Contacts of the helix formed by residues 1544 - 1566 (chain B) in PDB entry 5DKD
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 SER1544 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1540B ASN* 3.8 4.0 - - - +
1541B LEU* 2.7 32.3 + - - +
1542B GLU 3.4 0.4 + - - -
1543B GLY* 1.3 80.7 + - - +
1545B LEU* 1.3 65.6 + - - +
1546B ILE* 3.4 14.7 - - - +
1547B TYR* 3.2 17.2 + - - +
1548B GLU* 3.2 21.0 + - - +
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Residues in contact with LEU1545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1479B ARG* 3.5 38.1 - - - +
1543B GLY 4.1 0.6 + - - -
1544B SER* 1.3 73.9 - - - +
1546B ILE* 1.3 57.6 + - - +
1548B GLU* 3.0 8.8 + - + -
1549B ASP* 2.8 38.6 + - - +
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Residues in contact with ILE1546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1484B VAL* 3.6 27.8 - - + -
1485B PHE* 3.5 20.5 - - + -
1536B ALA* 5.0 0.7 - - + -
1540B ASN* 3.3 30.5 - - + +
1544B SER* 3.4 13.9 - - - +
1545B LEU* 1.3 77.9 - - - +
1547B TYR* 1.3 72.1 + - - +
1549B ASP* 3.2 9.2 + - - -
1550B SER* 3.1 18.7 + - - -
1605B 5BW 3.4 46.7 - - + +
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Residues in contact with TYR1547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1536B ALA 4.9 2.9 - - - -
1537B GLN* 3.3 42.4 + - + +
1540B ASN* 3.5 23.3 - - + -
1541B LEU 3.3 9.0 - - - +
1542B GLU* 3.6 46.7 + - + -
1543B GLY 4.5 1.8 - - - -
1544B SER* 3.2 19.9 + - - +
1546B ILE* 1.3 83.6 - - - +
1548B GLU* 1.3 72.5 + - - +
1550B SER* 2.6 26.6 + - - -
1551B ILE* 3.1 22.9 + - + +
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Residues in contact with GLU1548 (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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1543B GLY* 5.2 4.5 + - - -
1544B SER 3.2 10.1 + - - +
1545B LEU* 3.0 14.5 + - + +
1547B TYR* 1.3 92.4 - - - +
1549B ASP* 1.3 69.1 + - - +
1551B ILE* 3.0 24.6 + - - +
1552B VAL* 3.0 31.7 + - + +
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Residues in contact with ASP1549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1479B ARG* 2.6 45.2 + - - -
1481B LEU* 4.0 21.7 - - + +
1484B VAL* 5.7 3.0 - - + +
1485B PHE* 3.9 17.5 - - + -
1545B LEU* 2.8 29.8 + - - +
1546B ILE* 3.6 8.5 - - - +
1548B GLU* 1.3 76.7 - - - +
1550B SER* 1.3 55.6 + - - +
1552B VAL* 3.4 7.0 + - - +
1553B LEU* 3.0 31.9 + - - +
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Residues in contact with SER1550 (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 PHE* 3.9 11.3 - - - -
1533B CYS* 3.3 32.2 - - - -
1536B ALA* 3.7 26.8 - - - +
1537B GLN* 2.9 24.9 + - - +
1546B ILE 3.1 9.2 + - - -
1547B TYR* 2.6 20.5 + - - -
1549B ASP* 1.3 74.4 - - - +
1551B ILE* 1.3 64.2 + - - +
1553B LEU* 3.4 2.3 + - - -
1554B GLN* 3.3 9.2 + - - +
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Residues in contact with ILE1551 (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 GLN* 3.4 29.4 - - + +
1547B TYR* 3.1 31.8 + - + +
1548B GLU* 3.0 27.7 + - - +
1550B SER* 1.3 80.7 + - - +
1552B VAL* 1.3 65.9 + - + +
1554B GLN* 3.1 36.7 + - - +
1555B SER* 3.9 3.1 + - - -
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Residues in contact with VAL1552 (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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1472B TYR* 5.0 2.9 - - + +
1481B LEU* 3.4 29.6 - - + -
1548B GLU* 3.0 28.7 + - + +
1549B ASP* 3.7 6.5 - - - +
1551B ILE* 1.3 78.5 - - + +
1553B LEU* 1.3 62.5 + - - +
1555B SER* 3.1 19.9 + - - +
1556B VAL* 3.1 18.3 + - + +
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Residues in contact with LEU1553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1469B VAL* 3.9 35.9 - - + +
1472B TYR* 5.1 1.8 - - + -
1481B LEU* 4.0 29.2 - - + +
1482B SER* 4.0 8.1 - - - +
1485B PHE* 3.6 33.0 - - + -
1507B PHE* 4.7 9.6 - - + -
1529B VAL* 5.1 1.9 - - + +
1532B LEU* 6.2 0.4 - - + -
1533B CYS* 4.2 12.6 - - - -
1549B ASP 3.0 20.5 + - - +
1550B SER* 3.8 6.7 - - - +
1551B ILE 3.3 0.4 - - - -
1552B VAL* 1.3 72.9 - - - +
1554B GLN* 1.3 65.2 + - - +
1556B VAL* 3.7 14.7 - - + +
1557B PHE* 2.9 24.8 + - - +
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Residues in contact with GLN1554 (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 VAL* 5.8 0.2 - - - -
1530B MET* 3.4 39.5 - - + +
1533B CYS* 3.6 18.7 - - + +
1534B GLN* 4.7 1.6 + - - -
1537B GLN* 2.9 29.2 + - - +
1550B SER 3.3 7.8 + - - +
1551B ILE* 3.1 30.5 + - - +
1553B LEU* 1.3 78.5 - - - +
1555B SER* 1.3 59.1 + - - +
1557B PHE* 3.5 0.6 + - - +
1558B THR* 3.3 18.7 + - - +
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Residues in contact with SER1555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1551B ILE 4.4 1.4 + - - -
