Contacts of the helix formed by residues 1523 - 1545 (chain E) in PDB entry 5JCZ
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 ASP1523 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1479E LYS* 5.6 0.7 + - - -
1518E ALA 3.1 11.3 + - - +
1521E LEU* 3.1 17.6 - - + +
1522E ASN* 1.3 73.6 - - - +
1524E ASP* 1.3 63.5 + - - +
1525E GLN* 3.3 13.0 + - - +
1526E LYS* 3.2 37.6 + - + +
1527E VAL* 3.1 25.8 + - - +
1591E PHE* 3.8 2.7 - - - -
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Residues in contact with ASP1524 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1774C THR* 5.9 2.9 - - - +
1775C ALA* 3.5 19.7 - - + +
1813C PRO* 4.0 11.2 - - + +
1522E ASN 3.4 8.4 + - - +
1523E ASP* 1.3 70.5 - - - +
1525E GLN* 1.3 65.7 + - - +
1527E VAL* 3.7 1.9 - - - +
1528E ARG* 2.8 62.6 + - - +
1591E PHE* 3.4 28.2 - - + -
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Residues in contact with GLN1525 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1479E LYS* 3.9 17.9 - - - +
1523E ASP* 3.2 10.4 + - - +
1524E ASP* 1.3 85.8 - - - +
1526E LYS* 1.3 58.0 + - - +
1528E ARG* 3.4 25.6 + - - +
1529E SER* 3.0 28.4 + - - -
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Residues in contact with LYS1526 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1476E GLU* 5.1 2.0 + - - +
1477E TYR* 2.8 68.0 + - - +
1479E LYS* 4.0 29.3 - - + +
1514E CYS 6.0 0.2 - - - -
1517E HIS* 4.9 5.9 + - - -
1518E ALA* 4.2 20.6 - - + +
1521E LEU* 4.8 15.3 - - + +
1523E ASP* 3.2 32.2 + - + +
1525E GLN* 1.3 76.5 - - - +
1527E VAL* 1.3 60.0 + - - +
1529E SER* 3.8 0.5 - - - -
1530E LEU* 2.9 33.5 + - - +
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Residues in contact with VAL1527 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1813C PRO* 3.8 19.5 - - + -
1515E VAL* 4.9 8.5 - - + +
1518E ALA* 3.6 24.0 - - + -
1519E ASP* 4.1 2.2 - - + +
1523E ASP 3.1 17.1 + - - +
1524E ASP* 3.7 6.7 - - - +
1526E LYS* 1.3 76.9 - - - +
1528E ARG* 1.3 62.6 + - - +
1530E LEU* 4.0 2.6 - - - +
1531E LEU* 3.1 45.8 + - + +
1591E PHE* 3.6 26.0 - - + -
1593E LEU* 4.0 11.0 - - + -
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Residues in contact with ARG1528 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1775C ALA* 3.7 8.1 - - - +
1813C PRO* 2.8 41.2 + - + +
1814C GLN* 4.2 1.3 - - - +
1815C LEU* 3.7 42.8 - - - +
1816C LEU 5.4 0.4 - - - +
1524E ASP* 2.8 47.0 + - - +
1525E GLN* 3.5 32.7 + - - +
1527E VAL* 1.3 77.3 - - - +
1529E SER* 1.3 56.6 + - - +
1531E LEU* 4.0 2.2 - - - +
1532E THR* 2.8 38.1 + - - +
1596E TYR* 3.7 21.4 - - - +
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Residues in contact with SER1529 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1479E LYS* 3.8 16.7 - - - -
1482E GLU* 2.2 33.1 + - - -
1525E GLN* 3.0 18.6 + - - -
1526E LYS 3.8 0.9 - - - -
1528E ARG* 1.3 77.6 - - - +
1530E LEU* 1.3 55.3 + - - +
1532E THR* 3.8 4.1 - - - -
1533E SER* 2.7 38.8 + - - -
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Residues in contact with LEU1530 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1477E TYR* 3.5 20.9 - - + +
1482E GLU* 3.7 10.5 + - + +
1485E LEU* 4.0 20.6 - - + -
1486E VAL* 5.0 4.9 - - + -
1511E LEU* 4.2 10.3 - - + +
