Contacts of the helix formed by residues 1709 - 1730 (chain B) in PDB entry 5WBY
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 ARG1709 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1685B LEU* 6.0 6.7 - - + -
1704B MET* 3.0 42.1 + - + +
1707B SER* 3.5 4.3 - - - -
1708B ALA* 1.3 98.1 - - - +
1710B LYS* 1.3 58.6 + - - +
1711B ILE 3.8 0.9 - - - -
1712B ASP* 4.2 21.1 - - + +
1713B ALA 3.5 7.2 + - - -
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Residues in contact with LYS1710 (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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1705B TRP* 3.2 70.5 - - + +
1707B SER 5.1 1.6 - - - -
1708B ALA 2.7 15.7 + - - +
1709B ARG* 1.3 72.1 - - - +
1711B ILE* 1.3 65.0 + - + +
1712B ASP 3.3 0.4 - - - -
1713B ALA* 3.8 2.9 - - - -
1714B PHE* 3.1 20.4 + - - +
1760B ASN* 3.3 27.1 + - - +
1761B LEU* 4.2 15.2 - - + +
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Residues in contact with ILE1711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1710B LYS* 1.3 78.9 - - + +
1712B ASP* 1.3 63.5 + - - +
1714B PHE* 3.3 8.9 + - + +
1715B GLN* 3.1 27.6 + - + +
1761B LEU* 4.0 21.8 - - + -
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Residues in contact with ASP1712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1685B LEU* 3.8 25.1 - - - +
1704B MET* 4.2 10.7 - - - +
1709B ARG* 4.2 26.2 - - + +
1710B LYS 3.3 1.0 - - - +
1711B ILE* 1.3 77.3 - - - +
1713B ALA* 1.3 59.2 + - - +
1715B GLN* 3.4 7.9 + - - +
1716B HIS* 2.9 50.8 + - - -
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Residues in contact with ALA1713 (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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1701B MET* 3.2 21.6 - - - +
1704B MET* 4.0 14.7 - - + +
1705B TRP* 3.7 28.9 - - + +
1709B ARG 3.5 18.8 + - - +
1710B LYS 3.8 5.8 - - - +
1711B ILE 3.3 0.2 - - - -
1712B ASP* 1.3 79.6 - - - +
1714B PHE* 1.3 62.7 + - - +
1716B HIS 3.3 0.3 + - - -
1717B MET 3.1 18.7 + - - -
1757B TRP* 3.6 9.0 - - + -
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Residues in contact with PHE1714 (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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1705B TRP* 4.4 2.7 - - + -
1710B LYS 3.1 16.2 + - - +
1711B ILE* 3.6 7.2 - - + +
1713B ALA* 1.3 78.1 - - - +
1715B GLN* 1.3 64.3 + - + +
1717B MET* 3.4 2.8 + - - +
1718B GLN* 3.1 54.3 + - + +
1754B LEU* 3.5 38.6 - - + -
1757B TRP* 3.8 25.0 - + + -
1758B GLN* 3.5 37.7 - - + -
1761B LEU* 3.6 22.9 - - + -
1762B GLN* 6.4 0.2 - - - -
1775B TYR* 4.5 3.4 - - - -
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Residues in contact with GLN1715 (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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1711B ILE* 3.1 20.2 + - + +
1712B ASP* 3.7 9.9 - - - +
1713B ALA 3.3 0.2 - - - -
1714B PHE* 1.3 76.9 - - + +
1716B HIS* 1.3 63.6 + - - +
1717B MET 3.4 0.5 + - - -
1718B GLN* 3.5 26.6 + - - +
1719B HIS* 3.1 55.4 + - - -
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Residues in contact with HIS1716 (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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1685B LEU 4.7 6.0 + - - -
1686B ASP 5.9 0.2 - - - -
1687B HIS 3.8 16.1 + - - -
1688B PRO* 4.1 4.4 - - + +
1689B LEU* 3.3 45.1 + - + +
1701B MET* 3.2 23.6 - - + +
1704B MET* 3.6 20.5 - - + +
1712B ASP* 2.9 43.9 + - - +
1715B GLN* 1.3 76.4 - - - +
1717B MET* 1.3 56.4 + - - +
1719B HIS* 3.7 7.1 + - - +
1720B PHE* 3.0 28.1 + - - +
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Residues in contact with MET1717 (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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1698B TYR* 3.9 22.0 - - + +
1701B MET* 3.2 28.7 - - + +
1702B LYS* 5.1 1.1 - - + +
1713B ALA 3.1 14.5 + - - +
1714B PHE 3.8 5.2 - - - +
1715B GLN 3.2 0.4 - - - -
1716B HIS* 1.3 73.7 - - - +
1718B GLN* 1.3 67.4 + - - +
1720B PHE* 3.5 3.8 - - - +
1721B VAL* 3.0 24.8 + - - +
1750B CYS* 3.7 33.0 - - + +
1753B LYS* 4.2 7.6 - - + -
1754B LEU* 3.7 25.8 - - + +
1757B TRP* 3.5 34.5 - - + -
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Residues in contact with GLN1718 (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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1714B PHE* 3.1 46.7 + - + +
1715B GLN* 3.8 31.2 + - - +
1716B HIS 3.5 0.2 - - - -
1717B MET* 1.3 79.3 - - - +
1719B HIS* 1.3 64.0 + - + +
1721B VAL* 3.6 2.9 + - - +
1722B GLN* 3.4 32.3 + - - +
1754B LEU* 3.6 21.7 - - + +
1775B TYR* 4.0 15.1 + - - +
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Residues in contact with HIS1719 (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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1715B GLN* 3.1 44.9 + - - +
1716B HIS* 4.0 6.3 - - - +
1717B MET 3.3 0.2 - - - -
1718B GLN* 1.3 79.0 - - + +
1720B PHE* 1.3 62.9 + - - +
1722B GLN* 3.5 24.1 + - - +
1723B THR* 3.0 29.0 + - - +
