Contacts of the helix formed by residues 1331 - 1352 (chain B) in PDB entry 6V65
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 SER1331 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1326B LEU* 4.0 3.1 - - - -
1329B SER 5.3 0.7 - - - -
1330B GLU* 1.3 76.3 - - - +
1332B LEU* 1.3 63.2 + - - +
1333B GLU* 3.1 31.4 + - - +
1334B GLU* 4.0 21.9 + - - +
1335B ASN* 3.2 26.7 + - - +
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Residues in contact with LEU1332 (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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1320B GLU 4.4 3.4 - - - +
1321B VAL* 4.0 26.9 - - - +
1323B PRO* 4.3 24.7 - - + -
1326B LEU* 3.6 20.5 - - + +
1331B SER* 1.3 70.3 + - - +
1333B GLU* 1.3 68.6 + - - +
1335B ASN* 3.1 3.1 + - - -
1336B GLN* 2.9 52.8 + - + +
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Residues in contact with GLU1333 (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 SER* 3.1 18.7 + - - +
1332B LEU* 1.3 77.1 - - - +
1334B GLU* 1.3 64.6 + - + +
1336B GLN* 3.5 14.0 + - - +
1337B ARG* 3.3 33.8 + - - +
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Residues in contact with GLU1334 (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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1316B HIS 4.9 7.9 - - - +
1318B SER* 5.8 0.2 - - - -
1330B GLU* 5.3 2.8 - - - +
1331B SER* 3.6 24.5 + - - +
1332B LEU 3.2 0.6 - - - -
1333B GLU* 1.3 80.7 - - + +
1335B ASN* 1.3 76.0 + - - +
1337B ARG* 3.2 29.6 + - - +
1338B ASN* 3.1 33.8 + - - +
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Residues in contact with ASN1335 (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 SER* 3.0 51.2 + - - +
1319B PHE* 4.3 1.7 - - - -
1320B GLU 3.0 31.5 + - - +
1321B VAL* 4.1 3.2 - - + +
1326B LEU* 3.4 20.6 - - - +
1330B GLU* 3.7 5.2 + - - +
1331B SER 3.2 14.7 + - - +
1332B LEU 3.1 4.1 + - - +
1334B GLU* 1.3 86.5 - - - +
1336B GLN* 1.3 65.5 + - - +
1338B ASN* 3.2 5.4 + - - +
1339B LEU* 3.0 23.4 + - - +
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Residues in contact with GLN1336 (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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1321B VAL* 4.1 18.7 + - + +
1332B LEU* 2.9 45.0 + - + +
1333B GLU* 3.7 14.9 - - - +
1335B ASN* 1.3 77.6 - - - +
1337B ARG* 1.3 63.2 + - + +
1339B LEU* 3.4 2.9 + - - +
1340B LEU* 3.2 28.4 + - + +
1439B HIS 5.3 1.2 + - - -
1442B PRO* 3.8 33.1 - - - +
1443B PHE* 4.2 13.6 - - + -
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Residues in contact with ARG1337 (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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1333B GLU* 3.3 21.3 + - - +
1334B GLU* 3.2 35.8 + - - +
1336B GLN* 1.3 78.5 - - + +
1338B ASN* 1.3 70.0 + - - +
1340B LEU* 3.1 6.6 + - - -
1341B GLN* 3.0 39.4 + - + +
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Residues in contact with ASN1338 (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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1316B HIS 5.2 0.8 + - - -
1317B VAL* 4.6 12.6 - - - +
1318B SER 3.3 31.1 + - - +
1319B PHE* 3.3 23.2 - - + -
1334B GLU* 3.1 33.5 + - - +
1335B ASN* 3.2 9.8 + - - +
1337B ARG* 1.3 80.0 + - - +
1339B LEU* 1.3 61.8 + - - +
1341B GLN* 4.0 7.1 - - - +
1342B MET* 3.3 17.2 + - - +
