8 28.6 + - - -
1350A PRO 5.5 0.4 - - - -
1351A PRO* 3.6 26.3 - - + +
1362A MET* 3.9 18.3 - - - +
1366A TRP* 4.1 3.6 - + + -
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Residues in contact with GLU1321 (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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1205A LYS* 4.7 14.3 + - + +
1208A LEU* 3.8 2.5 - - - +
1252A ALA* 3.0 41.0 + - + +
1253A ARG 4.8 0.9 + - - -
1295A TRP* 2.9 41.0 + - - -
1317A VAL 2.8 18.6 + - - +
1318A LEU* 3.2 13.8 - - - +
1320A TRP* 1.3 77.0 - - + +
1322A ILE* 1.3 62.9 + - - +
1324A SER* 3.1 7.9 + - - -
1326A GLY* 2.9 29.0 + - - -
1327A TYR 4.0 15.5 - - - +
1328A MET* 6.1 0.2 - - - +
1329A PRO* 4.0 14.4 - - + +
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Residues in contact with ILE1322 (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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1204A LEU* 3.9 18.2 - - + -
1208A LEU* 3.8 10.9 - - + +
1226A LEU* 3.8 30.8 - - + +
1229A VAL* 3.6 26.0 - - + -
1230A ALA* 4.0 20.6 - - + +
1233A ILE* 5.6 0.2 - - + -
1318A LEU* 2.6 40.5 + - + +
1319A LEU* 3.6 9.6 - - + +
1321A GLU* 1.3 72.3 - - - +
1323A PHE* 1.3 77.0 + - + +
1325A LEU* 2.9 28.8 + - - +
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Residues in contact with PHE1323 (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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1223A MET* 3.4 37.2 - - + -
1226A LEU* 3.7 30.2 - - + +
1227A LEU* 3.8 21.5 - - + -
1230A ALA* 4.7 0.9 - - + -
1319A LEU* 2.9 35.1 + - + +
1322A ILE* 1.3 88.2 - - + +
1324A SER* 1.3 58.5 + - - +
1325A LEU* 3.2 11.1 + - - +
1351A PRO* 3.5 23.2 - - + +
1352A LYS 4.4 8.3 - - - +
1354A CYS* 4.3 9.7 - - + +
1355A PRO* 4.5 7.0 - - + -
1358A VAL* 3.7 36.3 - - + -
1362A MET* 4.3 0.9 - - + -
1397A LEU* 5.0 4.0 - - + +
1398A PRO* 5.5 1.6 - - - +
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Residues in contact with SER1324 (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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1320A TRP* 2.9 41.1 + - - -
1321A GLU 3.1 4.9 + - - -
1323A PHE* 1.3 76.6 - - - +
1325A LEU* 1.3 67.8 + - - +
1327A TYR* 3.1 48.1 + - - +
1351A PRO* 3.6 15.7 - - - -
1352A LYS 5.3 1.3 - - - +
1398A PRO* 6.3 1.1 - - - -
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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
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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