Contacts of the helix formed by residues 1525 - 1548 (chain B) in PDB entry 4J5L
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 ASP1525 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1520B ALA 3.0 10.8 + - - +
1523B LEU* 4.3 16.4 - - + +
1524B ASN* 1.3 74.1 - - - +
1526B ASP* 1.3 63.1 + - - +
1527B GLN* 3.3 14.4 + - - +
1528B LYS* 3.1 39.9 + - + +
1529B VAL* 3.1 25.3 + - - +
1593B PHE* 4.0 2.2 - - - -
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Residues in contact with ASP1526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1777A ALA* 3.6 16.6 - - + +
1815A PRO* 4.1 11.8 - - + +
1524B ASN* 3.5 7.5 + - - +
1525B ASP* 1.3 75.0 - - - +
1527B GLN* 1.3 59.1 + - - +
1529B VAL* 3.3 2.4 + - - +
1530B ARG* 2.5 69.7 + - - +
1593B PHE* 3.6 26.8 - - + -
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Residues in contact with GLN1527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1481B LYS* 2.6 36.6 + - + +
1525B ASP* 3.3 9.5 + - - +
1526B ASP* 1.3 85.4 - - - +
1528B LYS* 1.3 60.6 + - - +
1530B ARG* 3.3 18.7 + - - +
1531B SER* 3.0 25.3 + - - -
1901B SO4 3.7 30.3 + - - +
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Residues in contact with LYS1528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1478B GLU* 4.9 1.8 - - - +
1479B TYR* 2.6 68.3 + - + +
1481B LYS* 4.6 23.8 - - + +
1484B GLU* 5.1 0.4 - - - +
1519B HIS* 4.6 15.8 - - - -
1520B ALA* 4.2 19.5 - - + +
1523B LEU* 4.7 9.8 - - + +
1525B ASP* 3.1 32.6 + - + +
1527B GLN* 1.3 78.5 - - - +
1529B VAL* 1.3 63.5 + - - +
1531B SER* 3.3 6.4 + - - +
1532B LEU* 3.1 27.5 + - - +
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Residues in contact with VAL1529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1815A PRO* 4.0 20.2 - - + -
1517B VAL* 4.8 9.9 - - + +
1520B ALA* 3.6 22.4 - - + -
1521B ASP* 4.2 1.8 - - + +
1525B ASP 3.1 15.9 + - - +
1526B ASP* 3.6 8.7 - - - +
1527B GLN 3.3 0.2 - - - -
1528B LYS* 1.3 76.1 - - - +
1530B ARG* 1.3 63.8 + - - +
1532B LEU* 4.0 3.0 - - - +
1533B LEU* 3.2 45.5 + - + +
1593B PHE* 3.6 25.1 - - + -
1595B LEU* 4.2 10.8 - - + -
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Residues in contact with ARG1530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1777A ALA* 3.8 6.9 - - - +
1815A PRO* 2.6 43.7 + - + +
1816A GLN* 4.2 1.1 - - - +
1817A LEU* 3.6 35.9 - - - +
1818A LEU 5.3 0.7 - - - +
1526B ASP* 2.5 50.6 + - - +
1527B GLN* 3.5 19.8 - - - +
1529B VAL* 1.3 75.1 - - - +
1531B SER* 1.3 58.2 + - - +
1533B LEU* 3.9 3.3 - - - +
1534B THR* 2.9 35.8 + - - +
1598B TYR* 4.0 20.0 - - - +
1901B SO4 2.4 35.0 + - - +
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Residues in contact with SER1531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1481B LYS* 4.5 12.6 - - - -
1484B GLU* 2.6 31.7 + - - -
1527B GLN* 3.0 15.0 + - - -
1528B LYS* 3.3 10.4 + - - -
1530B ARG* 1.3 77.3 - - - +
1532B LEU* 1.3 54.1 + - - +
1534B THR* 3.7 5.1 - - - -
1535B SER* 2.7 40.3 + - - -
1901B SO4 5.6 5.6 - - - -
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Residues in contact with LEU1532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1479B TYR* 3.4 23.6 - - + +
1484B GLU* 3.9 12.1 - - + +
1487B LEU* 4.2 18.4 - - + -
1488B VAL* 5.6 4.3 - - + -
1513B LEU* 4.3 11.2 - - + +
1516B CYS* 3.7 28.9 - - + +
1517B VAL* 3.8 26.7 - - + +
1520B ALA* 5.6 2.7 - - + -
1528B LYS 3.1 16.4 + - - +
1529B VAL* 4.0 4.0 - - - +
1531B SER* 1.3 81.9 + - - +
1533B LEU* 1.3 59.5 + - + +
1535B SER* 3.8 3.2 - - - -
1536B THR* 2.8 43.7 + - - +
