Contacts of the helix formed by residues 1554 - 1577 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1552D ALA* 4.3 0.5 - - - +
1553D GLU* 1.3 82.5 - - - +
1555D ILE* 1.3 60.5 + - - +
1556D ASN* 3.6 18.4 + - - +
1557D GLU* 3.3 29.0 + - - +
1558D ARG* 2.9 34.8 + - - +
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Residues in contact with ILE1555 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1554D SER* 1.3 74.4 - - - +
1556D ASN* 1.3 57.6 + - - +
1558D ARG* 3.0 55.1 - - - +
1559D THR* 2.8 33.8 + - + +
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Residues in contact with ASN1556 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1554D SER* 3.1 15.4 + - - +
1555D ILE* 1.3 85.7 - - - +
1557D GLU* 1.3 59.6 + - + +
1559D THR* 3.8 4.4 + - - -
1560D ALA* 3.0 22.3 + - - +
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Residues in contact with GLU1557 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1465D HIS* 4.9 10.0 - - - +
1467D GLY* 4.2 13.7 - - - +
1552D ALA* 4.3 6.7 - - + -
1553D GLU* 3.1 43.6 - - - +
1554D SER* 3.3 17.9 + - - +
1556D ASN* 1.3 78.3 - - + +
1558D ARG* 1.3 65.7 + - - +
1560D ALA* 3.0 19.6 - - + +
1561D TRP* 3.0 27.2 + - + +
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Residues in contact with ARG1558 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1528D LEU* 6.2 3.6 - - + +
1530D THR* 5.3 15.4 + - - +
1539D PHE* 5.0 13.1 - - + -
1552D ALA* 3.8 18.5 - - + +
1554D SER 2.9 13.0 + - - +
1555D ILE* 3.0 64.0 - - - +
1557D GLU* 1.3 76.3 - - - +
1559D THR* 1.3 79.7 + - + +
1560D ALA 2.9 9.8 + - - -
1561D TRP* 3.3 7.8 + - - +
1562D VAL* 3.2 21.1 + - - +
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Residues in contact with THR1559 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1528D LEU* 4.7 16.4 - - + -
1555D ILE* 2.8 26.9 + - + +
1556D ASN* 3.8 6.2 + - - -
1558D ARG* 1.3 93.9 - - + +
1560D ALA* 1.3 57.5 + - - +
1562D VAL* 3.9 8.8 - - - +
1563D GLN* 3.1 29.1 + - - +
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Residues in contact with ALA1560 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1465D HIS* 4.6 17.3 - - + +
1556D ASN 3.0 17.3 - - - +
1557D GLU* 3.0 19.0 - - + +
1558D ARG 2.9 1.8 - - - -
1559D THR* 1.3 79.0 + - - +
1561D TRP* 1.3 61.3 + - - +
1563D GLN* 3.3 4.8 + - - +
1564D LYS* 3.0 35.7 + - - +
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Residues in contact with TRP1561 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1465D HIS* 3.4 27.3 - + - -
1466D SER* 3.6 7.2 - - - -
1467D GLY* 3.3 30.8 + - - -
1468D LYS 4.6 1.3 - - - -
1469D LEU* 4.4 34.5 - - + +
1480D GLY* 3.3 29.4 - - - -
1482D LEU* 4.2 16.6 - - + -
1487D LEU* 3.9 26.2 - - + -
1539D PHE* 4.1 18.8 - + + -
1552D ALA* 5.1 1.7 - - + +
1557D GLU* 3.0 37.6 + - + +
1558D ARG* 4.1 5.2 - - - +
1560D ALA* 1.3 75.7 - - + +
1562D VAL* 1.3 58.0 + - - +
1564D LYS* 4.8 4.5 - - - -
1565D ILE* 2.7 55.7 + - + +
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Residues in contact with VAL1562 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1526D VAL* 3.6 25.1 - - + +
1528D LEU* 4.4 30.3 - - + -
1539D PHE* 3.5 28.3 - - + -
1558D ARG* 3.2 20.0 - - + +
1559D THR* 3.9 8.3 - - - +
1560D ALA 3.2 0.2 - - - -
1561D TRP* 1.3 76.4 - - - +
1563D GLN* 1.3 64.6 + - - +
1565D ILE* 4.2 0.2 - - - +
1566D LYS* 3.0 37.1 + - + +
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Residues in contact with GLN1563 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1559D THR 3.1 18.1 + - - +
1560D ALA* 3.4 7.6 - - - +
1562D VAL* 1.3 80.8 - - - +
1564D LYS* 1.3 63.2 - - + +
1566D LYS* 3.8 3.7 - - - +
1567D ALA* 3.0 40.6 + - - +
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Residues in contact with LYS1564 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1464D LEU* 3.4 22.1 + - + +
1465D HIS* 3.0 45.1 - - + -
1482D LEU* 3.9 15.7 - - + -
1560D ALA* 3.0 19.5 + - - +
1561D TRP* 4.0 2.2 - - - +
1563D GLN* 1.3 81.0 - - + +
1565D ILE* 1.3 61.1 + - - +
1567D ALA* 3.8 3.9 - - - +
1568D ALA* 2.8 34.7 + - - +
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Residues in contact with ILE1565 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1482D LEU* 3.9 24.2 - - + -
1487D LEU* 4.4 18.8 - - + -
1521D LEU* 4.3 9.8 - - + +
1524D VAL* 4.6 19.1 - - + -
1526D VAL* 3.3 26.7 - - + -
1539D PHE* 3.7 28.5 - - + -
1541D ILE* 4.7 2.7 - - + -
1561D TRP* 2.7 44.2 + - + +
1562D VAL 4.2 0.2 - - - +
1564D LYS* 1.3 71.5 - - - +