1552B VAL* 3.1 18.9 + - - +
1554B GLN* 1.3 77.0 - - - +
1556B VAL* 1.3 65.0 + - - +
1558B THR* 3.0 19.4 + - - -
1559B SER* 3.0 19.2 + - - -
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Residues in contact with VAL1556 (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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1469B VAL* 4.2 20.4 - - + -
1472B TYR* 3.8 57.2 - - + -
1552B VAL* 3.1 25.7 + - + +
1553B LEU* 3.7 13.2 - - + +
1555B SER* 1.3 76.3 + - - +
1557B PHE* 1.3 64.4 + - - +
1559B SER* 3.6 3.8 - - - -
1560B VAL* 2.9 34.6 + - + +
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Residues in contact with PHE1557 (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 ILE* 3.7 22.9 - - + -
1466B VAL* 5.2 2.5 - - + -
1469B VAL* 3.7 22.8 - - + +
1522B LEU* 4.7 2.0 - - + -
1525B LEU* 4.1 13.5 - - + -
1526B GLU* 3.4 56.1 - - + -
1529B VAL* 3.8 39.5 - - + -
1530B MET* 4.1 7.2 - - + -
1553B LEU 2.9 17.7 + - - +
1554B GLN 3.6 4.9 - - - +
1555B SER 3.2 0.2 - - - -
1556B VAL* 1.3 75.9 - - - +
1558B THR* 1.3 62.1 + - - +
1560B VAL* 3.8 1.4 - - - +
1561B ARG* 2.8 41.7 + - + +
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Residues in contact with THR1558 (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 GLU* 4.4 13.2 - - - +
1530B MET* 3.9 16.4 - - + -
1554B GLN 3.3 9.1 + - - +
1555B SER* 3.0 26.3 + - - -
1557B PHE* 1.3 86.2 - - + +
1559B SER* 1.3 54.9 + - - +
1561B ARG* 3.7 5.5 - - - +
1562B GLN* 3.1 44.5 + - - +
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Residues in contact with SER1559 (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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1555B SER* 3.0 19.9 + - - -
1556B VAL* 3.6 6.1 - - - -
1558B THR* 1.3 74.4 + - - +
1560B VAL* 1.3 68.1 + - - +
1562B GLN* 3.3 8.3 + - - +
1563B LYS* 3.0 24.7 + - - +
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Residues in contact with VAL1560 (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 ILE* 3.6 38.1 - - + +
1468B ALA* 3.8 21.5 - - + +
1469B VAL* 4.0 14.1 - - + +
1472B TYR* 6.0 2.0 - - + -
1556B VAL* 2.9 30.2 + - + +
1557B PHE 3.8 2.7 - - - +
1559B SER* 1.3 78.6 - - - +
1561B ARG* 1.3 66.3 + - - +
1563B LYS* 3.3 16.4 + - - +
1564B ILE* 3.0 28.8 + - + +
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Residues in contact with ARG1561 (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 ILE* 3.9 25.6 - - + +
1522B LEU* 3.6 31.7 + - + +
1523B ASN* 2.9 31.1 + - - +
1526B GLU* 2.8 36.7 + - - -
1557B PHE* 2.8 36.2 + - + +
1558B THR* 3.7 6.7 - - - +
1559B SER 3.3 0.2 - - - -
1560B VAL* 1.3 74.7 - - - +
1562B GLN* 1.3 58.4 + - + +
1564B ILE* 3.3 2.1 + - - +
1565B GLU* 2.8 62.7 + - - +
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Residues in contact with GLN1562 (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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1558B THR* 3.1 30.7 + - - +
1559B SER* 3.6 6.8 - - - +
1560B VAL 3.3 0.2 - - - -
1561B ARG* 1.3 75.7 - - + +
1563B LYS* 1.3 69.5 + - - +
1565B GLU* 3.3 20.7 + - - +
1566B LYS* 3.4 15.2 + - - +
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Residues in contact with LYS1563 (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 SER 3.0 12.2 + - - +
1560B VAL* 3.6 18.7 - - - +
1562B GLN* 1.3 80.0 - - - +
1564B ILE* 1.3 74.5 + - + +
1566B LYS* 3.1 26.3 + - + +
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Residues in contact with ILE1564 (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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1461B LYS* 4.2 30.5 - - + +
1464B LYS* 3.5 42.0 - - + +
1465B ILE* 3.9 29.2 - - + -
1560B VAL* 3.0 25.2 + - + +
1561B ARG 3.7 3.6 - - - +
1563B LYS* 1.3 92.1 - - + +
1565B GLU* 1.3 62.5 + - - +
1566B LYS 3.0 9.9 + - - +
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Residues in contact with GLU1565 (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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1461B LYS* 5.1 7.6 - - + +
1465B ILE* 5.8 0.2 - - + -
1522B LEU* 3.6 22.0 - - + +
1561B ARG* 2.8 61.4 + - - +
1562B GLN* 3.7 13.5 - - - +
1563B LYS 3.3 0.2 - - - -
1564B ILE* 1.3 74.4 - - - +
1566B LYS* 1.3 61.7 + - - +
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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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1562B GLN 3.4 11.0 + - - +
1563B LYS* 3.3 18.1 - - + +
1564B ILE 3.0 10.0 + - - +
1565B GLU* 1.3 82.2 - - - +
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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
------------------------------------------------------------
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