Contacts of the helix formed by residues 1548 - 1569 (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 ASP1548 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1545E ARG* 3.6 15.7 - - + +
1546E GLY 3.3 0.6 - - - -
1547E ASP* 1.3 77.9 - - - +
1549E PHE* 1.3 66.0 + - - +
1550E GLU* 3.4 11.8 + - - +
1551E THR* 2.7 38.2 + - - +
1552E VAL* 3.1 25.4 + - - +
1614E VAL* 4.5 0.2 - - - -
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Residues in contact with PHE1549 (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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1547E ASP 3.9 3.6 + - - -
1548E ASP* 1.3 72.3 + - - +
1550E GLU* 1.3 65.9 + - + +
1552E VAL* 3.2 4.4 + - - +
1553E SER* 2.8 51.1 + - - -
1611E LEU* 3.5 33.0 - - + -
1614E VAL* 3.9 23.6 - - + +
1615E LEU* 4.2 26.0 - - + -
1618E ILE* 4.5 12.5 - - + +
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Residues in contact with GLU1550 (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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1495E PRO* 4.4 14.7 - - + +
1496E ARG* 3.0 51.9 + - - +
1548E ASP* 3.4 9.9 + - - +
1549E PHE* 1.3 86.3 - - + +
1551E THR* 1.3 57.5 + - - +
1553E SER* 3.8 4.3 - - - -
1554E PHE* 2.9 32.6 + - - +
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Residues in contact with THR1551 (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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1495E PRO* 4.5 15.8 - - + +
1541E VAL* 3.7 31.4 - - + +
1542E LEU* 4.7 3.8 - - + -
1545E ARG* 3.6 35.8 + - + +
1548E ASP* 2.7 31.8 + - - +
1549E PHE 3.2 0.2 - - - -
1550E GLU* 1.3 77.1 - - - +
1552E VAL* 1.3 61.9 + - - +
1554E PHE* 3.4 0.3 + - - +
1555E TRP* 3.2 30.8 + - + +
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Residues in contact with VAL1552 (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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1542E LEU* 4.0 17.7 - - + -
1545E ARG 4.7 0.4 - - - +
1546E GLY* 3.5 28.3 - - - +
1548E ASP 3.1 15.6 + - - +
1549E PHE* 3.7 4.9 - - - +
1551E THR* 1.3 73.2 - - - +
1553E SER* 1.3 60.9 + - - +
1555E TRP 3.4 0.5 + - - -
1556E LEU* 2.9 29.1 + - - +
1607E ILE* 3.6 32.5 - - + +
1610E GLN* 4.3 5.2 - - + -
1611E LEU* 3.7 26.5 - - + +
1614E VAL* 4.3 6.3 - - + -
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Residues in contact with SER1553 (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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1549E PHE* 2.8 41.6 + - - -
1550E GLU* 3.8 5.4 - - - -
1552E VAL* 1.3 73.7 - - - +
1554E PHE* 1.3 61.4 + - - +
1556E LEU* 3.7 5.5 - - - +
1557E SER* 2.8 33.8 + - - -
1611E LEU* 3.8 13.8 - - - +
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Residues in contact with PHE1554 (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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1493E LEU* 3.5 33.2 - - + -
1495E PRO* 3.9 28.7 - - + -
1500E VAL* 3.4 27.6 - - + -
1505E GLY 5.7 2.5 - - - -
1507E PRO* 3.7 12.8 - - + -
1550E GLU 2.9 18.8 + - - +
1551E THR 3.7 3.8 - - - +
1552E VAL 3.3 0.2 - - - -
1553E SER* 1.3 77.7 - - - +
1555E TRP* 1.3 87.7 + + - +
1557E SER* 3.5 4.8 + - - -
1558E ASN* 2.7 58.7 + - - -
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Residues in contact with TRP1555 (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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1489E LEU 3.4 21.5 - - - -
1490E ILE* 3.5 46.6 + - + -
1493E LEU* 4.4 10.8 + - + -
1495E PRO* 5.5 2.0 - - - +
1507E PRO* 4.2 9.9 - - + -
1511E LEU* 5.3 4.9 - - + -
1538E ILE* 4.4 31.2 - - + -
1541E VAL* 3.7 28.9 - - + +
