Contacts of the strand formed by residues 1710 - 1716 (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 GLY1710 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1705B TYR* 3.5 6.8 - - - +
1706B CYS* 3.0 44.3 + - - +
1707B HIS 4.5 0.4 + - - -
1708B GLY 3.2 4.6 + - - -
1709B GLY* 1.3 81.6 - - - +
1711B SER* 1.3 64.1 + - - -
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Residues in contact with SER1711 (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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1703B THR* 3.9 10.4 - - - +
1704B VAL 3.3 9.4 - - - -
1705B TYR* 3.8 24.4 - - - +
1706B CYS* 4.3 3.2 - - - +
1709B GLY 3.9 3.2 + - - -
1710B GLY* 1.3 75.7 - - - -
1712B CYS* 1.3 61.3 + - - +
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Residues in contact with CYS1712 (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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1703B THR* 3.2 9.5 - - - +
1704B VAL* 2.6 49.9 + - + +
1711B SER* 1.3 76.8 - - - +
1713B LYS* 1.3 81.8 + - - +
1714B ILE* 4.8 0.7 - - - -
1729B LEU* 4.1 22.4 - - + -
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Residues in contact with LYS1713 (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 THR* 4.0 27.7 - - - +
1702B SER 3.5 9.6 - - - +
1703B THR* 4.7 3.4 - - - +
1712B CYS* 1.3 89.6 - - - +
1714B ILE* 1.3 69.3 + - - +
1715B THR* 5.4 2.4 + - - +
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Residues in contact with ILE1714 (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 THR* 3.1 10.4 - - - -
1702B SER* 3.0 56.4 + - - +
1704B VAL* 3.5 34.5 - - + -
1712B CYS* 4.7 0.9 - - - +
1713B LYS* 1.3 82.0 - - - +
1715B THR* 1.3 62.0 + - - +
1716B ILE* 3.9 23.5 + - + -
1725B VAL* 4.3 20.4 - - + -
1728B LYS* 6.2 2.0 - - - +
1729B LEU* 4.6 12.3 - - + -
1744B LEU* 5.8 0.7 - - + -
1761B VAL* 4.4 12.1 - - + -
1784B PHE* 4.7 4.0 - - + -
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Residues in contact with THR1715 (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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1699B GLU* 2.9 41.8 - - + +
1700B MET 3.5 5.8 - - - +
1701B THR* 4.7 10.6 - - + +
1713B LYS* 5.9 2.3 - - - +
1714B ILE* 1.3 74.0 - - - +
1716B ILE* 1.3 67.1 + - - +
1720B THR* 4.7 1.6 + - - -
1728B LYS* 4.1 17.3 + - - +
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Residues in contact with ILE1716 (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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1699B GLU* 3.4 7.1 - - - +
1700B MET* 2.8 62.3 + - + +
1701B THR* 5.5 1.1 - - - -
1702B SER* 5.2 1.8 - - - -
1714B ILE* 3.9 26.2 - - + +
1715B THR* 1.3 81.0 - - - +
1717B ASN* 1.3 60.6 + - - +
1720B THR* 3.6 27.4 - - + +
1725B VAL* 4.1 6.3 - - + -
1761B VAL* 3.2 31.0 - - + -
1762B ALA* 3.6 23.6 - - + +
1765B LEU* 4.4 8.7 - - + -
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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