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Residues in contact with LEU1339 (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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1319B PHE* 3.7 24.1 - - + +
1321B VAL* 3.9 24.0 - - + -
1335B ASN 3.0 13.5 + - - +
1336B GLN 3.7 8.7 - - - +
1337B ARG 3.2 0.2 - - - -
1338B ASN* 1.3 78.6 - - - +
1340B LEU* 1.3 54.8 + - - +
1342B MET* 3.8 6.6 - - + +
1343B THR* 2.7 44.6 + - - +
1417B GLY 3.8 21.5 - - - +
1420B LEU* 3.7 23.8 - - + -
1421B MET 4.3 3.6 - - - +
1424B ILE* 4.2 13.7 - - + -
1440B MET* 5.9 0.2 - - + -
1443B PHE* 4.2 13.9 - - + -
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Residues in contact with LEU1340 (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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1336B GLN* 3.2 15.1 + - + +
1337B ARG* 3.1 6.7 + - - +
1339B LEU* 1.3 79.7 - - - +
1341B GLN* 1.3 65.1 + - - +
1343B THR* 3.7 2.5 - - - -
1344B GLU* 2.8 31.5 + - - +
1424B ILE* 4.6 8.3 - - + -
1442B PRO 5.8 1.3 - - - +
1443B PHE* 3.5 32.1 - - + -
1446B PHE* 3.8 50.5 - - + -
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Residues in contact with GLN1341 (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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1337B ARG* 3.0 29.1 + - + +
1338B ASN* 4.0 7.0 - - - +
1339B LEU 3.3 0.2 - - - -
1340B LEU* 1.3 82.3 - - - +
1342B MET* 1.3 63.8 + - - +
1344B GLU* 3.2 26.8 + - - +
1345B LYS* 3.3 18.2 + - - +
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Residues in contact with MET1342 (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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1308B VAL* 4.2 24.0 - - + -
1319B PHE* 3.7 30.5 - - + -
1338B ASN 3.3 14.0 + - - +
1339B LEU* 3.8 8.7 - - + +
1341B GLN* 1.3 79.3 - - - +
1343B THR* 1.3 63.0 + - - +
1345B LYS* 3.6 2.3 + - - +
1346B PHE* 3.1 38.5 + - + +
1414B ILE* 5.5 0.7 - - - -
1417B GLY* 3.6 33.7 - - - +
1418B LEU* 4.1 17.3 - - + +
1421B MET* 3.8 20.9 - - + -
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Residues in contact with THR1343 (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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1339B LEU* 2.7 28.0 + - - +
1340B LEU* 3.8 7.6 - - - -
1342B MET* 1.3 75.6 - - - +
1344B GLU* 1.3 59.0 + - - +
1346B PHE* 3.8 0.7 - - - +
1347B PHE* 2.9 27.9 + - + +
1421B MET* 3.3 36.2 - - + +
1424B ILE* 4.0 24.1 - - + +
1425B LEU* 4.1 14.3 - - + +
1446B PHE* 3.9 21.1 - - + -
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Residues in contact with GLU1344 (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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1340B LEU 2.8 19.2 + - - +
1341B GLN* 3.5 18.9 + - - +
1342B MET 3.2 0.8 - - - -
1343B THR* 1.3 76.1 - - - +
1345B LYS* 1.3 76.8 + - + +
1347B PHE* 3.2 5.7 + - - +
1348B HIS* 2.8 31.9 + - + +
1446B PHE* 4.1 25.0 - - + -
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Residues in contact with LYS1345 (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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1304B LEU* 4.0 13.9 - - + +
1341B GLN 3.3 12.6 + - - +
1342B MET* 4.4 2.7 - - - +
1344B GLU* 1.3 91.9 + - + +
1346B PHE* 1.3 61.2 + - + +
1348B HIS* 3.9 25.5 + - + +
1349B ALA* 3.0 29.1 + - - +
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Residues in contact with PHE1346 (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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1301B LEU* 4.1 26.2 - - + -
