Contacts of the helix formed by residues 1760 - 1772 (chain B) in PDB entry 3AU5
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 VAL1760 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1681B CYS 5.8 4.0 - - - +
1682B ARG* 4.4 11.4 - - - -
1683B GLU* 5.2 1.4 + - - -
1718B SER 3.5 24.2 - - - +
1719B HIS* 3.9 19.1 - - - +
1720B THR 3.4 10.8 - - - +
1721B THR* 5.0 0.4 - - + -
1758B ARG 4.2 7.0 - - - +
1759B THR* 1.3 76.5 - - - +
1761B VAL* 1.3 67.3 + - - +
1762B ALA* 3.7 11.9 - - + +
1763B ASP* 3.2 21.5 - - + +
1764B VAL* 3.2 22.5 + - - +
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Residues in contact with VAL1761 (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 ILE* 4.4 5.6 - - + -
1716B ILE* 3.2 31.6 - - + -
1720B THR 2.8 20.5 + - - +
1722B ALA* 3.8 18.8 - - + +
1725B VAL* 3.7 28.3 - - + -
1744B LEU* 4.4 8.1 - - + -
1759B THR 3.7 0.6 + - - -
1760B VAL* 1.3 69.3 - - - +
1762B ALA* 1.3 65.9 + - - +
1764B VAL* 2.9 10.8 + - - +
1765B LEU* 2.9 20.2 + - + +
1784B PHE* 3.6 28.0 - - + -
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Residues in contact with ALA1762 (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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1682B ARG* 3.6 12.9 + - - +
1687B SER* 5.2 0.7 + - - -
1690B GLU* 3.5 34.0 - - + +
1700B MET* 4.4 1.7 - - - +
1716B ILE* 3.6 13.7 - - + +
1717B ASN 3.9 18.8 + - - +
1720B THR 4.6 0.4 + - - -
1760B VAL* 3.4 5.2 - - + +
1761B VAL* 1.3 78.5 - - - +
1763B ASP* 1.3 56.8 + - - +
1765B LEU* 3.1 9.2 - - - +
1766B ALA* 2.9 29.3 + - - +
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Residues in contact with ASP1763 (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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1681B CYS 4.6 0.3 - - - +
1682B ARG* 3.0 36.4 + - - +
1683B GLU* 2.6 44.8 + - - +
1684B PHE* 2.9 25.7 + - - +
1760B VAL* 3.2 23.4 + - + +
1762B ALA* 1.3 77.4 - - - +
1764B VAL* 1.3 65.3 + - + +
1766B ALA* 3.4 4.0 + - - +
1767B LYS* 3.1 20.4 + - - +
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Residues in contact with VAL1764 (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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1683B GLU* 6.5 0.2 - - - -
1746B GLU* 4.4 11.7 - - - +
1755B ILE* 4.5 18.6 - - + -
1759B THR* 3.5 21.8 - - + -
1760B VAL 3.4 15.5 - - - +
1761B VAL* 2.9 8.6 + - - +
1763B ASP* 1.3 73.2 - - + +
1765B LEU* 1.3 66.8 + - - +
1767B LYS* 3.2 12.3 - - + +
1768B PHE* 3.0 37.7 + - + -
1784B PHE* 3.5 24.2 - - + -
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Residues in contact with LEU1765 (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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1687B SER* 4.8 7.4 - - - +
1689B ASP* 5.6 2.0 - - + +
1700B MET* 3.2 33.7 - - + -
1701B THR 4.9 1.3 - - - +
1702B SER* 3.4 25.4 - - - +
1716B ILE* 4.4 12.3 - - + -
1761B VAL 2.9 8.8 + - - +
1762B ALA 3.1 9.6 - - - +
1764B VAL* 1.3 74.6 - - - +
1766B ALA* 1.3 61.0 + - - +
1768B PHE* 2.8 33.8 + - + +
1769B GLU* 3.1 11.8 + - - +
1784B PHE* 3.3 29.2 - - + -
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Residues in contact with ALA1766 (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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1682B ARG* 4.4 3.6 - - - +
1684B PHE* 3.8 13.3 - - + -
1685B VAL 3.4 27.1 - - - +
1687B SER* 3.8 23.5 - - - +
1762B ALA 2.9 16.0 + - - +
1763B ASP 3.6 6.1 - - - +
1765B LEU* 1.3 75.0 - - - +
1767B LYS* 1.3 63.2 + - - +
1769B GLU* 3.2 5.1 + - - +
1770B LYS* 3.1 22.7 + - - +
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Residues in contact with LYS1767 (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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1683B GLU* 6.0 0.9 - - - +
1684B PHE* 3.6 41.4 - - + -
1746B GLU* 2.6 44.4 + - - +
1753B LYS* 5.0 8.9 - - - +
1763B ASP 3.1 14.3 + - - +
1764B VAL* 3.2 19.3 - - + +
1766B ALA* 1.3 77.1 - - - +
1768B PHE* 1.3 60.7 + - + +
1770B LYS* 3.9 0.9 - - - +
1771B LEU* 3.0 51.3 + - + +
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Residues in contact with PHE1768 (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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1746B GLU* 3.3 41.3 - - + -
1764B VAL* 3.0 28.1 + - + -
1765B LEU* 2.8 24.1 + - + +
1767B LYS* 1.3 79.7 - - + +
1769B GLU* 1.3 56.9 + - - +
1771B LEU* 3.3 10.0 + - + +
1772B ALA* 2.8 30.2 + - - +
1782B TRP* 3.5 38.5 - + + +
1783B LYS* 3.9 30.1 - - - -
1784B PHE* 4.1 20.0 - + - -
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Residues in contact with GLU1769 (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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1590B GLN* 3.2 27.5 + - - +
1687B SER* 3.5 11.2 - - - -
1688B ARG* 2.8 47.7 + - - +
1689B ASP* 4.6 0.7 + - - +
1765B LEU 3.1 8.8 + - - +
1766B ALA* 3.2 9.6 + - - +
1768B PHE* 1.3 75.8 - - - +
1770B LYS* 1.3 63.3 + - - +
1772B ALA* 3.3 17.8 + - - +
1773B ALA* 3.9 5.5 + - - +
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Residues in contact with LYS1770 (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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1594B GLN* 4.2 24.2 - - - +
1684B PHE* 4.2 24.2 - - + -
1766B ALA 3.1 12.6 + - - +
1767B LYS* 3.9 5.2 - - - +
1769B GLU* 1.3 75.9 + - - +
1771B LEU* 1.3 55.5 + - + +
1772B ALA 3.0 4.3 - - - -
1773B ALA* 2.7 38.4 + - - +
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Residues in contact with LEU1771 (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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1684B PHE* 6.0 1.6 - - + -
1746B GLU* 4.7 3.8 - - - +
1767B LYS* 3.0 57.7 + - + +
1768B PHE* 3.7 8.5 - - + +
1770B LYS* 1.3 76.3 - - + +
1772B ALA* 1.3 57.2 + - - +
1773B ALA 2.9 12.1 + - - +
1782B TRP* 4.6 28.0 + - + +
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Residues in contact with ALA1772 (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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1768B PHE 2.8 14.1 + - - +
1769B GLU* 3.3 16.6 - - + +
1770B LYS 2.9 0.6 + - - -
1771B LEU* 1.3 75.7 - - - +
1773B ALA* 1.3 60.2 + - + +
1782B TRP* 6.3 0.7 - - - -
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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