Contacts of the helix formed by residues 1523 - 1545 (chain B) 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 ASP1523 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1479B LYS* 5.2 6.4 - - - +
1518B ALA* 3.1 11.8 + - - +
1521B LEU* 4.0 18.2 - - + +
1522B ASN* 1.3 74.0 - - - +
1524B ASP* 1.3 62.6 + - - +
1525B GLN* 3.2 15.9 + - - +
1526B LYS* 3.0 39.2 + - + +
1527B VAL* 3.1 25.3 + - - +
1591B PHE* 3.8 1.8 - - - -
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Residues in contact with ASP1524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1522B ASN 3.3 9.0 + - - +
1523B ASP* 1.3 73.9 + - - +
1525B GLN* 1.3 61.6 + - - +
1527B VAL* 3.6 3.7 + - - +
1528B ARG* 3.1 59.4 + - - +
1591B PHE* 3.5 27.3 - - + -
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Residues in contact with GLN1525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1479B LYS* 4.9 12.1 - - - +
1523B ASP* 3.2 11.7 + - - +
1524B ASP* 1.3 83.8 + - - +
1526B LYS* 1.3 66.4 + - - +
1528B ARG* 3.5 28.2 + - - +
1529B SER* 3.0 36.8 + - - -
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Residues in contact with LYS1526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1477B TYR* 3.1 57.9 + - + +
1479B LYS* 3.7 32.8 - - - +
1482B GLU* 4.7 4.9 - - - +
1517B HIS* 5.6 5.3 + - - +
1518B ALA* 3.7 24.2 - - + +
1521B LEU* 5.6 9.2 - - + +
1523B ASP* 3.0 31.8 + - + +
1525B GLN* 1.3 80.4 + - - +
1527B VAL* 1.3 61.8 + - - +
1529B SER* 3.8 4.2 - - - +
1530B LEU* 2.9 31.2 + - + +
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Residues in contact with VAL1527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1515B VAL* 4.8 7.4 - - + +
1518B ALA* 3.6 24.9 - - + -
1519B ASP* 4.0 2.2 - - + +
1523B ASP 3.1 17.5 + - - +
1524B ASP* 3.8 7.9 - - - +
1526B LYS* 1.3 76.3 - - - +
1528B ARG* 1.3 64.4 + - + +
1530B LEU* 4.2 2.5 - - - +
1531B LEU* 3.2 45.6 + - + +
1591B PHE* 3.8 30.3 - - + -
1593B LEU* 3.8 21.1 - - + -
1596B TYR* 5.6 1.1 - - + -
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Residues in contact with ARG1528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1524B ASP* 3.1 44.1 + - + +
1525B GLN* 3.5 29.0 + - - +
1526B LYS 3.2 0.2 - - - -
1527B VAL* 1.3 80.0 - - + +
1529B SER* 1.3 58.4 + - - +
1531B LEU* 4.1 1.6 - - - +
1532B THR* 2.6 35.1 + - - +
1596B TYR* 3.2 27.9 + - + +
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Residues in contact with SER1529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1482B GLU* 2.4 32.9 + - - -
1525B GLN* 3.0 31.8 + - - -
1526B LYS* 3.3 4.0 + - - -
1528B ARG* 1.3 75.0 - - - +
1530B LEU* 1.3 55.9 + - - +
1532B THR* 3.3 5.6 + - - -
1533B SER* 2.7 39.8 + - - -
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Residues in contact with LEU1530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1477B TYR* 3.5 23.8 - - + +
1482B GLU* 3.5 12.5 + - + -
1485B LEU* 4.2 20.0 - - + -
1486B VAL* 6.4 2.0 - - + -
1511B LEU* 4.3 9.9 - - + +
1514B CYS* 3.8 24.0 - - + +
1515B VAL* 3.7 33.7 - - + +
1518B ALA* 5.3 4.3 - - + -
1526B LYS 2.9 18.5 + - - +
1527B VAL* 4.2 3.1 - - - +
1529B SER* 1.3 77.1 - - - +
1531B LEU* 1.3 54.2 + - + +
1533B SER* 3.2 3.5 + - - -
1534B THR* 2.6 46.8 + - - +
