Contacts of the helix formed by residues 1718 - 1723 (chain A) in PDB entry 5V7W
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 ASN1718 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1635A LYS* 5.3 2.8 + - - +
1638A GLN* 4.8 7.6 - - - +
1639A THR* 3.8 19.7 - - + +
1681A PHE* 3.8 2.5 - - - -
1716A ALA* 3.5 14.4 - - - +
1717A VAL* 1.3 95.0 - - - +
1719A ALA* 1.3 65.8 + - - +
1720A ASN* 3.3 17.8 + - - +
1721A TYR* 3.3 17.3 + - + +
1781A SER* 4.6 4.4 + - - -
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Residues in contact with ALA1719 (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 LYS 4.8 1.5 + - - +
1636A PHE* 3.8 24.8 - - + +
1639A THR* 3.3 11.5 + - - +
1640A CYS* 3.7 13.7 - - - -
1681A PHE* 3.4 41.2 - - + -
1718A ASN* 1.3 70.8 - - - +
1720A ASN* 1.3 58.2 + - - +
1722A SER* 2.9 22.9 + - - -
1723A ALA* 3.1 10.7 + - - +
1738A VAL* 5.2 2.8 - - + +
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Residues in contact with ASN1720 (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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1639A THR* 2.8 43.1 + - - +
1640A CYS* 3.4 10.3 - - - -
1642A HIS* 5.1 4.5 - - + +
1643A PHE* 5.8 0.4 - - + -
1718A ASN* 3.4 18.2 + - - +
1719A ALA* 1.3 71.2 - - - +
1721A TYR* 1.3 72.0 + - - +
1723A ALA* 3.3 15.4 + - + +
1724A ASN* 3.7 4.7 + - - +
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Residues in contact with TYR1721 (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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1716A ALA* 3.8 10.8 - - + -
1718A ASN* 3.5 18.2 - - + +
1719A ALA 3.1 0.4 - - - -
1720A ASN* 1.3 90.0 + - - +
1722A SER* 1.3 59.8 + - - +
1723A ALA 3.1 0.6 + - - -
1724A ASN* 3.4 20.3 + - + +
1727A TYR* 3.5 15.4 - + - -
1781A SER* 4.5 30.1 + - - -
1782A LEU* 5.9 4.3 - - + -
1901A 91J 3.8 25.1 - - + -
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Residues in contact with SER1722 (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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1681A PHE* 3.3 30.9 + - - +
1682A HIS 4.1 0.2 - - - -
1683A GLY* 3.4 28.1 - - - -
1716A ALA* 3.4 11.8 - - - +
1719A ALA 2.9 9.2 + - - -
1721A TYR* 1.3 74.8 - - - +
1723A ALA* 1.3 56.7 + - - +
1724A ASN 3.2 7.0 + - - +
1727A TYR* 4.1 3.2 - - - +
1728A SER* 2.9 17.5 + - - -
1738A VAL* 3.6 7.0 - - - +
1901A 91J 3.0 20.6 + - - -
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Residues in contact with ALA1723 (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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1640A CYS* 4.0 4.9 - - - -
1643A PHE* 3.7 32.8 - - + -
1719A ALA 3.1 9.4 + - - +
1720A ASN* 3.4 16.8 - - - +
1721A TYR 3.1 0.8 - - - -
1722A SER* 1.3 77.0 - - - +
1724A ASN* 1.3 58.9 + - - +
1725A ASP* 3.5 1.9 + - - +
1728A SER* 3.7 5.8 - - - -
1736A LYS* 2.8 25.1 + - - +
1738A VAL* 4.5 0.9 - - + -
1799A PHE* 4.3 13.9 - - + -
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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