1564B PHE* 6.4 0.2 - - + -
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Residues in contact with LEU1533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1517B VAL* 3.8 28.7 - - + -
1529B VAL* 3.2 37.7 + - + +
1530B ARG 3.9 2.5 - - - +
1532B LEU* 1.3 77.5 - - + +
1534B THR* 1.3 60.5 + - - +
1536B THR* 3.5 5.2 + - - +
1537B ILE* 3.4 29.8 + - + +
1564B PHE* 3.9 22.7 - - + -
1568B LEU* 5.1 4.7 - - + -
1595B LEU* 4.0 20.9 - - + -
1598B TYR* 3.9 39.9 - - + -
1602B LEU* 6.3 0.2 - - + -
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Residues in contact with THR1534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1530B ARG* 2.9 22.6 + - - +
1531B SER* 3.7 6.7 - - - -
1533B LEU* 1.3 75.5 - - - +
1535B SER* 1.3 66.6 + - - +
1536B THR 3.3 0.3 + - - -
1537B ILE* 3.4 4.4 + - - +
1538B ASN* 3.2 41.6 + - - +
1598B TYR* 5.2 6.4 - - - -
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Residues in contact with SER1535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1484B GLU* 2.7 28.2 + - - -
1485B GLN* 3.4 18.3 + - - -
1488B VAL* 3.6 13.0 - - - +
1531B SER* 2.7 20.0 + - - -
1532B LEU* 3.9 4.7 - - - -
1534B THR* 1.3 75.2 - - - +
1536B THR* 1.3 59.2 + - - +
1538B ASN* 4.5 5.1 - - - +
1539B SER* 2.6 33.8 + - - -
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Residues in contact with THR1536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1488B VAL* 4.2 1.8 - - - +
1492B ILE* 3.9 8.6 - - + +
1513B LEU* 3.8 41.7 - - + +
1532B LEU* 2.8 27.5 + - - +
1533B LEU* 3.6 8.8 - - - +
1534B THR 3.1 0.2 - - - -
1535B SER* 1.3 76.6 - - - +
1537B ILE* 1.3 64.2 + - + +
1539B SER* 3.3 2.1 + - - -
1540B ILE* 3.0 49.9 + - + +
1564B PHE* 4.5 20.1 - - + -
1602B LEU* 5.7 0.9 - - + -
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Residues in contact with ILE1537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1533B LEU 3.4 17.8 + - - +
1534B THR* 3.4 4.9 + - - +
1536B THR* 1.3 78.6 - - + +
1538B ASN* 1.3 62.7 + - - +
1540B ILE* 3.4 7.4 + - + +
1541B LYS* 3.0 52.1 + - + +
1564B PHE* 6.5 0.2 - - + -
1598B TYR* 5.3 6.1 - - + +
1601B VAL* 3.5 34.5 - - + -
1602B LEU* 3.9 31.0 - - + +
1605B LEU* 4.2 11.9 - - + -
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Residues in contact with ASN1538 (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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1534B THR* 3.2 35.3 + - - +
1535B SER* 4.5 4.2 - - - +
1537B ILE* 1.3 83.7 - - - +
1539B SER* 1.3 58.1 + - - +
1541B LYS* 3.6 13.1 + - - +
1542B LYS* 2.9 28.8 + - - +
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Residues in contact with SER1539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1485B GLN* 5.6 0.3 + - - -
1488B VAL* 3.3 25.9 - - - +
1492B ILE* 3.6 19.3 - - - -
1493B LEU* 3.3 22.7 - - - +
1535B SER 2.6 24.5 + - - -
1536B THR 3.7 2.7 - - - -
1537B ILE 3.2 0.2 - - - -
1538B ASN* 1.3 75.4 - - - +
1540B ILE* 1.3 64.5 + - - +
1542B LYS* 3.3 2.5 + - - -
1543B VAL* 3.0 27.7 + - - +
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Residues in contact with ILE1540 (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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1492B ILE* 4.1 19.1 - - + -
1513B LEU* 5.7 1.6 - - + -
1536B THR* 3.0 38.2 + - + +
1537B ILE* 3.8 5.2 - - - +
1539B SER* 1.3 76.3 - - - +
1541B LYS* 1.3 61.9 + - - +
1543B VAL* 3.2 5.4 + - - +
1544B LEU* 3.0 39.2 + - + +
1557B TRP* 4.3 26.9 - - + -
1560B ASN 6.0 0.4 - - - -
1561B THR* 3.8 29.6 - - + +
1564B PHE* 6.3 1.1 - - + -
1602B LEU* 5.7 2.9 - - + -
