Contacts of the helix formed by residues 1664 - 1668 (chain A) in PDB entry 4ASI
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 LEU1664 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1662A PRO 4.0 0.9 + - - +
1663A PRO* 1.3 75.4 - - - +
1665A PRO* 1.3 77.9 - - + +
1666A SER* 3.2 8.5 - - - +
1667A ASP* 2.9 34.1 + - - +
1668A MET* 3.0 9.2 + - - +
1618B ASP* 5.4 7.4 - - - +
1620B LEU* 6.0 2.5 - - + -
1621B GLN* 6.0 5.6 - - + +
1624B ARG* 4.3 15.3 - - - +
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Residues in contact with PRO1665 (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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1643A ARG* 2.8 32.9 + - - -
1647A ILE* 4.2 24.9 - - + -
1663A PRO 4.1 3.1 - - - +
1664A LEU* 1.3 94.2 - - + +
1666A SER* 1.3 59.7 + - - +
1668A MET* 3.2 26.7 + - + +
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Residues in contact with SER1666 (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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1643A ARG* 3.6 16.4 + - - +
1664A LEU* 4.3 7.1 - - - +
1665A PRO* 1.3 78.0 - - - +
1667A ASP* 1.3 73.9 + - - +
1669A LEU 3.7 7.4 - - - +
1624B ARG* 5.1 1.4 + - - -
1640B GLU* 5.4 13.2 - - - -
1671B TYR* 6.1 0.9 - - - -
1689B PRO* 4.4 7.7 - - - +
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Residues in contact with ASP1667 (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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1663A PRO* 4.6 7.4 - - + +
1664A LEU* 2.9 21.5 + - - +
1666A SER* 1.3 90.6 + - - +
1668A MET* 1.3 63.5 + - - +
1669A LEU 3.4 1.6 - - - -
1704A LYS* 3.3 19.6 + - - +
1620B LEU* 3.0 24.5 - - + +
1624B ARG* 2.6 32.7 + - - -
1688B LEU* 3.3 16.3 - - - +
1689B PRO* 4.0 18.4 - - + +
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Residues in contact with MET1668 (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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1643A ARG* 4.6 3.4 - - + +
1646A LEU* 4.0 21.3 - - + -
1647A ILE* 3.9 31.0 - - + -
1650A TRP* 4.1 13.7 - - + +
1662A PRO* 4.7 5.4 - - + -
1663A PRO* 3.1 45.5 - - + +
1664A LEU 3.0 3.9 + - - +
1665A PRO* 3.2 28.9 + - + +
1667A ASP* 1.3 80.3 - - - +
1669A LEU* 1.3 61.4 + - + +
1703A PHE* 3.1 6.1 - - - +
1704A LYS* 2.8 43.9 + - - +
1688B LEU* 3.6 1.8 - - - -
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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