Contacts of the helix formed by residues 1554 - 1577 (chain B) in PDB entry 1KI1
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 SER1554 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1552B ALA* 4.3 0.5 - - - +
1553B GLU* 1.3 82.9 - - - +
1555B ILE* 1.3 60.3 + - - +
1556B ASN* 3.6 18.4 + - - +
1557B GLU* 3.3 28.8 + - - +
1558B ARG* 2.9 34.7 + - - +
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Residues in contact with ILE1555 (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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1554B SER* 1.3 74.6 - - - +
1556B ASN* 1.3 57.4 + - - +
1558B ARG* 3.0 55.1 - - - +
1559B THR* 2.8 33.6 + - + +
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Residues in contact with ASN1556 (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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1554B SER* 3.1 15.6 + - - +
1555B ILE* 1.3 85.9 - - - +
1557B GLU* 1.3 59.8 + - + +
1559B THR* 3.8 4.4 + - - -
1560B ALA* 3.0 22.3 + - - +
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Residues in contact with GLU1557 (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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1465B HIS* 4.9 10.0 - - - +
1467B GLY* 4.2 13.7 - - - +
1552B ALA* 4.3 6.7 - - + -
1553B GLU* 3.1 43.7 - - - +
1554B SER* 3.3 18.1 + - - +
1556B ASN* 1.3 77.9 - - + +
1558B ARG* 1.3 65.9 + - - +
1560B ALA* 3.0 19.5 - - + +
1561B TRP* 3.0 27.2 + - + +
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Residues in contact with ARG1558 (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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1528B LEU* 6.2 3.6 - - + +
1530B THR* 5.3 15.4 + - - +
1539B PHE* 5.0 13.1 - - + -
1552B ALA* 3.8 18.5 - - + +
1554B SER 2.9 13.0 + - - +
1555B ILE* 3.0 63.8 - - - +
1557B GLU* 1.3 76.1 - - - +
1559B THR* 1.3 79.1 + - + +
1560B ALA 2.9 9.8 + - - -
1561B TRP* 3.3 7.8 + - - +
1562B VAL* 3.2 21.1 + - - +
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Residues in contact with THR1559 (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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1528B LEU* 4.7 16.4 - - + -
1555B ILE* 2.8 26.9 + - + +
1556B ASN* 3.8 6.2 + - - -
1558B ARG* 1.3 94.3 - - + +
1560B ALA* 1.3 57.5 + - - +
1562B VAL* 3.9 8.8 - - - +
1563B GLN* 3.1 28.9 + - - +
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Residues in contact with ALA1560 (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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1465B HIS* 4.6 17.3 - - + +
1556B ASN 3.0 17.3 - - - +
1557B GLU* 3.0 19.2 - - + +
1558B ARG 2.9 1.8 - - - -
1559B THR* 1.3 79.2 + - - +
1561B TRP* 1.3 61.5 + - - +
1563B GLN* 3.3 4.8 + - - +
1564B LYS* 3.0 35.3 + - - +
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Residues in contact with TRP1561 (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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1465B HIS* 3.4 27.3 - + - -
1466B SER* 3.6 7.2 - - - -
1467B GLY* 3.3 30.8 + - - -
1468B LYS 4.6 1.1 - - - -
1469B LEU* 4.4 35.6 - - + +
1480B GLY* 3.3 29.4 - - - -
1482B LEU* 4.2 16.2 - - + -
1487B LEU* 3.9 26.2 - - + -
1539B PHE* 4.1 19.1 - + + -
1552B ALA* 5.1 1.7 - - + +
1557B GLU* 3.0 37.6 + - + +
1558B ARG* 4.1 5.2 - - - +
1560B ALA* 1.3 75.3 - - + +
1562B VAL* 1.3 58.2 + - - +
1564B LYS* 4.8 4.5 - - - -
1565B ILE* 2.7 55.5 + - + +
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Residues in contact with VAL1562 (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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1526B VAL* 3.6 25.1 - - + +
1528B LEU* 4.4 30.3 - - + -
1539B PHE* 3.5 28.5 - - + -
1558B ARG* 3.2 20.0 - - + +
1559B THR* 3.9 8.3 - - - +
1560B ALA 3.2 0.2 - - - -
1561B TRP* 1.3 76.2 - - - +
1563B GLN* 1.3 64.0 - - - +
1565B ILE* 4.2 0.2 - - - +
1566B LYS* 3.0 37.1 + - + +
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Residues in contact with GLN1563 (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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1559B THR 3.1 18.1 + - - +
1560B ALA* 3.4 7.6 - - - +
1562B VAL* 1.3 81.0 - - - +
1564B LYS* 1.3 63.2 - - + +
1566B LYS* 3.8 3.7 - - - +
1567B ALA* 3.0 40.5 + - - +
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Residues in contact with LYS1564 (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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1464B LEU* 3.4 22.1 + - + +
1465B HIS* 3.0 45.3 - - + -
1482B LEU* 3.9 15.7 - - + -
1560B ALA* 3.0 19.8 + - - +
1561B TRP* 4.0 2.5 - - - +
1563B GLN* 1.3 81.0 - - + +
1565B ILE* 1.3 61.1 + - - +
1567B ALA* 3.8 3.9 - - - +
1568B ALA* 2.8 34.5 + - - +
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Residues in contact with ILE1565 (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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1482B LEU* 3.9 24.2 - - + -
1487B LEU* 4.4 18.8 - - + -
1521B LEU* 4.3 9.8 - - + +
1524B VAL* 4.6 19.1 - - + -
1526B VAL* 3.3 26.7 - - + -
1539B PHE* 3.7 28.7 - - + -
1541B ILE* 4.7 2.7 - - + -
1561B TRP* 2.7 44.4 + - + +
1562B VAL 4.2 0.2 - - - +
1564B LYS* 1.3 71.1 - - - +
1566B LYS* 1.3 58.7 + - - +