1542E LEU* 4.5 13.5 - - + -
1545E ARG* 5.6 0.8 - - - +
1551E THR* 3.2 26.9 + - + +
1552E VAL 4.3 1.3 - - - +
1554E PHE* 1.3 100.2 - + - +
1556E LEU* 1.3 60.0 + - - +
1557E SER 3.3 0.2 - - - -
1558E ASN* 3.8 23.1 - - + +
1559E THR* 2.5 35.7 + - - -
1607E ILE* 3.8 4.0 - - - +
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Residues in contact with LEU1556 (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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1552E VAL 2.9 18.8 + - - +
1553E SER* 3.7 5.2 - - - +
1555E TRP* 1.3 78.4 - - - +
1557E SER* 1.3 62.8 + - - +
1559E THR* 3.9 0.5 - - - -
1560E CYS* 3.1 45.2 + - - -
1604E ALA* 3.6 28.3 - - + +
1607E ILE* 3.7 17.8 - - + +
1608E TYR* 4.1 25.8 - - + +
1611E LEU* 3.8 28.0 - - + -
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Residues in contact with SER1557 (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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1505E GLY* 6.0 1.3 - - - -
1553E SER* 2.8 25.4 + - - -
1554E PHE* 3.6 7.3 - - - -
1556E LEU* 1.3 79.1 - - - +
1558E ASN* 1.3 61.3 + - - +
1560E CYS* 3.4 7.0 + - - +
1561E ARG* 3.0 27.1 + - - +
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Residues in contact with ASN1558 (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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1505E GLY* 3.3 21.4 - - - +
1507E PRO* 3.2 25.5 - - - +
1508E ALA* 3.3 15.3 + - + +
1538E ILE* 6.0 0.4 - - - -
1554E PHE* 2.7 60.7 + - - +
1555E TRP* 3.8 20.9 - - + -
1556E LEU 3.4 0.2 - - - -
1557E SER* 1.3 78.0 - - - +
1559E THR* 1.3 60.5 + - - +
1561E ARG* 4.3 1.8 - - - -
1562E PHE* 2.9 29.1 + - - +
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Residues in contact with THR1559 (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* 3.7 22.1 - - + +
1555E TRP* 2.5 26.3 + - - -
1556E LEU 3.9 3.1 - - - -
1558E ASN* 1.3 76.5 - - - +
1560E CYS* 1.3 57.1 + - - +
1562E PHE* 3.4 7.1 + - - +
1563E LEU* 3.0 27.5 + - + +
1600E LEU* 3.9 40.0 - - + +
1603E LEU* 4.3 9.2 - - + -
1604E ALA* 4.2 12.1 - - + -
1607E ILE* 3.5 13.9 - - + +
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Residues in contact with CYS1560 (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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1556E LEU* 3.1 41.0 + - - +
1557E SER* 3.5 6.7 - - - +
1559E THR* 1.3 78.2 - - - +
1561E ARG* 1.3 51.1 + - - +
1563E LEU* 3.1 12.2 + - - +
1564E HIS* 2.7 54.1 + - + +
1604E ALA* 4.5 13.0 - - - -
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Residues in contact with ARG1561 (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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1504E PRO 5.8 0.2 + - - -
1505E GLY* 4.1 9.1 - - - +
1508E ALA* 3.6 21.3 - - + -
1509E TYR* 3.5 44.7 + - + -
1557E SER 3.0 17.2 + - - +
1558E ASN* 3.9 2.0 - - - +
1560E CYS* 1.3 75.6 - - - +
1562E PHE* 1.3 56.4 + - - +
1564E HIS* 3.4 39.7 - - - +
1565E CYS* 2.9 32.4 + - - -
1568E GLN* 4.9 9.3 + - - -
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Residues in contact with PHE1562 (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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1508E ALA* 3.6 23.7 - - + +
1511E LEU* 3.8 15.0 - - + -
1512E PHE* 3.6 31.6 - - + -
1515E VAL* 4.1 8.7 - - + -
1530E LEU* 6.3 0.2 - - + -
1531E LEU* 3.9 25.8 - - + -
1534E THR* 4.1 24.9 - - + -
1535E ILE* 6.1 0.7 - - + -
1538E ILE* 5.8 1.8 - - + -
1558E ASN 2.9 18.3 + - - +
1559E THR* 3.6 6.7 - - - +
1561E ARG* 1.3 76.4 - - - +
1563E LEU* 1.3 62.0 + - - +
1565E CYS* 3.4 3.5 + - - +
1566E LEU* 3.1 38.6 + - + +
1600E LEU* 3.5 37.9 - - + -
