Contacts of the strand formed by residues 1759 - 1763 (chain B) 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 ASN1759 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1660B ASN* 3.2 32.4 + - - +
1661B CYS 2.9 13.0 + - - +
1662B ASN* 3.3 16.8 + - - +
1742B GLN* 3.1 32.6 + - - +
1743B VAL 3.5 10.1 + - - -
1744B THR* 2.7 30.6 + - + +
1757B PHE 5.1 1.6 - - - +
1758B LEU* 1.3 76.2 - - - +
1760B ASP* 1.3 60.1 + - - +
1761B ILE* 3.7 15.8 + - - +
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Residues in contact with ASP1760 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1662B ASN* 3.2 8.6 - - - +
1663B SER* 2.7 52.7 + - - -
1664B TRP 4.5 0.5 + - - -
1724B LYS* 4.6 9.5 + - - -
1742B GLN* 3.3 3.6 - - - -
1743B VAL* 2.8 50.5 + - + +
1758B LEU* 4.1 2.8 - - - +
1759B ASN* 1.3 73.3 + - - +
1761B ILE* 1.3 59.1 + - - +
1762B TYR* 3.4 30.5 + - + +
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Residues in contact with ILE1761 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1625B THR* 4.0 5.6 - - - -
1626B HIS* 3.3 43.5 - - + +
1660B ASN* 3.9 24.2 - - - +
1662B ASN* 5.4 3.0 - - - +
1712B LEU* 4.4 13.7 - - + -
1740B ALA* 4.2 15.5 - - + -
1741B VAL 3.6 2.7 - - - +
1742B GLN* 4.0 22.7 - - + +
1759B ASN* 3.7 23.5 + - - +
1760B ASP* 1.3 78.3 - - - +
1762B TYR* 1.3 72.8 + - - +
1763B TYR* 4.1 17.3 - - + -
1766B GLU* 3.9 1.2 - - - +
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Residues in contact with TYR1762 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1724B LYS* 4.8 4.7 + - - -
1740B ALA* 3.4 2.4 - - - -
1741B VAL* 2.8 53.5 + - + +
1743B VAL* 3.4 30.5 - - + +
1760B ASP* 3.4 34.3 + - + +
1761B ILE* 1.3 80.2 - - - +
1763B TYR* 1.3 66.1 + - - +
1766B GLU* 3.4 8.3 - - + +
1767B ILE* 4.4 7.6 - - + +
1780B LEU* 5.5 2.9 - - + -
1782B ILE* 3.8 41.1 - - + -
1785B GLN* 4.4 13.6 + - - -
1789B LEU* 3.5 33.3 - - + +
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Residues in contact with TYR1763 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1813A SER 6.0 1.6 - - - -
1814A GLN 5.1 3.4 - - - -
1815A PRO* 5.0 8.5 - - + -
1816A ASP* 2.7 32.7 + - - -
1590B ARG* 3.7 8.7 + - - -
1625B THR* 4.9 0.7 + - - -
1626B HIS* 3.2 52.7 + + + +
1712B LEU* 4.6 16.8 - - + +
1739B THR* 3.6 9.0 - - - +
1740B ALA* 3.9 12.1 - - + -
1761B ILE* 4.3 9.0 - - + -
1762B TYR* 1.3 76.1 - - - +
1764B ALA* 1.3 65.9 + - - +
1765B SER* 3.9 19.5 - - - +
1766B GLU* 2.7 29.6 + - + +
1767B ILE* 3.5 7.4 + - - +
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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