1304B LEU* 3.6 39.9 - - + +
1305B LEU* 3.9 28.0 - - + -
1308B VAL* 4.4 11.2 - - + -
1342B MET* 3.1 38.3 + - + +
1343B THR 3.8 1.1 - - - +
1345B LYS* 1.3 77.7 - - + +
1347B PHE* 1.3 63.1 + - - +
1349B ALA* 3.4 3.3 + - - +
1350B ILE* 3.3 29.9 + - + +
1397B ILE* 4.4 15.7 - - + -
1418B LEU* 4.7 1.1 - - + -
1421B MET* 3.6 35.7 - - + -
1425B LEU* 4.9 4.9 - - + -
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Residues in contact with PHE1347 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1343B THR* 2.9 21.4 + - + +
1344B GLU* 3.7 5.4 - - - +
1346B PHE* 1.3 75.8 - - - +
1348B HIS* 1.3 64.7 + - - +
1350B ILE* 3.3 5.6 + - + +
1351B ILE* 3.1 61.6 + - + +
1389B PHE* 4.9 11.2 - + - -
1425B LEU* 3.7 27.1 - - + +
1428B ILE* 3.7 20.4 - - + -
1446B PHE* 5.6 0.4 - - + -
1450B ASN* 3.6 55.2 - - + +
1453B ALA* 4.1 8.5 - - + -
1454B ALA* 3.8 10.8 - - + -
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Residues in contact with HIS1348 (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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1344B GLU* 2.8 22.6 + - + +
1345B LYS* 3.9 28.2 + - + +
1346B PHE 3.3 0.2 - - - -
1347B PHE* 1.3 78.2 - - + +
1349B ALA* 1.3 59.4 + - - +
1351B ILE* 3.4 4.8 + - - +
1352B SER* 2.9 58.0 + - - -
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Residues in contact with ALA1349 (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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1300B LEU* 3.6 19.0 - - + +
1304B LEU* 3.6 26.9 - - + -
1345B LYS 3.0 18.1 + - - +
1346B PHE 3.8 1.8 - - - +
1347B PHE 3.3 0.2 - - - -
1348B HIS* 1.3 81.3 - - + +
1350B ILE* 1.3 61.9 + - + +
1352B SER* 4.0 3.9 - - - +
1353B SER* 3.2 23.0 + - - -
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Residues in contact with ILE1350 (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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1296B TYR* 5.1 2.5 - - - +
1300B LEU* 4.2 15.9 - - + -
1301B LEU* 5.1 7.0 - - + -
1304B LEU* 6.5 0.2 - - + -
1346B PHE* 3.3 17.8 + - + +
1347B PHE* 3.3 8.6 + - - +
1348B HIS 3.2 0.4 - - - -
1349B ALA* 1.3 76.4 - - + +
1351B ILE* 1.3 67.9 + - + +
1353B SER* 2.4 27.1 + - - +
1388B MET* 5.9 0.7 - - + -
1389B PHE* 3.8 31.6 - - + -
1393B ILE* 3.6 36.3 - - + -
1397B ILE* 4.7 9.2 - - + -
1425B LEU* 4.7 4.5 - - + -
1457B PHE* 3.1 28.3 - - + -
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Residues in contact with ILE1351 (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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1347B PHE* 3.1 47.4 + - + +
1348B HIS* 4.1 5.6 - - - +
1350B ILE* 1.3 81.1 - - + +
1352B SER* 1.3 61.8 + - - +
1353B SER 3.2 1.3 + - - -
1354B SER* 4.0 5.0 + - - -
1389B PHE* 5.5 2.2 - - + -
1453B ALA* 3.7 20.9 - - + +
1454B ALA* 3.6 28.7 - - + -
1456B ARG* 6.2 0.2 - - + -
1457B PHE* 3.3 34.8 - - + +
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Residues in contact with SER1352 (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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1348B HIS* 2.9 47.6 + - - -
1349B ALA* 4.0 4.9 - - - -
1351B ILE* 1.3 75.1 - - - +
1353B SER* 1.3 55.4 + - - +
1354B SER* 3.3 8.3 + - - -
1355B SER* 4.5 8.1 + - - -
1356B GLU* 4.6 2.1 - - - +
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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