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Residues in contact with LEU1531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1515B VAL* 4.2 16.8 - - + -
1527B VAL* 3.2 26.5 + - + +
1528B ARG 4.1 0.2 - - - +
1530B LEU* 1.3 79.3 - - + +
1532B THR* 1.3 61.1 + - - +
1534B THR* 3.6 4.5 - - - +
1535B ILE* 3.1 34.9 + - + +
1562B PHE* 3.9 30.5 - - + -
1566B LEU* 4.9 6.5 - - + -
1593B LEU* 3.7 31.6 - - + -
1596B TYR* 3.7 45.3 - - + -
1600B LEU* 5.8 0.9 - - + -
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Residues in contact with THR1532 (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 ARG* 2.6 26.3 + - - +
1529B SER* 3.6 5.6 - - - -
1531B LEU* 1.3 75.9 - - - +
1533B SER* 1.3 63.9 + - - +
1535B ILE* 3.6 5.2 + - - +
1536B ASN* 3.1 48.9 + - - +
1596B TYR* 4.9 7.9 + - - -
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Residues in contact with SER1533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1482B GLU* 2.6 34.3 + - - +
1483B GLN* 5.9 2.8 - - - +
1486B VAL* 4.7 13.2 - - - -
1529B SER* 2.7 19.4 + - - -
1530B LEU* 3.6 6.5 - - - -
1532B THR* 1.3 73.4 - - - +
1534B THR* 1.3 55.9 + - - +
1536B ASN* 4.0 4.5 - - - +
1537B SER* 2.5 37.0 + - - -
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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
----------------------------------------------------------
1486B VAL* 5.6 0.7 - - - -
1490B ILE* 3.9 10.2 - - + +
1511B LEU* 3.7 35.3 - - + +
1530B LEU* 2.6 37.1 + - - +
1531B LEU* 3.6 8.5 - - - -
1532B THR 3.2 0.4 - - - -
1533B SER* 1.3 75.3 - - - +
1535B ILE* 1.3 67.0 + - + +
1537B SER* 3.2 3.5 + - - -
1538B ILE* 3.1 38.4 + - + +
1562B PHE* 4.4 23.8 - - + -
1600B LEU* 5.7 0.4 - - + -
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Residues in contact with ILE1535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1531B LEU* 3.1 22.5 + - + +
1532B THR* 4.2 5.2 - - - +
1534B THR* 1.3 77.0 - - + +
1536B ASN* 1.3 61.6 + - - +
1538B ILE* 3.4 7.7 + - - +
1539B LYS* 3.1 50.7 + - - +
1562B PHE* 6.1 0.9 - - + -
1596B TYR* 4.8 15.5 - - + +
1599B VAL* 3.7 34.3 - - + -
1600B LEU* 3.9 25.6 - - + -
1603B LEU* 4.1 14.1 - - + +
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Residues in contact with ASN1536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1532B THR* 3.1 38.2 + - - +
1533B SER* 4.2 4.2 - - - +
1535B ILE* 1.3 82.1 - - - +
1537B SER* 1.3 58.2 + - - +
1539B LYS* 3.6 18.9 + - - +
1540B LYS* 3.1 27.4 + - - +
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Residues in contact with SER1537 (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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1486B VAL* 3.5 16.2 - - - +
1490B ILE* 3.6 25.1 - - - -
1491B LEU* 3.4 21.9 - - - +
1533B SER* 2.5 24.6 + - - -
1534B THR 3.2 4.7 + - - -
1536B ASN* 1.3 74.5 - - - +
1538B ILE* 1.3 65.4 + - - +
1540B LYS* 3.3 1.2 + - - -
1541B VAL* 3.2 27.5 + - - +
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Residues in contact with ILE1538 (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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1490B ILE* 4.0 18.4 - - + -
1511B LEU* 5.5 2.7 - - + -
1534B THR* 3.1 29.0 + - + +
1535B ILE* 3.7 7.0 - - - +
1537B SER* 1.3 75.8 - - - +
1539B LYS* 1.3 64.3 + - - +
