Contacts of the helix formed by residues 1517 - 1539 (chain B) in PDB entry 4LX0
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 ASP1517 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1512B ALA 3.0 9.6 + - - +
1515B THR* 3.4 23.4 + - - +
1516B ASN* 1.3 74.2 - - - +
1518B ASP* 1.3 57.1 + - - +
1519B LEU* 3.4 11.6 + - - +
1520B LYS* 3.0 43.8 + - + +
1521B VAL* 3.1 13.5 + - - +
1585B PHE* 4.2 1.1 - - - -
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Residues in contact with ASP1518 (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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1516B ASN 3.3 7.1 + - - +
1517B ASP* 1.3 70.7 - - - +
1519B LEU* 1.3 67.9 + - - +
1520B LYS 3.3 0.2 - - - -
1521B VAL* 3.8 7.1 - - + +
1522B HIS* 3.1 26.0 + - - +
1585B PHE* 3.5 30.9 - - + -
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Residues in contact with LEU1519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1517B ASP* 3.2 9.1 + - - +
1518B ASP* 1.3 84.2 + - - +
1520B LYS* 1.3 56.7 + - - +
1522B HIS* 4.0 3.9 - - - +
1523B SER* 2.9 33.0 + - - -
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Residues in contact with LYS1520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1472B TYR* 4.1 13.5 + - + +
1512B ALA* 3.7 17.5 - - + -
1517B ASP* 3.0 33.3 + - + +
1519B LEU* 1.3 73.1 - - - +
1521B VAL* 1.3 61.0 + - - +
1523B SER* 3.7 4.9 - - - -
1524B LEU* 2.8 35.7 + - - +
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Residues in contact with VAL1521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1509B ILE* 4.6 11.4 - - + +
1512B ALA* 3.9 17.3 - - + -
1513B ASP* 4.2 6.3 - - + +
1517B ASP 3.1 11.2 + - - +
1518B ASP* 3.8 8.7 - - + +
1519B LEU 3.4 0.2 - - - -
1520B LYS* 1.3 79.3 - - - +
1522B HIS* 1.3 64.7 + - - +
1524B LEU* 3.8 2.9 - - - +
1525B LEU* 3.1 36.9 + - + +
1585B PHE* 4.0 26.0 - - + -
1587B LEU* 3.7 32.3 - - + -
1590B TYR* 4.8 4.5 - - + -
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Residues in contact with HIS1522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1518B ASP 3.1 15.2 + - - +
1519B LEU* 4.0 4.3 - - - +
1521B VAL* 1.3 79.0 - - - +
1523B SER* 1.3 66.9 + - - +
1526B THR* 2.9 52.6 + - + +
1590B TYR* 3.0 30.8 + + - +
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Residues in contact with SER1523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1477B GLU* 2.6 35.4 + - - -
1519B LEU 2.9 22.6 + - - -
1520B LYS* 3.7 3.8 - - - -
1522B HIS* 1.3 81.7 - - - +
1524B LEU* 1.3 63.2 - - - +
1526B THR* 4.0 1.4 - - - -
1527B SER* 2.9 28.1 + - - -
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Residues in contact with LEU1524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1472B TYR* 3.5 21.8 - - + +
1477B GLU* 3.7 8.5 + - + +
1480B LEU* 4.0 20.9 - - + -
1481B ILE* 4.2 9.4 - - + -
1505B LEU* 4.5 11.0 - - + +
1508B CYS* 3.5 31.6 - - + -
1509B ILE* 3.9 24.2 - - + +
1512B ALA* 5.7 2.7 - - + -
1520B LYS 2.8 22.7 + - - +
1521B VAL* 3.8 3.6 - - - +
1523B SER* 1.3 74.2 + - - +
1525B LEU* 1.3 53.6 + - - +
1527B SER* 3.5 2.1 - - - -
1528B THR* 2.8 49.3 + - - +
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Residues in contact with LEU1525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1509B ILE* 3.8 32.3 - - + -
1521B VAL* 3.1 30.8 + - + +
1524B LEU* 1.3 75.8 - - + +
1526B THR* 1.3 67.3 + - - +