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Residues in contact with LEU1563 (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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1559E THR* 3.0 15.2 + - + +
1560E CYS* 3.3 13.0 - - - +
1562E PHE* 1.3 75.4 - - - +
1564E HIS* 1.3 69.5 + - + +
1566E LEU* 3.3 6.4 + - - +
1567E LYS* 3.1 51.2 + - + +
1597E ARG* 3.4 43.3 - - + +
1600E LEU* 4.5 11.4 - - + +
1601E SER* 4.1 27.8 - - - +
1604E ALA* 5.5 4.5 - - + -
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Residues in contact with HIS1564 (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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1560E CYS* 2.7 42.2 + - + +
1561E ARG* 3.4 42.6 - - - +
1563E LEU* 1.3 79.4 - - + +
1565E CYS* 1.3 53.4 + - - +
1567E LYS* 3.3 14.9 + - - +
1568E GLN* 2.8 39.8 + - - +
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Residues in contact with CYS1565 (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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1508E ALA 4.7 3.6 - - - -
1509E TYR* 3.7 36.1 - - - -
1512E PHE* 3.8 34.6 - - + -
1561E ARG* 2.9 30.7 + - - +
1562E PHE 3.6 6.1 - - - +
1564E HIS* 1.3 77.2 - - - +
1566E LEU* 1.3 57.0 + - - +
1568E GLN* 4.4 4.3 - - - -
1569E TYR* 2.9 48.6 + - + +
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Residues in contact with LEU1566 (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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1512E PHE* 3.8 26.7 - - + -
1515E VAL* 4.5 6.5 - - + -
1531E LEU* 5.0 5.4 - - + -
1562E PHE* 3.1 34.0 + - + +
1563E LEU* 3.3 5.8 + - - +
1565E CYS* 1.3 76.4 - - - +
1567E LYS* 1.3 58.0 + - - +
1569E TYR 3.9 0.3 - - - -
1570E SER* 3.1 27.2 + - - -
1588E LEU* 4.8 3.6 - - + +
1593E LEU* 3.9 29.6 - - + -
1596E TYR* 5.6 2.7 - - + -
1597E ARG* 3.8 30.1 + - + +
1600E LEU* 3.5 31.2 - - + -
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Residues in contact with LYS1567 (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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1563E LEU* 3.1 48.4 + - + +
1564E HIS* 3.6 15.5 + - - +
1566E LEU* 1.3 75.0 - - - +
1568E GLN* 1.3 65.6 + - - +
1570E SER* 2.8 25.0 + - - -
1575E PHE* 3.1 51.1 - - + +
1576E MET* 5.7 0.2 - - - +
1597E ARG* 3.7 22.0 - - - +
1601E SER* 6.1 0.8 - - - -
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Residues in contact with GLN1568 (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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1561E ARG* 4.9 10.7 + - - -
1564E HIS* 2.8 22.0 + - - +
1565E CYS* 3.9 5.4 - - - +
1567E LYS* 1.3 74.1 - - - +
1569E TYR* 1.3 78.3 + - + +
1570E SER 3.8 0.7 + - - -
1575E PHE* 3.9 15.3 - - - +
1576E MET* 4.1 6.1 - - - +
1578E HIS* 5.2 3.0 + - - +
1579E ASN* 2.9 54.9 + - - +
1583E GLN* 3.5 27.5 + - - +
1587E CYS* 4.1 0.2 - - - -
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Residues in contact with TYR1569 (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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1509E TYR* 6.0 4.4 - + - -
1512E PHE* 3.3 35.2 - + + -
1565E CYS* 2.9 33.4 + - + -
1566E LEU 3.9 3.1 - - - -
1568E GLN* 1.3 103.1 + - + +
1570E SER* 1.3 58.0 + - - +
1571E GLY 3.2 2.7 - - - -
1579E ASN* 5.1 0.4 - - - -
1583E GLN* 3.3 60.7 + - + +
1586E HIS* 3.7 30.9 - + + +
1587E CYS* 3.7 7.0 - - - -
1588E LEU* 2.9 30.6 + - - +
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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
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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