1605B LEU* 4.4 14.6 - - + -
1609B ILE* 4.4 6.3 - - + -
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Residues in contact with LYS1541 (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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1537B ILE* 3.0 33.6 + - + +
1538B ASN* 3.8 13.1 + - - +
1540B ILE* 1.3 76.2 - - - +
1542B LYS* 1.3 57.2 + - - +
1544B LEU* 3.3 8.2 + - - +
1545B LYS* 2.9 29.2 + - - +
1605B LEU* 3.8 31.2 - - + -
1608B GLN* 4.4 10.9 + - - -
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Residues in contact with LYS1542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1493B LEU* 4.0 24.5 - - + +
1538B ASN 2.9 19.2 + - - +
1539B SER* 3.5 6.3 - - - +
1540B ILE 3.2 0.2 - - - -
1541B LYS* 1.3 74.9 - - - +
1543B VAL* 1.3 64.2 + - - +
1545B LYS* 3.3 19.2 + - + +
1546B LYS* 3.4 14.4 + - - +
1902B SO4 4.1 24.8 + - - +
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Residues in contact with VAL1543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1492B ILE* 3.4 30.5 - - + +
1493B LEU* 3.7 19.1 - - + +
1539B SER 3.0 18.8 + - - +
1540B ILE* 3.2 7.6 + - - +
1542B LYS* 1.3 75.0 - - - +
1544B LEU* 1.3 59.6 + - + +
1546B LYS* 3.4 4.1 + - - +
1547B ARG* 2.9 44.6 + - - +
1553B THR* 3.8 19.5 - - + -
1557B TRP* 3.8 24.9 - - + +
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Residues in contact with LEU1544 (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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1540B ILE* 3.0 24.6 + - + +
1541B LYS* 3.9 6.5 - - - +
1543B VAL* 1.3 75.8 - - + +
1545B LYS* 1.3 60.6 + - - +
1548B GLY* 3.0 27.6 + - - +
1553B THR* 4.2 19.3 - - + +
1554B VAL* 4.2 32.3 - - + -
1557B TRP* 4.4 7.0 - - + -
1605B LEU* 5.7 2.2 - - + -
1609B ILE* 3.6 44.0 - - + -
1612B GLN* 5.5 5.1 + - + +
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Residues in contact with LYS1545 (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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1541B LYS 2.9 16.9 + - - +
1542B LYS* 3.5 13.7 - - + +
1543B VAL 3.2 0.2 - - - -
1544B LEU* 1.3 80.3 - - - +
1546B LYS* 1.3 62.5 + - + +
1548B GLY 4.5 1.4 + - - -
1902B SO4 2.9 36.5 + - - +
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Residues in contact with LYS1546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1542B LYS 3.4 11.4 + - - +
1543B VAL* 4.1 3.1 - - - +
1545B LYS* 1.3 83.9 - - + +
1547B ARG* 1.3 82.8 + - + +
1548B GLY 3.6 1.2 + - - -
1549B ASP* 4.1 8.7 - - - +
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Residues in contact with ARG1547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1492B ILE 5.0 0.8 + - - -
1493B LEU 3.0 26.7 + - - -
1494B GLU* 5.1 0.8 - - - +
1495B LEU 5.5 3.8 + - - -
1496B LYS* 3.6 27.4 - - - +
1497B PRO* 5.9 4.0 - - - +
1498B ARG* 3.4 27.9 - - - +
1543B VAL* 2.9 37.3 + - - +
1544B LEU* 4.4 1.6 - - - -
1546B LYS* 1.3 104.6 - - + +
1548B GLY* 1.3 55.3 + - - +
1549B ASP* 3.1 17.2 + - - +
1550B ASP* 3.3 13.1 + - + +
1553B THR* 3.8 28.9 + - + +
1554B VAL* 4.2 0.3 - - - +
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Residues in contact with GLY1548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1544B LEU* 3.0 26.0 + - - -
1545B LYS 4.5 1.4 + - - -
1546B LYS 3.6 1.8 - - - -
1547B ARG* 1.3 76.6 - - - +
1549B ASP* 1.3 57.8 + - - +
1550B ASP 3.5 0.2 - - - -
1554B VAL* 3.6 16.0 - - - +
1612B GLN* 2.8 32.4 + - - -
1616B VAL* 3.4 11.1 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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