1514E CYS* 3.7 30.1 - - + +
1515E VAL* 3.7 30.3 - - + +
1518E ALA* 5.2 4.5 - - + -
1526E LYS 2.9 18.8 + - - +
1527E VAL* 4.0 3.4 - - - +
1529E SER* 1.3 75.6 - - - +
1531E LEU* 1.3 55.2 + - + +
1533E SER* 3.4 1.7 + - - -
1534E THR* 2.7 47.8 + - - +
1562E PHE* 6.3 0.2 - - + -
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Residues in contact with LEU1531 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1515E VAL* 3.9 19.7 - - + -
1527E VAL* 3.1 36.6 + - + +
1528E ARG 4.0 2.0 - - - +
1530E LEU* 1.3 77.3 - - + +
1532E THR* 1.3 61.9 + - - +
1534E THR* 3.5 4.6 + - - -
1535E ILE* 3.1 33.1 + - + +
1562E PHE* 3.9 32.1 - - + -
1566E LEU* 5.0 5.8 - - + -
1593E LEU* 4.0 18.4 - - + -
1596E TYR* 3.8 42.4 - - + -
1600E LEU* 5.8 1.1 - - + -
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Residues in contact with THR1532 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1528E ARG* 2.8 24.4 + - - +
1529E SER* 3.8 4.5 - - - -
1531E LEU* 1.3 75.2 - - - +
1533E SER* 1.3 60.7 - - - +
1535E ILE* 3.5 5.6 + - - +
1536E ASN* 3.0 50.1 + - - +
1596E TYR* 5.0 7.3 + - - -
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Residues in contact with SER1533 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1482E GLU* 3.1 18.0 + - - +
1486E VAL* 4.0 22.0 - - - -
1529E SER* 2.7 25.1 + - - -
1530E LEU* 3.8 4.3 - - - -
1532E THR* 1.3 78.4 - - - +
1534E THR* 1.3 56.6 + - - +
1536E ASN* 4.1 5.1 - - - +
1537E SER* 2.6 38.1 + - - -
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Residues in contact with THR1534 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1486E VAL* 4.3 1.6 - - - +
1490E ILE* 4.0 10.4 - - + +
1511E LEU* 3.7 41.4 - - + +
1530E LEU* 2.7 30.8 + - - +
1531E LEU* 3.6 8.6 - - - -
1533E SER* 1.3 77.5 - - - +
1535E ILE* 1.3 64.3 + - + +
1537E SER* 3.3 2.9 + - - -
1538E ILE* 3.1 42.0 + - + +
1562E PHE* 4.1 23.0 - - + -
1600E LEU* 5.6 0.4 - - + -
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Residues in contact with ILE1535 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1531E LEU* 3.1 22.2 + - + +
1532E THR* 4.0 4.7 - - - +
1534E THR* 1.3 76.5 - - - +
1536E ASN* 1.3 68.2 + - - +
1538E ILE* 3.4 8.4 + - - +
1539E LYS* 3.1 50.0 + - + +
1562E PHE* 6.1 0.7 - - + -
1596E TYR* 5.0 12.3 - - + +
1599E VAL* 3.7 31.0 - - + -
1600E LEU* 3.9 30.7 - - + -
1603E LEU* 4.4 8.9 - - + +
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Residues in contact with ASN1536 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1532E THR* 3.0 42.4 + - - +
1533E SER* 4.1 4.8 - - - +
1535E ILE* 1.3 83.2 - - - +
1537E SER* 1.3 58.8 + - - +
1539E LYS* 3.6 13.6 + - - +
1540E LYS* 3.0 28.2 + - - +
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Residues in contact with SER1537 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1486E VAL* 3.5 20.5 - - - +
1490E ILE* 3.8 20.6 - - - -
1491E LEU* 3.5 22.2 - - - +
1533E SER* 2.6 24.3 + - - -
1534E THR 3.7 4.0 - - - -
1536E ASN* 1.3 75.4 - - - +
1538E ILE* 1.3 58.8 + - - +
1540E LYS* 3.2 4.2 + - - +
1541E VAL* 2.9 33.6 + - - +
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Residues in contact with ILE1538 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1490E ILE* 4.1 19.3 - - + -