1568B ALA* 4.0 2.1 - - - +
1569B SER* 2.8 33.5 + - - -
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Residues in contact with LYS1566 (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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1526B VAL* 4.9 16.8 - - + +
1562B VAL* 3.0 27.7 + - + +
1563B GLN* 3.8 3.8 - - - +
1565B ILE* 1.3 75.7 - - - +
1567B ALA* 1.3 65.2 + - - +
1569B SER* 3.6 4.6 - - - -
1570B GLU* 2.9 57.3 + - + +
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Residues in contact with ALA1567 (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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1563B GLN* 3.0 30.6 + - - +
1564B LYS* 3.8 5.2 - - - +
1566B LYS* 1.3 78.1 - - - +
1568B ALA* 1.3 63.3 - - - +
1570B GLU* 3.3 9.4 + - - +
1571B LEU* 3.0 25.9 + - - +
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Residues in contact with ALA1568 (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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1458B LEU* 5.6 0.2 - - - +
1464B LEU* 3.6 26.0 - - + -
1482B LEU* 5.1 0.2 - - + -
1484B ASN* 4.4 8.5 - - + +
1521B LEU* 3.4 23.6 - - + -
1564B LYS 2.8 21.7 + - - +
1565B ILE* 4.0 0.4 - - - +
1567B ALA* 1.3 73.3 - - - +
1569B SER* 1.3 63.2 + - - +
1571B LEU* 3.4 9.0 + - - +
1572B TYR* 3.0 22.9 + - - +
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Residues in contact with SER1569 (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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1521B LEU* 2.4 41.6 + - - +
1524B VAL* 3.4 18.2 + - - +
1565B ILE* 2.8 22.4 + - - -
1566B LYS* 3.6 6.5 - - - -
1568B ALA* 1.3 77.6 - - - +
1570B GLU* 1.3 57.6 + - - +
1572B TYR* 3.1 5.5 + - - +
1573B ILE* 2.9 37.3 + - - +
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Residues in contact with GLU1570 (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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1566B LYS* 2.9 54.2 + - + +
1567B ALA* 3.8 6.9 - - - +
1569B SER* 1.3 75.5 - - - +
1571B LEU* 1.3 58.1 + - - +
1573B ILE* 3.1 20.2 + - + +
1574B GLU* 2.9 37.9 + - + +
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Residues in contact with LEU1571 (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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1458B LEU* 5.1 2.7 - - + -
1567B ALA 3.0 17.6 + - - +
1568B ALA* 3.7 8.3 - - - +
1570B GLU* 1.3 77.1 - - - +
1572B TYR* 1.3 57.5 + - - +
1574B GLU* 3.2 17.3 + - + +
1575B THR* 2.7 47.4 + - - +
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Residues in contact with TYR1572 (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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1456B ASN* 4.8 11.1 - - - +
1457B CYS* 3.7 26.2 - - - -
1458B LEU* 3.7 33.0 - - + -
1484B ASN 4.1 0.4 - - - +
1485B ASP* 3.6 30.7 - - + +
1520B PHE* 4.5 9.6 - - + -
1521B LEU* 3.9 10.1 - - + -
1522B ASN* 3.5 52.8 + - + +
1568B ALA 3.0 13.4 + - - +
1569B SER* 3.2 11.2 - - - +
1571B LEU* 1.3 76.0 - - - +
1573B ILE* 1.3 59.7 + - - +
1575B THR* 3.4 1.2 + - - -
1576B GLU* 2.9 33.9 + - + +
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Residues in contact with ILE1573 (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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1521B LEU 5.0 3.6 - - - +
1522B ASN* 5.1 10.8 - - - +
1524B VAL 6.1 0.4 - - - +
1569B SER* 2.9 25.0 + - - +
1570B GLU* 3.2 29.6 - - + +
1572B TYR* 1.3 75.4 - - - +
1574B GLU* 1.3 67.4 + - + +
1576B GLU* 2.9 12.8 + - - +
1577B LYS* 2.8 35.4 + - + +
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Residues in contact with GLU1574 (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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1570B GLU* 2.9 16.7 + - + +
1571B LEU* 3.2 32.1 + - + +
1573B ILE* 1.3 77.9 - - + +
1575B THR* 1.3 58.0 + - - +
1577B LYS* 2.8 35.5 + - - +
1578B LYS* 3.8 6.7 + - - +
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Residues in contact with THR1575 (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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1457B CYS* 3.2 30.0 - - - +
1458B LEU* 3.7 16.8 - - + +
1571B LEU* 2.7 36.4 + - - +
1572B TYR 3.8 0.9 - - - -
1573B ILE 3.2 0.2 - - - -
1574B GLU* 1.3 76.8 - - - +
1576B GLU* 1.3 60.0 + - - +
1578B LYS* 3.7 20.7 + - + +
1579B LYS* 4.4 5.0 - - - +
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Residues in contact with GLU1576 (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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1457B CYS* 4.8 6.4 - - - -
1522B ASN* 3.5 38.7 + - - +
1572B TYR* 2.9 31.4 + - + +
1573B ILE* 2.9 8.1 + - - +
1575B THR* 1.3 75.1 - - - +
1577B LYS* 1.3 53.6 + - + +
1578B LYS 2.7 17.0 + - - -
1579B LYS* 3.2 32.4 + - + +
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Residues in contact with LYS1577 (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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1573B ILE* 2.8 26.5 + - + +
1574B GLU* 2.8 14.7 + - - +
1576B GLU* 1.3 74.3 - - + +
1578B LYS* 1.3 63.8 + - + +
1579B LYS 3.6 2.2 - - - -
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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