1566D LYS* 1.3 58.7 + - - +
1568D ALA* 4.0 2.1 - - - +
1569D SER* 2.8 33.7 + - - -
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Residues in contact with LYS1566 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1526D VAL* 4.9 16.1 - - + +
1562D VAL* 3.0 27.7 + - + +
1563D GLN* 3.8 3.8 - - - +
1565D ILE* 1.3 75.5 - - - +
1567D ALA* 1.3 65.6 + - - +
1569D SER* 3.6 4.6 - - - -
1570D GLU* 2.9 57.6 + - + +
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Residues in contact with ALA1567 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1563D GLN* 3.0 30.6 + - - +
1564D LYS* 3.8 5.2 - - - +
1566D LYS* 1.3 77.9 - - - +
1568D ALA* 1.3 63.1 - - - +
1570D GLU* 3.3 9.4 + - - +
1571D LEU* 3.0 26.1 + - - +
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Residues in contact with ALA1568 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1458D LEU* 5.6 0.2 - - - +
1464D LEU* 3.6 25.8 - - + -
1482D LEU* 5.1 0.2 - - + -
1484D ASN* 4.4 8.7 - - + +
1521D LEU* 3.4 23.3 - - + -
1564D LYS 2.8 21.5 + - - +
1565D ILE* 4.0 0.4 - - - +
1567D ALA* 1.3 73.3 - - - +
1569D SER* 1.3 63.1 + - - +
1571D LEU* 3.4 9.2 + - - +
1572D TYR* 3.0 22.9 + - - +
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Residues in contact with SER1569 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1521D LEU* 2.4 41.6 + - - +
1524D VAL* 3.4 17.8 + - - +
1565D ILE* 2.8 22.4 + - - -
1566D LYS* 3.6 6.5 - - - -
1568D ALA* 1.3 77.7 - - - +
1570D GLU* 1.3 58.0 + - - +
1572D TYR* 3.1 5.5 + - - +
1573D ILE* 2.9 37.3 + - - +
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Residues in contact with GLU1570 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1566D LYS* 2.9 53.7 + - + +
1567D ALA* 3.8 6.8 - - - +
1569D SER* 1.3 75.1 - - - +
1571D LEU* 1.3 58.5 + - - +
1573D ILE* 3.1 20.2 + - + +
1574D GLU* 2.9 38.1 + - + +
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Residues in contact with LEU1571 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1458D LEU* 5.1 2.7 - - + -
1567D ALA 3.0 17.8 + - - +
1568D ALA* 3.7 8.3 - - - +
1570D GLU* 1.3 76.7 - - - +
1572D TYR* 1.3 57.3 + - - +
1574D GLU* 3.2 17.3 + - + +
1575D THR* 2.7 47.6 + - - +
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Residues in contact with TYR1572 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1456D ASN* 4.8 11.1 - - - +
1457D CYS* 3.7 26.2 - - - -
1458D LEU* 3.7 33.2 - - + -
1484D ASN 4.1 0.4 - - - +
1485D ASP* 3.6 30.7 - - + +
1520D PHE* 4.5 9.3 - - + -
1521D LEU* 3.9 10.1 - - + -
1522D ASN* 3.5 52.6 + - + +
1568D ALA 3.0 13.4 + - - +
1569D SER* 3.2 11.2 - - - +
1571D LEU* 1.3 76.4 - - - +
1573D ILE* 1.3 59.7 + - - +
1575D THR* 3.4 1.2 + - - -
1576D GLU* 2.9 34.1 + - + +
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Residues in contact with ILE1573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1521D LEU 5.0 3.8 - - - +
1522D ASN* 5.1 10.5 - - - +
1524D VAL 6.1 0.4 - - - +
1569D SER* 2.9 25.0 + - - +
1570D GLU* 3.2 29.6 - - + +
1572D TYR* 1.3 75.6 - - - +
1574D GLU* 1.3 67.8 + - + +
1576D GLU* 2.9 12.8 + - - +
1577D LYS* 2.8 35.4 + - + +
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Residues in contact with GLU1574 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1570D GLU* 2.9 16.7 + - + +
1571D LEU* 3.2 32.0 + - + +
1573D ILE* 1.3 77.7 - - + +
1575D THR* 1.3 58.0 + - - +
1577D LYS* 2.8 35.5 + - - +
1578D LYS* 3.8 7.1 + - - +
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Residues in contact with THR1575 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1457D CYS* 3.2 30.0 - - - +
1458D LEU* 3.7 16.8 - - + +
1571D LEU* 2.7 36.4 + - - +
1572D TYR 3.8 0.7 - - - -
1573D ILE 3.2 0.2 - - - -
1574D GLU* 1.3 76.8 - - - +
1576D GLU* 1.3 59.5 + - - +
1578D LYS* 3.7 20.6 + - + +
1579D LYS* 4.4 5.0 - - - +
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Residues in contact with GLU1576 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1457D CYS* 4.8 6.4 - - - -
1522D ASN* 3.5 38.4 + - - +
1572D TYR* 2.9 31.4 + - + +
1573D ILE* 2.9 8.1 + - - +
1575D THR* 1.3 75.3 - - - +
1577D LYS* 1.3 53.6 + - + +
1578D LYS 2.7 17.3 + - - -
1579D LYS* 3.2 32.4 + - + +
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Residues in contact with LYS1577 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1573D ILE* 2.8 26.5 + - + +
1574D GLU* 2.8 14.7 + - - +
1576D GLU* 1.3 73.7 - - + +
1578D LYS* 1.3 63.9 + - + +
1579D 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