1511E LEU* 5.6 1.8 - - + -
1534E THR* 3.1 33.9 + - + +
1535E ILE* 3.4 5.1 + - - +
1537E SER* 1.3 76.5 - - - +
1539E LYS* 1.3 61.7 + - - +
1541E VAL* 3.3 4.9 + - - +
1542E LEU* 3.1 40.0 + - + +
1555E TRP* 4.4 23.6 - - + -
1559E THR* 3.7 31.6 - - + +
1562E PHE* 5.8 2.0 - - + -
1600E LEU* 5.1 4.3 - - + -
1603E LEU* 4.1 18.8 - - + -
1607E ILE* 4.1 1.1 - - + -
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Residues in contact with LYS1539 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1535E ILE* 3.1 40.4 + - + +
1536E ASN* 3.7 13.8 + - - +
1538E ILE* 1.3 76.7 - - - +
1540E LYS* 1.3 58.5 + - - +
1542E LEU* 3.5 8.8 + - - +
1543E LYS* 3.0 28.2 + - - +
1599E VAL* 5.7 4.8 - - - +
1603E LEU* 3.8 28.9 - - + -
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Residues in contact with LYS1540 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1491E LEU* 4.3 24.8 - - + +
1536E ASN 3.0 18.5 + - - +
1537E SER* 3.2 8.0 + - - +
1539E LYS* 1.3 76.0 - - - +
1541E VAL* 1.3 65.7 + - - +
1543E LYS* 3.1 9.5 + - + +
1544E LYS* 3.0 51.2 + - + +
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Residues in contact with VAL1541 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1490E ILE* 3.5 25.8 - - + +
1491E LEU* 3.7 11.2 - - + -
1537E SER 2.9 19.6 + - - +
1538E ILE* 3.6 7.6 - - - +
1540E LYS* 1.3 75.0 - - - +
1542E LEU* 1.3 58.4 + - + +
1544E LYS* 3.4 7.9 + - - +
1545E ARG* 2.8 57.1 + - - +
1551E THR* 3.7 25.1 - - + -
1555E TRP* 3.7 19.1 - - + +
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Residues in contact with LEU1542 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1538E ILE* 3.1 26.8 + - + +
1539E LYS* 3.7 7.9 - - - +
1541E VAL* 1.3 77.8 - - + +
1543E LYS* 1.3 59.3 + - - +
1546E GLY* 3.1 24.2 - - - -
1551E THR* 4.4 9.9 - - + +
1552E VAL* 4.0 41.1 - - + +
1555E TRP* 4.5 8.5 - - + -
1603E LEU* 5.2 2.5 - - + -
1607E ILE* 3.5 40.4 - - + -
1610E GLN* 5.4 8.8 + - + +
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Residues in contact with LYS1543 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1539E LYS 3.0 17.2 + - - +
1540E LYS* 3.1 11.6 + - + +
1542E LEU* 1.3 79.7 - - - +
1544E LYS* 1.3 64.1 + - + +
1546E GLY 4.6 1.0 + - - -
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Residues in contact with LYS1544 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1491E LEU* 3.9 24.9 + - - +
1492E GLU* 5.8 1.4 - - - +
1540E LYS* 3.0 38.8 + - + +
1541E VAL* 4.0 11.2 - - - +
1543E LYS* 1.3 83.7 - - + +
1545E ARG* 1.3 88.7 + - + +
1546E GLY 3.5 1.1 + - - -
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Residues in contact with ARG1545 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1490E ILE 4.3 0.6 + - - -
1491E LEU 2.4 32.1 + - - -
1492E GLU* 4.9 3.2 - - - +
1493E LEU 4.4 14.1 + - - -
1495E PRO* 5.6 4.4 - - - +
1541E VAL* 2.8 50.3 + - - +
1544E LYS* 1.3 95.9 - - + +
1546E GLY* 1.3 58.7 + - - +
1547E ASP 3.2 7.4 + - - +
1548E ASP* 3.3 20.6 + - + +
1551E THR* 3.6 31.6 + - + +
1555E TRP* 5.6 1.0 - - - +
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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
------------------------------------------------------------
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