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Residues in contact with PHE1720 (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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1689B LEU* 5.9 1.3 - - + -
1691B THR* 4.6 9.9 - - + -
1694B PRO* 3.5 24.9 - - + -
1697B THR* 3.6 37.0 - - + -
1698B TYR* 4.4 7.6 - + + -
1701B MET* 4.0 9.9 - - - -
1716B HIS 3.0 20.3 + - - +
1717B MET* 3.2 10.7 + - - +
1719B HIS* 1.3 76.2 - - - +
1721B VAL* 1.3 59.2 + - - +
1723B THR* 3.2 5.8 + - - -
1724B MET* 2.9 63.2 + - + +
1746B LEU* 4.2 7.9 - - + -
1750B CYS* 3.7 31.4 - - - -
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Residues in contact with VAL1721 (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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1717B MET* 3.0 20.3 + - - +
1718B GLN 4.1 3.8 - - - +
1720B PHE* 1.3 75.8 - - - +
1722B GLN* 1.3 58.5 + - + +
1724B MET* 3.2 6.5 + - - +
1725B GLN* 3.0 34.9 + - - +
1747B MET* 4.6 8.0 - - + +
1750B CYS* 3.4 35.9 - - + -
1751B PHE* 3.5 41.7 - - + +
1754B LEU* 3.9 16.8 - - + -
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Residues in contact with GLN1722 (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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1718B GLN* 3.4 23.4 + - - +
1719B HIS* 3.6 27.1 + - - +
1720B PHE 3.3 0.6 - - - -
1721B VAL* 1.3 79.0 - - + +
1723B THR* 1.3 59.5 + - - +
1725B GLN* 3.3 31.3 + - - +
1726B GLN* 3.4 22.0 + - - +
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Residues in contact with THR1723 (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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1691B THR* 3.8 30.3 - - + +
1719B HIS* 3.0 15.8 + - - +
1720B PHE* 3.2 10.0 + - - -
1722B GLN* 1.3 75.6 - - - +
1724B MET* 1.3 60.7 + - - +
1726B GLN* 3.8 6.3 - - + +
1727B GLN* 2.9 29.9 + - + +
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Residues in contact with MET1724 (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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1691B THR* 3.6 20.0 - - + -
1694B PRO* 3.9 25.8 - - - -
1720B PHE* 2.9 61.1 + - + +
1721B VAL* 3.2 7.4 + - - +
1723B THR* 1.3 77.2 - - - +
1725B GLN* 1.3 59.6 + - - +
1727B GLN* 3.3 9.5 + - - +
1728B ALA* 2.8 27.5 + - - +
1743B LEU* 3.9 25.5 - - + +
1746B LEU* 4.6 4.5 - - + -
1747B MET* 3.8 26.4 - - + +
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Residues in contact with GLN1725 (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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1721B VAL* 3.0 28.2 + - - +
1722B GLN* 3.3 25.7 + - - +
1724B MET* 1.3 74.8 - - - +
1726B GLN* 1.3 63.5 - - + +
1728B ALA* 3.6 4.5 - - - +
1729B GLN* 3.1 37.0 + - - +
1747B MET* 3.7 22.2 - - + +
1751B PHE* 4.4 9.2 - - - -
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Residues in contact with GLN1726 (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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1722B GLN* 3.4 21.9 + - - +
1723B THR* 3.9 6.2 - - - +
1724B MET 3.3 0.6 - - - -
1725B GLN* 1.3 80.8 - - + +
1727B GLN* 1.3 63.9 + - - +
1728B ALA 3.2 0.9 + - - -
1729B GLN* 4.1 19.7 - - - +
1730B HIS* 3.5 35.2 + - - +
1731B ALA* 4.2 1.6 + - - +
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Residues in contact with GLN1727 (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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1691B THR* 3.3 27.5 - - - +
1694B PRO* 4.0 21.8 - - - +
1723B THR* 2.9 20.9 + - + +
1724B MET* 3.3 9.6 + - - +
1726B GLN* 1.3 75.8 - - - +
1728B ALA* 1.3 62.0 + - - +
1731B ALA* 3.4 24.1 - - + +
1732B ILE* 4.4 2.1 + - - +
1739B HIS* 4.5 10.6 + - - +
1743B LEU* 4.2 19.3 - - + +
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Residues in contact with ALA1728 (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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1724B MET 2.8 16.6 + - - +
1725B GLN* 3.6 8.5 - - - +
1726B GLN 3.2 0.2 - - - -
1727B GLN* 1.3 75.2 - - - +
1729B GLN* 1.3 68.3 + - - +
1730B HIS 3.1 0.9 + - - -
1732B ILE* 2.9 47.7 + - + +
1743B LEU* 3.9 13.7 - - + +
1744B HIS* 4.3 20.0 - - + +
1747B MET* 5.1 2.7 - - - -
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Residues in contact with GLN1729 (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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1725B GLN* 3.1 21.2 + - - +
1726B GLN* 3.7 22.2 + - - +
1728B ALA* 1.3 78.4 - - + +
1730B HIS* 1.3 94.3 + - + +
1732B ILE* 4.2 12.0 + - - +
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Residues in contact with HIS1730 (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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1726B GLN* 3.5 19.4 + - - +
1728B ALA 3.3 0.4 - - - -
1729B GLN* 1.3 108.2 + - + +
1731B ALA* 1.3 66.5 + - - +
1732B ILE 3.2 8.9 + - - +
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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