Contacts of the helix formed by residues 1767 - 1783 (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 SER1767 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1765B ASN* 2.7 20.5 + - - -
1766B GLU* 1.3 77.3 - - - +
1768B THR* 1.3 65.5 + - - +
1770B PRO* 3.5 10.0 - - - +
1771B LYS* 3.5 30.8 - - - +
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Residues in contact with THR1768 (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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1758B GLN* 4.2 16.2 - - + +
1759B LEU* 5.0 1.9 - - - +
1762B GLN* 3.6 28.9 - - + -
1763B GLY 2.7 29.3 + - - +
1764B ILE* 3.6 2.1 - - - -
1765B ASN* 2.9 30.9 + - - +
1767B SER* 1.3 79.4 - - - +
1769B ILE* 1.3 64.2 + - - +
1771B LYS* 3.1 11.0 + - + +
1772B VAL* 3.0 28.8 + - - +
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Residues in contact with ILE1769 (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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1759B LEU* 6.3 0.2 - - - -
1764B ILE* 3.9 23.3 - - + -
1765B ASN 3.1 20.5 + - - +
1766B GLU 4.5 1.6 - - - +
1768B THR* 1.3 75.7 + - - +
1770B PRO* 1.4 64.3 - - + +
1772B VAL* 3.4 8.2 - - - +
1773B LEU* 3.1 51.4 + - + +
1796B MET* 4.7 6.5 - - - -
1800B ALA* 3.8 21.3 - - + -
1803B HIS* 3.6 31.4 - - + +
1804B TYR* 4.3 15.0 - - + +
1880B TYR* 3.9 16.2 - - - +
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Residues in contact with PRO1770 (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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1766B GLU 3.5 18.2 - - - +
1767B SER* 3.5 12.1 - - - +
1769B ILE* 1.4 96.3 - - + +
1771B LYS* 1.3 60.7 + - + +
1773B LEU* 3.8 9.2 - - + +
1774B GLN* 2.9 29.8 + - - +
1880B TYR* 5.3 4.9 - - - +
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Residues in contact with LYS1771 (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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1758B GLN* 3.8 31.3 + - - +
1767B SER* 3.5 26.2 - - - +
1768B THR* 3.1 9.3 + - + +
1770B PRO* 1.3 78.5 - - + +
1772B VAL* 1.3 57.4 + - - +
1774B GLN* 3.3 10.0 + - - +
1775B TYR* 2.9 37.7 + - + -
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Residues in contact with VAL1772 (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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1755B GLY* 3.4 28.5 - - - +
1758B GLN* 3.5 28.0 - - + -
1759B LEU* 3.9 12.1 - - + -
1768B THR* 3.0 19.7 + - - +
1769B ILE* 3.4 8.5 - - - +
1771B LYS* 1.3 72.6 - - - +
1773B LEU* 1.3 59.2 + - - +
1775B TYR* 3.5 7.4 - - + +
1776B TYR* 2.7 44.7 + - + -
1796B MET* 3.5 33.9 - - + -
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Residues in contact with LEU1773 (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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1769B ILE* 3.1 34.2 + - + +
1770B PRO* 3.8 7.2 - - + +
1772B VAL* 1.3 75.7 - - - +
1774B GLN* 1.3 54.6 + - - +
1776B TYR* 4.0 2.6 - - - +
1777B SER* 2.7 39.3 + - - -
1793B TRP* 4.0 13.1 - - + +
1796B MET* 3.7 23.1 - - + -
1797B ASN* 3.4 40.6 - - - +
1800B ALA* 5.0 1.1 - - + -
1880B TYR* 3.7 31.2 - - + -
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Residues in contact with GLN1774 (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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1751B PHE* 5.3 2.6 - - + -
1770B PRO 2.9 21.1 + - - +
1771B LYS* 3.4 8.7 - - - +
1773B LEU* 1.3 75.5 - - - +
1775B TYR* 1.3 66.0 + - + +
1777B SER* 3.1 21.9 + - - -
1778B ALA* 3.3 14.3 + - - +
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Residues in contact with TYR1775 (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* 4.5 4.4 - + - -
1718B GLN* 4.0 25.1 + - - +
1751B PHE* 3.6 37.5 - + - +
1754B LEU* 3.6 39.9 - - + -
1755B GLY* 3.8 21.5 - - - +
1758B GLN* 4.0 23.0 + - - -
1771B LYS* 2.9 27.5 + - + +
1772B VAL* 3.5 7.9 - - + +
1773B LEU 3.2 0.2 - - - -
1774B GLN* 1.3 80.0 - - + +