1541B VAL* 3.5 5.0 + - - +
1542B LEU* 3.3 39.1 + - + +
1555B TRP* 4.5 23.6 - - + -
1558B ASN 5.9 0.2 - - - -
1559B THR* 3.6 34.5 - - + +
1562B PHE* 5.9 3.4 - - + -
1600B LEU* 5.1 4.3 - - + -
1603B LEU* 4.3 19.3 - - + -
1607B ILE* 4.3 1.3 - - + -
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Residues in contact with LYS1539 (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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1535B ILE* 3.1 39.9 + - + +
1536B ASN* 3.8 17.2 + - - +
1537B SER 3.4 0.2 - - - -
1538B ILE* 1.3 77.1 - - - +
1540B LYS* 1.3 62.1 + - - +
1542B LEU* 3.6 7.2 + - - +
1543B LYS* 3.2 24.0 + - - +
1599B VAL* 5.7 4.3 - - - +
1603B LEU* 3.9 26.5 - - + -
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Residues in contact with LYS1540 (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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1491B LEU* 3.8 35.9 - - + +
1536B ASN 3.1 17.6 + - - +
1537B SER* 3.5 6.1 - - - +
1538B ILE 3.1 0.4 - - - -
1539B LYS* 1.3 75.4 - - - +
1541B VAL* 1.3 60.7 + - - +
1543B LYS* 3.2 7.3 + - + +
1544B LYS* 3.0 30.5 + - + +
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Residues in contact with VAL1541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1490B ILE* 3.5 28.3 - - + +
1491B LEU* 3.8 22.4 - - + +
1537B SER 3.2 15.6 + - - +
1538B ILE* 3.9 6.3 - - - +
1539B LYS 3.4 0.2 - - - -
1540B LYS* 1.3 75.6 - - - +
1542B LEU* 1.3 55.5 + - - +
1544B LYS* 4.7 3.8 - - - -
1545B ARG* 2.7 40.6 + - + +
1551B THR* 3.8 24.0 - - + -
1555B TRP* 3.8 19.7 - - + +
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Residues in contact with LEU1542 (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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1538B ILE* 3.3 25.4 + - + +
1539B LYS* 3.9 6.7 - - - +
1540B LYS 3.3 0.4 - - - -
1541B VAL* 1.3 77.6 - - + +
1543B LYS* 1.3 57.0 + - - +
1545B ARG 4.2 3.1 - - - -
1546B GLY* 3.2 10.0 - - - -
1551B THR* 4.4 7.6 - - + +
1552B VAL* 3.9 36.6 - - + +
1555B TRP* 4.3 14.6 - - + -
1603B LEU* 5.3 2.7 - - + -
1607B ILE* 3.6 42.4 - - + -
1610B GLN* 2.9 38.4 + - - +
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Residues in contact with LYS1543 (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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1539B LYS 3.2 18.1 + - - +
1540B LYS* 3.6 7.4 - - + +
1541B VAL 3.2 0.2 - - - -
1542B LEU* 1.3 79.0 - - - +
1544B LYS* 1.3 62.7 + - - +
1546B GLY* 4.4 3.0 + - - -
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Residues in contact with LYS1544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1540B LYS* 3.0 18.2 + - + +
1541B VAL* 3.9 3.8 - - - +
1543B LYS* 1.3 79.9 - - - +
1545B ARG* 1.3 66.2 + - + +
1546B GLY 3.1 5.2 + - - -
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Residues in contact with ARG1545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1541B VAL* 2.7 25.1 + - + +
1542B LEU* 4.0 3.5 - - - +
1544B LYS* 1.3 75.9 - - + +
1546B GLY* 1.3 60.7 + - - +
1547B ASP 3.6 1.8 - - - -
1548B ASP* 4.1 13.7 + - + -
1551B THR* 3.7 40.2 - - + +
1552B VAL* 4.4 3.5 - - - +
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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