Contacts of the strand formed by residues 1757 - 1763 (chain A) in PDB entry 2H04
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 TYR1757 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1721A ILE* 3.9 18.2 - - + -
1722A ALA* 3.1 27.3 - - + +
1727A ASN* 3.4 37.0 - - + +
1730A LYS* 3.8 32.0 + - + +
1731A ASN* 2.9 30.1 + - - -
1738A PRO* 3.1 30.7 - - + +
1743A ARG* 4.0 11.2 - - - +
1746A LEU* 3.9 9.8 - - - +
1755A SER* 3.2 6.6 + - - +
1756A ASP* 1.3 84.0 + - - +
1758A ILE* 1.3 69.4 + - - +
1759A ASN* 3.6 17.2 - - - -
1785A ASP* 4.5 5.5 - - - +
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Residues in contact with ILE1758 (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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1730A LYS* 5.9 0.7 - - - -
1738A PRO* 4.1 1.9 - - - +
1743A ARG* 5.0 1.2 - - - +
1744A VAL* 3.4 26.7 + - + +
1746A LEU* 4.0 22.4 - - + +
1756A ASP 3.5 1.2 + - - -
1757A TYR* 1.3 89.7 - - - +
1759A ASN* 1.3 63.8 + - - +
1760A ALA* 3.0 27.3 + - + +
1775A THR* 4.3 5.8 - - - +
1782A THR* 5.1 5.4 - - - +
1785A ASP* 3.8 32.3 - - + +
1786A PHE* 3.9 18.2 - - + +
1789A MET* 4.0 23.8 - - + -
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Residues in contact with ASN1759 (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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1730A LYS 4.1 2.9 + - - +
1731A ASN* 3.1 27.3 + - - +
1736A ILE 2.8 26.1 + - - +
1738A PRO* 3.6 12.0 - - - +
1757A TYR* 3.6 10.1 - - - -
1758A ILE* 1.3 70.2 - - - +
1760A ALA* 1.3 53.0 + - - +
1775A THR* 2.6 29.9 + - - -
1776A GLN* 3.4 36.7 + - - +
1943A ARG* 2.8 35.4 + - - -
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Residues in contact with ALA1760 (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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1738A PRO* 3.7 5.4 - - - +
1743A ARG* 3.4 7.6 - - - +
1744A VAL* 3.0 29.1 + - + -
1758A ILE* 3.0 11.3 + - + +
1759A ASN* 1.3 76.8 + - - +
1761A SER* 1.3 64.1 + - - +
1773A ILE* 4.3 1.1 - - + -
1774A VAL 2.9 12.1 - - - +
1775A THR* 3.6 10.3 - - - +
1789A MET* 3.7 28.7 - - + -
1943A ARG* 4.1 1.9 - - - +
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Residues in contact with SER1761 (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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1738A PRO* 3.7 9.5 - - - +
1742A THR* 3.5 11.2 + - - -
1743A ARG* 4.3 0.2 - - - +
1744A VAL* 3.7 5.6 - - - -
1760A ALA* 1.3 74.5 + - - +
1762A TYR* 1.3 62.4 + - - +
1763A ILE* 3.8 8.4 + - - +
1773A ILE* 3.4 1.7 - - - -
1774A VAL* 2.6 35.0 + - - -
1942A HIS 4.0 15.4 + - - -
1943A ARG* 2.9 42.4 + - - +
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Residues in contact with TYR1762 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1742A THR* 2.8 32.4 + - - +
1743A ARG 3.9 16.6 - - - -
1744A VAL* 3.8 23.9 - - + +
1745A LYS 4.7 2.0 + - - -
1761A SER* 1.3 72.7 - - - +
1763A ILE* 1.3 68.8 + - - +
1764A PRO* 4.0 3.0 - - - +
1769A ARG 5.1 1.3 - - - +
1770A ARG* 3.2 72.4 + - + +
1772A TYR 3.7 3.4 - - - -
1773A ILE* 3.9 13.2 - - + -
1793A GLN* 3.0 36.5 + - - -
1899A PRO* 4.7 3.4 - - + -
1942A HIS* 3.8 14.8 - - + +
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Residues in contact with ILE1763 (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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1761A SER* 3.8 13.9 - - - +
1762A TYR* 1.3 89.1 - - - +
1764A PRO* 1.3 81.7 - - + +
1769A ARG 3.7 4.2 + - - -
1771A GLU 3.1 5.2 + - - -
1772A TYR* 2.9 49.7 + - + -
1774A VAL* 3.7 29.2 - - + +
1915A ILE* 4.4 4.3 - - + -
1939A LEU* 3.5 29.8 - - + +
1942A HIS* 3.7 17.5 - - + -
1943A ARG* 4.2 7.0 - - + -
1946A MET* 4.2 14.6 - - + -
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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