1776B TYR* 1.3 64.9 + - - +
1778B ALA* 3.2 6.1 + - - +
1779B ALA 3.1 17.0 + - - -
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Residues in contact with TYR1776 (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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1752B LEU* 3.6 37.2 - - + -
1755B GLY* 4.0 10.8 - - - -
1756B GLU* 3.5 13.9 + - + +
1759B LEU* 3.5 25.8 - - + +
1772B VAL* 2.7 27.6 + - + +
1773B LEU* 4.0 2.2 - - - +
1775B TYR* 1.3 70.8 - - - +
1777B SER* 1.3 65.4 + - - +
1779B ALA* 3.3 7.6 + - - +
1780B THR* 3.0 21.8 + - - -
1789B ALA 4.2 4.6 - - - +
1792B ALA* 3.3 44.5 - - + +
1793B TRP* 3.9 19.3 - - + +
1796B MET* 3.7 24.0 - - + -
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Residues in contact with SER1777 (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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1773B LEU 2.7 19.5 + - - -
1774B GLN* 3.1 20.8 + - - -
1776B TYR* 1.3 71.8 - - - +
1778B ALA* 1.3 60.5 + - - +
1780B THR* 3.0 14.5 + - - +
1781B GLU* 2.9 33.1 + - - +
1793B TRP* 3.8 22.1 - - - -
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Residues in contact with ALA1778 (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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1751B PHE* 3.5 33.2 - - + -
1774B GLN* 3.3 14.1 + - - +
1775B TYR 3.2 10.9 + - - +
1777B SER* 1.3 81.9 + - - +
1779B ALA* 1.3 56.3 + - - +
1781B GLU* 3.2 11.9 + - - +
1782B HIS* 3.0 38.2 + - + +
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Residues in contact with ALA1779 (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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1748B ALA* 3.4 37.7 - - + +
1751B PHE* 3.8 8.6 - - + +
1752B LEU* 4.1 15.0 - - + +
1775B TYR 3.1 8.4 + - - +
1776B TYR 3.5 9.0 - - - +
1777B SER 3.3 0.2 - - - -
1778B ALA* 1.3 74.3 - - - +
1780B THR* 1.3 62.4 + - - +
1782B HIS 3.2 0.5 + - - -
1783B ASP* 3.1 22.5 + - - -
1786B TRP* 4.8 0.4 - - + -
1789B ALA* 3.9 19.4 - - + +
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Residues in contact with THR1780 (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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1776B TYR 3.0 11.7 + - - -
1777B SER* 3.0 18.6 + - - +
1779B ALA* 1.3 76.1 - - - +
1781B GLU* 1.3 71.5 + - - +
1783B ASP 4.8 0.9 - - - -
1784B ARG* 3.5 27.7 + - - +
1789B ALA* 3.8 9.7 + - - +
1790B TRP* 3.2 66.0 + - + -
1793B TRP* 4.5 6.7 - - + +
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Residues in contact with GLU1781 (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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1777B SER* 2.9 20.6 + - - +
1778B ALA* 3.2 13.4 + - - +
1780B THR* 1.3 86.6 - - - +
1782B HIS* 1.3 70.3 + - + +
1783B ASP 3.5 0.3 + - - -
1784B ARG* 2.9 46.0 + - - +
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Residues in contact with HIS1782 (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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1744B HIS* 3.4 67.2 + + - +
1745B LYS* 4.1 3.6 + - - +
1747B MET* 3.5 28.1 - - + +
1748B ALA* 3.9 10.8 - - + +
1751B PHE* 3.5 25.5 - + - -
1778B ALA* 3.0 29.7 + - + +
1779B ALA 3.2 0.2 + - - -
1781B GLU* 1.3 82.9 - - + +
1783B ASP* 1.3 60.5 + - - +
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Residues in contact with ASP1783 (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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1745B LYS* 3.8 37.6 - - + +
1748B ALA* 3.8 17.5 - - + -
1779B ALA 3.1 10.9 + - - +
1780B THR 4.0 4.1 - - - +
1782B HIS* 1.3 77.5 - - - +
1784B ARG* 1.3 65.3 + - - +
1785B SER* 3.1 18.3 + - - +
1786B TRP* 3.2 41.4 + - + +
1789B ALA* 4.6 2.9 - - - +
1790B TRP* 4.8 0.5 + - - -
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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
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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