1527B SER 3.0 1.6 - - - -
1528B THR* 2.9 8.1 + - - -
1529B ILE* 2.8 35.5 + - + +
1556B LEU* 4.6 9.9 - - + -
1560B LEU* 4.4 13.7 - - + -
1587B LEU* 4.4 8.5 - - + -
1590B TYR* 3.7 41.5 - - + -
1594B LEU* 4.6 12.6 - - + -
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Residues in contact with THR1526 (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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1522B HIS* 2.9 49.7 + - + +
1523B SER* 4.1 2.0 - - - -
1525B LEU* 1.3 74.2 - - - +
1527B SER* 1.3 61.2 + - - +
1529B ILE* 4.0 8.7 - - - +
1530B ASN* 3.3 36.2 + - - +
1590B TYR* 4.4 8.1 - - - -
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Residues in contact with SER1527 (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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1477B GLU* 3.9 14.9 + - - +
1481B ILE* 3.5 27.4 - - - +
1523B SER 2.9 20.4 + - - -
1524B LEU* 3.5 3.8 - - - -
1526B THR* 1.3 77.3 - - - +
1528B THR* 1.3 59.8 + - - +
1530B ASN* 3.6 6.5 + - - +
1531B GLY* 3.0 23.6 + - - -
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Residues in contact with THR1528 (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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1481B ILE* 3.3 18.7 - - - +
1485B VAL* 4.4 8.1 - - + +
1505B LEU* 3.5 41.8 - - + +
1524B LEU* 2.8 21.3 + - - +
1525B LEU* 2.9 8.9 + - + -
1527B SER* 1.3 75.2 - - - +
1529B ILE* 1.3 68.1 + - + +
1531B GLY* 3.2 2.0 + - - +
1532B ILE* 3.0 39.6 + - + +
1556B LEU* 4.9 8.7 - - + -
1594B LEU* 6.3 0.2 - - + -
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Residues in contact with ILE1529 (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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1525B LEU* 2.8 31.5 + - + +
1526B THR* 4.0 6.7 - - - +
1528B THR* 1.3 79.2 - - + +
1530B ASN* 1.3 65.4 + - - +
1532B ILE* 3.3 4.6 + - + +
1533B LYS* 3.1 43.3 + - + +
1590B TYR* 5.2 7.2 - - + +
1593B VAL* 3.6 35.2 - - + -
1594B LEU* 4.1 29.2 - - + -
1597B LEU* 4.1 20.3 - - + +
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Residues in contact with ASN1530 (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 THR* 3.3 30.3 + - - +
1527B SER* 3.9 6.2 - - - +
1528B THR 3.3 0.4 - - - -
1529B ILE* 1.3 78.6 - - - +
1531B GLY* 1.3 60.4 - - - +
1533B LYS* 3.5 17.6 + - - +
1534B LYS* 2.9 30.5 + - - +
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Residues in contact with GLY1531 (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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1481B ILE* 4.4 11.0 - - - -
1485B VAL* 3.6 13.5 - - - -
1486B THR* 4.7 6.1 + - - -
1527B SER 3.0 16.0 + - - -
1528B THR 3.2 4.2 + - - -
1530B ASN* 1.3 76.0 - - - +
1532B ILE* 1.3 57.4 + - - +
1534B LYS* 3.3 8.7 + - - +
1535B VAL* 2.9 32.2 + - - +
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Residues in contact with ILE1532 (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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1485B VAL* 3.7 17.7 - - + -
1505B LEU* 5.6 1.3 - - + -
1528B THR* 3.0 35.9 + - + +
1529B ILE* 3.7 5.6 - - + +
1530B ASN 3.2 0.2 - - - -
1531B GLY* 1.3 71.8 - - - +
1533B LYS* 1.3 69.0 + - - +
1535B VAL* 3.1 6.3 + - - +
1536B LEU* 2.9 37.9 + - + +
1549B TRP* 3.8 48.5 - - + -
1553B THR* 3.9 14.4 - - + +
1556B LEU* 6.0 2.9 - - + -
