Contacts of the strand formed by residues 1764 - 1768 (chain D) in PDB entry 1T2V
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 LEU1764 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1760D ILE 4.9 0.7 - - - +
1761D PHE* 3.2 48.9 + - + +
1762D ARG 3.8 0.2 - - - -
1763D GLY* 1.3 86.9 - - - +
1765D GLU* 1.3 60.4 + - - +
1766D ILE* 4.0 8.3 - - + -
1789D ALA* 3.8 2.0 - - - +
1790D SER* 3.0 28.2 + - - -
1804D VAL* 4.0 4.1 - - - +
1805D HIS* 3.7 24.9 - - + +
1807D ILE* 3.8 27.4 - - + -
1837D TRP* 4.0 10.3 - - + -
1847D CYS* 4.2 9.0 - - - -
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Residues in contact with GLU1765 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1764D LEU* 1.3 72.0 - - - +
1766D ILE* 1.3 58.7 + - - +
1790D SER* 3.6 16.7 + - - +
1792D VAL* 3.8 25.3 - - + +
1798D PHE* 3.3 16.6 - - + -
1799D THR* 2.8 57.5 + - - +
1804D VAL* 4.0 18.3 - - + +
1805D HIS 3.1 8.4 + - - +
1806D PRO* 4.1 8.9 - - + +
1807D ILE* 2.7 34.8 + - - +
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Residues in contact with ILE1766 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1761D PHE* 4.4 6.3 - - + -
1764D LEU* 4.0 12.8 - - + -
1765D GLU* 1.3 74.3 - - - +
1767D CYS* 1.3 61.9 + - - +
1768D CYS* 4.3 12.9 + - - -
1781D GLU* 6.4 0.2 - - + -
1784D VAL* 3.9 35.9 - - + -
1789D ALA* 4.1 21.1 - - + -
1790D SER 2.9 11.1 + - - +
1791D VAL* 3.6 6.1 - - + +
1792D VAL 3.0 23.7 + - - +
1798D PHE* 4.6 0.9 - - - -
1807D ILE* 3.5 7.4 - - + -
1809D VAL* 3.8 19.1 - - + -
1837D TRP* 3.7 39.3 - - + -
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Residues in contact with CYS1767 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1766D ILE* 1.3 73.8 - - - +
1768D CYS* 1.3 74.3 + - - +
1769D TYR* 3.6 6.1 + - - -
1792D VAL* 3.4 21.8 - - + +
1793D LYS 4.9 2.0 - - - -
1794D GLU 4.5 2.5 - - - -
1795D LEU* 3.9 37.5 - - + -
1798D PHE* 3.6 24.9 - - + -
1807D ILE 2.9 9.5 + - - +
1808D VAL* 3.4 5.7 - - - +
1809D VAL 2.8 25.0 + - - -
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Residues in contact with CYS1768 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1766D ILE* 4.3 12.1 + - - -
1767D CYS* 1.3 82.6 - - - +
1769D TYR* 1.3 60.9 + - - +
1770D GLY 4.4 0.2 + - - -
1772D PHE* 3.8 17.7 - - + -
1777D THR* 4.3 11.9 - - + -
1780D LEU* 3.8 29.2 - - - -
1781D GLU* 4.4 24.9 + - - +
1784D VAL* 6.2 0.4 - - - -
1792D VAL 4.2 3.5 + - - +
1793D LYS* 5.3 4.3 - - - +
1809D VAL* 3.4 16.2 - - - -
1838D VAL* 6.4 0.2 - - - -
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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