Contacts of the helix formed by residues 1634 - 1641 (chain A) in PDB entry 2D4Q
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 LYS1634 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1594A THR* 3.8 17.7 - - - +
1595A GLY* 5.4 7.9 - - - +
1632A ARG* 3.4 39.8 + - + +
1633A PHE* 1.3 75.1 - - - +
1635A THR* 1.3 57.5 + - - +
1636A ASP* 3.4 4.3 - - + +
1637A PHE* 3.0 15.1 + - + +
1638A LEU* 2.6 33.3 + - - +
1672A HIS* 5.5 0.7 - - - -
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Residues in contact with THR1635 (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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1633A PHE 3.8 0.8 + - - -
1634A LYS* 1.3 73.6 - - - +
1636A ASP* 1.3 66.3 + - - +
1638A LEU* 3.7 4.2 - - - +
1639A SER* 3.0 30.1 + - - -
1671A TYR* 5.6 1.2 - - - -
1672A HIS* 3.4 26.8 - - + +
1675A LEU* 3.8 20.4 - - + +
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Residues in contact with ASP1636 (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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1634A LYS* 3.4 2.9 - - + +
1635A THR* 1.3 84.8 - - - +
1637A PHE* 1.3 57.1 + - - +
1639A SER* 3.7 6.7 - - - -
1640A LYS* 3.0 32.0 + - - +
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Residues in contact with PHE1637 (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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1592A PHE* 4.1 11.0 - + - -
1599A GLY* 3.0 47.3 - - - -
1600A ASP* 4.2 1.1 - - - -
1602A LEU* 4.3 9.0 - - + -
1603A ILE* 3.6 16.8 - - + -
1633A PHE* 3.8 39.7 - + + -
1634A LYS* 3.0 18.6 + - + +
1636A ASP* 1.3 74.5 - - - +
1638A LEU* 1.3 66.1 + - - +
1639A SER 3.1 1.6 - - - -
1640A LYS* 3.1 11.2 + - + +
1641A TRP* 2.9 54.8 + + - -
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Residues in contact with LEU1638 (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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701A OXN 4.9 9.6 - - + -
1633A PHE* 4.0 20.4 - - + -
1634A LYS 2.6 20.1 + - - +
1635A THR 3.7 3.1 - - - +
1637A PHE* 1.3 73.4 - - - +
1639A SER* 1.3 61.1 + - - +
1641A TRP* 3.5 9.4 + - + +
1642A PHE* 3.2 32.7 - - + -
1668A TYR* 3.2 28.9 - - + +
1672A HIS* 3.9 32.8 - - + +
1675A LEU* 4.2 16.4 - - + -
1676A LEU* 4.2 24.7 - - + -
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Residues in contact with SER1639 (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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1635A THR* 3.0 17.9 + - - -
1636A ASP* 3.7 8.3 - - - -
1638A LEU* 1.3 76.7 - - - +
1640A LYS* 1.3 65.4 + - - +
1642A PHE* 2.9 23.5 + - - +
1643A VAL* 3.7 9.0 + - - +
1675A LEU* 4.1 23.7 - - - +
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Residues in contact with LYS1640 (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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1600A ASP* 4.0 20.9 - - - +
1603A ILE* 4.2 13.7 - - + -
1636A ASP* 3.0 21.6 + - - +
1637A PHE* 3.1 12.5 + - + +
1639A SER* 1.3 77.2 - - - +
1641A TRP* 1.3 54.7 + - - +
1643A VAL* 3.2 6.0 + - + +
1644A VAL* 2.7 60.2 + - + +
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Residues in contact with TRP1641 (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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701A OXN 3.4 44.4 - + + +
1587A TYR* 5.8 0.4 - + - -
1602A LEU* 4.1 20.0 - - + -
1603A ILE* 3.6 29.0 - - + +
1606A VAL* 3.6 28.5 - - + -
1633A PHE* 3.8 20.3 - + + -
1637A PHE* 2.9 61.7 + + - -
1638A LEU* 3.7 11.9 - - + +
1639A SER 3.1 1.4 + - - -
1640A LYS* 1.3 75.4 - - - +
1642A PHE* 1.3 65.0 + - + +
1643A VAL 3.4 0.4 - - - -
1644A VAL* 4.4 4.3 - - - -
1645A PHE* 3.4 42.8 - + - -
1650A TYR* 2.8 21.8 + - - -
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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