Contacts of the strand formed by residues 1733 - 1736 (chain A) in PDB entry 4W8F
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 LYS1733 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1657A THR* 3.4 11.2 - - + +
1728A TRP* 3.3 58.7 + - + +
1729A ALA* 3.9 15.2 + - - +
1731A VAL 2.9 28.8 + - - +
1732A GLN* 1.3 76.7 - - - +
1734A PHE* 1.3 64.1 - - - +
1735A TYR* 3.4 25.5 - - + +
1749A ILE* 3.4 6.4 - - - +
1750A SER* 2.9 61.9 + - - +
1751A GLN* 3.9 2.4 - - - +
1752A SER 4.5 1.2 - - - +
1753A GLY 5.5 0.8 - - - +
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Residues in contact with PHE1734 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1650A LEU* 3.7 11.9 - - + -
1653A GLN* 3.1 51.6 - - + -
1654A VAL* 3.2 44.6 - - + +
1656A TRP* 5.2 4.5 - + - -
1657A THR* 2.9 24.0 + - - +
1704A GLU* 5.4 0.2 - - - -
1708A PHE* 6.4 0.2 - + - -
1732A GLN* 3.7 42.8 - - + -
1733A LYS* 1.3 76.0 - - - +
1735A TYR* 1.3 60.9 + - - +
1747A VAL* 5.8 0.7 - - + -
1748A PHE 4.0 2.9 - - - +
1749A ILE* 3.6 20.9 - - + -
1771A TYR* 5.3 2.0 - - - -
1812A ASN* 3.5 26.0 - - - -
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Residues in contact with TYR1735 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1654A VAL* 4.4 3.4 - - - -
1657A THR* 3.8 14.6 - - + -
1658A GLU* 6.2 0.4 - - - -
1661A GLU* 2.6 34.5 + - + +
1728A TRP* 4.4 0.3 + - - -
1733A LYS* 3.4 40.3 - - + +
1734A PHE* 1.3 76.3 - - - +
1736A GLN* 1.3 62.2 + - - +
1747A VAL* 3.7 5.5 - - - +
1748A PHE* 3.0 64.9 + + + +
1750A SER* 3.6 26.7 - - - -
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Residues in contact with GLN1736 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1620A PHE* 5.3 3.0 - - - -
1623A PHE* 3.4 26.9 - - - -
1624A ARG* 5.2 7.1 - - - +
1627A LEU* 3.6 17.3 - - - +
1631A LYS* 5.3 5.5 + - - -
1654A VAL* 4.0 17.6 - - + +
1735A TYR* 1.3 76.0 - - - +
1737A LYS* 1.3 72.5 + - - +
1738A ASN* 3.4 25.1 + - - +
1746A SER* 3.7 18.0 + - - +
1747A VAL* 4.4 9.0 - - + +
1748A PHE* 4.6 2.7 - - - -
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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