1594B LEU* 6.0 2.7 - - + -
1597B LEU* 4.2 20.4 - - + -
1601B ILE* 4.3 3.4 - - + -
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Residues in contact with LYS1533 (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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1529B ILE* 3.1 31.2 + - + +
1530B ASN* 3.7 16.5 + - - +
1532B ILE* 1.3 77.6 - - - +
1534B LYS* 1.3 63.6 + - - +
1536B LEU* 3.0 9.7 + - - +
1537B LYS* 2.9 26.7 + - - +
1593B VAL* 6.0 2.2 - - - +
1597B LEU* 3.9 28.9 - - + +
1600B GLN* 6.4 1.3 - - - -
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Residues in contact with LYS1534 (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 ARG* 5.9 2.0 - - - +
1486B THR* 4.8 22.1 - - + +
1530B ASN 2.9 18.9 + - - +
1531B GLY* 3.5 7.4 - - - +
1532B ILE 3.2 0.2 - - - -
1533B LYS* 1.3 77.3 - - - +
1535B VAL* 1.3 64.4 + - + +
1537B LYS* 3.4 30.6 - - + +
1538B LYS* 3.2 27.4 + - + +
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Residues in contact with VAL1535 (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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1485B VAL* 4.0 10.5 - - + +
1486B THR* 3.7 38.6 - - + +
1489B LYS* 5.8 0.2 - - - +
1531B GLY 2.9 19.2 + - - +
1532B ILE* 3.1 8.0 + - - +
1534B LYS* 1.3 77.5 - - + +
1536B LEU* 1.3 59.3 + - - +
1538B LYS* 3.4 3.7 + - - +
1539B HIS* 2.9 36.4 + - + +
1545B MET* 3.7 38.1 - - + -
1549B TRP* 4.0 11.2 - - + +
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Residues in contact with LEU1536 (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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1532B ILE* 2.9 28.6 + - + +
1533B LYS* 3.0 7.4 + - - +
1535B VAL* 1.3 78.3 - - - +
1537B LYS* 1.3 63.0 + - - +
1539B HIS 3.8 1.8 - - - +
1540B ASN* 3.1 24.8 + - - -
1545B MET* 4.2 6.5 - - + +
1546B THR* 3.9 29.2 - - - +
1549B TRP* 4.2 17.9 - - + -
1597B LEU* 5.1 2.2 - - + -
1601B ILE* 3.5 44.0 - - + -
1604B GLN* 3.3 25.0 + - - +
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Residues in contact with LYS1537 (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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1533B LYS* 2.9 10.4 + - - +
1534B LYS* 3.4 44.0 - - + +
1536B LEU* 1.3 76.6 - - - +
1538B LYS* 1.3 65.4 + - + +
1540B ASN* 2.8 31.0 + - - +
1604B GLN* 5.4 0.4 - - - -
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Residues in contact with LYS1538 (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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1489B LYS* 6.3 0.2 - - - +
1534B LYS* 3.2 19.6 + - + +
1535B VAL* 3.7 5.2 - - - +
1537B LYS* 1.3 87.0 - - + +
1539B HIS* 1.3 74.6 + - + +
1540B ASN* 3.3 7.2 + - - +
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Residues in contact with HIS1539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1489B LYS* 3.3 32.0 + - - +
1535B VAL* 2.9 27.7 + - + +
1536B LEU* 3.4 4.9 - - + -
1537B LYS 3.5 0.2 - - - -
1538B LYS* 1.3 94.9 - - + +
1540B ASN* 1.3 55.4 + - - -
1541B ASP 3.0 11.5 + - - -
1542B ASP* 3.1 43.4 + - + +
1545B MET* 4.0 25.2 - - + +
1546B THR* 3.9 2.3 + - - -
1604B GLN* 3.6 8.1 + - - -
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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) + - + + + + + -
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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