Contacts of the strand formed by residues 1783 - 1790 (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 LYS1783 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1705B TYR* 3.5 51.9 - - + -
1745B PHE 3.5 0.9 - - - +
1746B GLU* 4.2 0.3 - - - -
1747B TYR 2.9 35.4 + - - +
1768B PHE* 3.9 11.9 - - - -
1781B PRO* 4.0 26.1 - - + +
1782B TRP* 1.3 84.9 - - - +
1784B PHE* 1.3 63.7 + - - +
1785B TYR* 3.4 19.2 + - + -
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Residues in contact with PHE1784 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1702B SER* 4.0 12.6 - - - -
1703B THR 3.4 22.9 + - - +
1704B VAL* 4.1 11.0 - - + -
1705B TYR* 2.7 38.4 + - - -
1714B ILE* 4.7 6.5 - - + -
1744B LEU* 4.2 16.8 - - + -
1745B PHE 3.7 4.3 - - - -
1755B ILE* 4.0 19.7 - - + -
1761B VAL* 3.6 38.4 - - + -
1764B VAL* 3.5 29.4 - - + -
1765B LEU* 3.3 32.5 - - + -
1768B PHE* 4.1 9.4 - + - -
1783B LYS* 1.3 71.7 - - - +
1785B TYR* 1.3 54.9 + - - +
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Residues in contact with TYR1785 (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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1704B VAL* 4.4 0.7 - - - -
1705B TYR* 3.1 34.8 - + + +
1706B CYS* 4.1 2.0 - - - -
1707B HIS* 3.7 49.8 - + - -
1743B ALA 3.8 0.5 - - - +
1744B LEU* 3.4 9.7 - - - +
1745B PHE* 3.0 35.6 + - + +
1747B TYR* 3.5 41.7 - + + -
1783B LYS* 3.7 26.0 + - + -
1784B PHE* 1.3 80.1 - - - +
1786B PHE* 1.3 59.5 + - - +
1787B LYS* 3.9 16.2 - - + +
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Residues in contact with PHE1786 (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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1704B VAL* 3.8 18.6 - - + -
1705B TYR 2.7 10.8 + - - +
1706B CYS* 3.9 12.6 - - + +
1707B HIS* 5.0 1.9 + - - -
1726B VAL* 4.4 9.6 - - + -
1729B LEU* 3.5 32.5 - - + -
1730B ILE* 3.7 20.9 - - + -
1733B LEU* 3.8 23.3 - - + -
1735B MET* 3.9 11.2 - - + -
1742B PHE* 3.6 35.9 - + + -
1743B ALA 3.8 15.0 - - - -
1744B LEU* 4.8 1.6 - - + -
1785B TYR* 1.3 73.7 - - - +
1787B LYS* 1.3 65.3 + - - +
1806B PHE* 3.7 28.6 - + - -
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Residues in contact with LYS1787 (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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1707B HIS* 3.0 43.4 + - + +
1742B PHE* 3.4 11.6 - - - -
1743B ALA 3.2 28.4 + - - -
1745B PHE* 3.4 28.8 - - + -
1747B TYR* 3.8 16.7 - - - -
1752B ASP* 2.9 31.3 + - - +
1785B TYR* 3.9 15.1 - - + +
1786B PHE* 1.3 79.6 - - - +
1788B LEU* 1.3 67.0 + - - +
1806B PHE* 5.0 4.3 - - + -
1810B GLN* 3.2 26.0 - - + +
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Residues in contact with LEU1788 (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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1740B ASN* 3.4 23.3 - - + +
1741B MET 3.8 3.6 - - - +
1742B PHE* 3.2 43.9 - - + -
1745B PHE* 3.8 7.4 - - - -
1787B LYS* 1.3 72.1 - - - +
1789B TYR* 1.3 63.0 + - - +
1790B CYS 3.2 32.1 - - - +
1791B PHE* 3.7 29.9 - - + -
1803B GLU* 4.8 1.1 - - + +
1806B PHE* 5.2 3.8 - - + -
1807B MET* 4.6 15.7 - - + +
1810B GLN* 2.9 38.0 + - - +
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Residues in contact with TYR1789 (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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1741B MET* 2.5 23.2 + - + +
1742B PHE 4.4 0.4 - - - -
1743B ALA* 4.3 18.2 - - + -
1745B PHE* 3.3 28.0 - + + -
1754B ALA* 3.4 31.8 - - + +
1787B LYS 3.3 1.0 + - - -
1788B LEU* 1.3 75.7 - - - +
1790B CYS* 1.3 67.9 + - - +
1791B PHE* 4.2 4.6 + - - -
1956B THR* 4.5 7.1 + - - -
2028B ASP* 4.2 2.9 + - - +
2031B LYS* 3.6 10.4 - - + +
2032B LEU* 3.3 59.7 + - + +
2035B ALA* 4.3 15.5 - - + -
2036B TYR* 4.1 4.0 + - - -
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Residues in contact with CYS1790 (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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1740B ASN* 3.0 26.2 - - - +
1741B MET* 3.0 31.6 + - + -
1788B LEU* 3.2 3.0 - - - +
1789B TYR* 1.3 93.4 - - - +
1791B PHE* 1.3 60.0 + - - +
1792B LEU* 3.3 9.1 + - + -
2032B LEU* 4.1 8.3 - - - -
2035B ALA* 3.7 32.1 - - - -
2036B TYR* 3.8 20.6 - - + -
2039B MET* 5.2 2.2 - - - -
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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
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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