Contacts of the strand formed by residues 1730 - 1736 (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 THR1730 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1723A LEU* 3.5 5.2 - - - -
1724A LYS* 2.7 54.3 + - + +
1728A LYS* 3.9 7.1 + - - +
1729A ASP* 1.3 76.5 + - - +
1731A LYS* 1.3 74.4 + - - +
1732A VAL* 3.4 10.8 + - + -
1745A SER* 4.5 12.1 - - - -
1747A GLU* 4.1 11.0 - - + +
1749A THR* 6.6 0.2 - - + -
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Residues in contact with LYS1731 (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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1722A ALA 3.7 7.0 - - - +
1723A LEU* 3.8 18.6 - - + -
1730A THR* 1.3 77.2 - - - +
1732A VAL* 1.3 56.9 + - - +
1745A SER* 3.6 1.4 - - - -
1746A ALA* 2.7 43.9 + - + -
1747A GLU* 3.3 30.9 + - + +
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Residues in contact with VAL1732 (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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1720A HIS 3.6 5.5 - - - +
1721A ASN* 4.2 0.2 - - - -
1722A ALA* 2.9 50.9 + - + +
1724A LYS* 4.1 17.7 - - + +
1730A THR* 3.8 19.5 - - + +
1731A LYS* 1.3 80.3 - - - +
1733A SER* 1.3 62.0 + - - +
1734A ILE* 4.4 3.4 - - + -
1743A VAL* 3.8 30.7 - - + -
1744A THR 3.3 13.5 - - - +
1745A SER* 4.1 6.1 - - - -
1746A ALA* 4.0 5.8 - - - +
1791A PHE* 4.2 9.0 - - + -
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Residues in contact with SER1733 (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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1718A VAL* 4.6 3.4 - - - -
1719A PHE 3.3 12.6 - - - -
1720A HIS* 3.9 27.9 + - - -
1732A VAL* 1.3 76.0 - - - +
1734A ILE* 1.3 60.4 + - - +
1735A LYS* 3.7 22.0 + - - +
1742A GLN 3.7 2.8 - - - +
1743A VAL* 3.7 2.4 - - - -
1744A THR* 3.0 38.1 + - - +
1746A ALA* 5.0 2.2 - - - +
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Residues in contact with ILE1734 (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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1718A VAL* 3.6 0.7 - - - -
1719A PHE* 2.7 49.8 + - + +
1722A ALA* 3.5 26.0 - - + -
1732A VAL* 4.4 7.2 - - + -
1733A SER* 1.3 74.1 - - - +
1735A LYS* 1.3 61.3 + - - +
1736A VAL* 4.4 7.9 - - + -
1741A VAL* 4.4 20.2 - - + -
1742A GLN 3.7 2.7 - - - -
1743A VAL* 4.7 5.6 - - + -
1778A PHE* 3.9 17.3 - - + -
1791A PHE* 3.8 34.8 - - + -
1793A HIS* 5.6 0.2 - - + -
1799A ILE* 4.2 25.1 - - + -
1803A ILE* 5.0 0.4 - - + -
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Residues in contact with LYS1735 (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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1713A GLU* 5.8 2.6 + - - +
1716A LEU* 4.3 28.7 - - + -
1717A LYS 3.4 4.5 - - - +
1718A VAL* 3.9 27.8 - - + -
1720A HIS* 5.8 1.3 - - - -
1733A SER* 3.7 19.5 - - - +
1734A ILE* 1.3 75.4 - - - +
1736A VAL* 1.3 62.6 + - - +
1737A GLY 4.1 0.2 - - - -
1740A ALA 3.9 0.7 - - - +
1741A VAL* 3.3 5.7 - - - +
1742A GLN* 2.8 57.1 + - + +
1744A THR* 3.4 28.2 + - - +
1759A ASN* 6.0 0.4 - - - -
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Residues in contact with VAL1736 (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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1715A ASP 4.1 1.2 - - - +
1716A LEU* 3.7 2.1 - - - -
1717A LYS* 2.8 42.6 + - + +
1719A PHE* 4.4 13.0 - - + -
1734A ILE* 4.4 15.0 - - + -
1735A LYS* 1.3 76.7 - - - +
1737A GLY* 1.3 68.9 + - - +
1740A ALA 3.8 1.8 - - - -
1741A VAL* 4.2 9.2 - - + +
1799A ILE* 4.8 1.3 - - + -
1802A SER* 3.2 40.4 - - - +
1803A ILE* 4.0 24.9 - - + -
1806A ILE* 4.0 7.1 - - + +
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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