Contacts of the helix formed by residues 1562 - 1570 (chain B) in PDB entry 5TWV
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 LYS1562 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1546B ALA 4.8 3.4 - - - +
1547B ASP 3.9 20.2 - - - +
1548B LEU* 4.6 2.0 - - - +
1549B VAL* 5.3 0.2 - - - -
1561B ASP* 1.3 79.0 - - - +
1563B PRO* 1.3 61.7 - - - +
1564B GLU* 3.4 4.7 - - + +
1565B THR* 3.4 9.3 + - - +
1566B LEU* 2.9 27.2 + - - +
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Residues in contact with PRO1563 (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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1543B ILE 3.9 7.6 - - - +
1544B LEU* 3.6 39.9 - - + +
1546B ALA* 4.9 4.7 - - - +
1549B VAL* 5.2 7.1 - - + -
1562B LYS* 1.3 74.5 - - - +
1564B GLU* 1.3 58.4 + - - +
1566B LEU* 3.8 6.0 - - + +
1567B LEU* 2.9 30.7 + - - +
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Residues in contact with GLU1564 (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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1562B LYS* 3.4 2.1 - - + +
1563B PRO* 1.3 77.5 - - - +
1565B THR* 1.3 58.2 + - - +
1567B LEU* 3.4 7.7 + - - +
1568B SER* 2.9 27.6 + - - -
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Residues in contact with THR1565 (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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1561B ASP* 4.4 14.4 - - - -
1562B LYS* 3.4 13.0 + - - +
1563B PRO 3.3 0.4 - - - -
1564B GLU* 1.3 77.3 - - - +
1566B LEU* 1.3 59.3 + - - +
1568B SER* 3.1 10.1 + - - -
1569B GLN* 2.9 27.4 + - - +
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Residues in contact with LEU1566 (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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1549B VAL* 5.8 4.9 - - + +
1561B ASP* 4.8 10.9 - - + +
1562B LYS 2.9 19.1 + - - +
1563B PRO* 3.8 7.4 - - + +
1565B THR* 1.3 73.4 - - - +
1567B LEU* 1.3 64.5 + - - +
1569B GLN* 3.3 21.8 + - - +
1570B LYS 3.6 4.0 + - - -
1571B ASP* 4.4 1.2 + - - +
1573B VAL* 4.7 17.8 - - + +
1574B PHE* 3.6 11.5 + - - +
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Residues in contact with LEU1567 (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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1563B PRO 2.9 17.9 + - - +
1564B GLU* 3.6 7.6 - - - +
1566B LEU* 1.3 76.3 - - - +
1568B SER* 1.3 62.4 + - - +
1570B LYS* 3.2 15.9 + - - +
1574B PHE* 3.7 17.0 - - + +
1577B PHE* 5.4 8.3 - - + +
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Residues in contact with SER1568 (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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1564B GLU 2.9 15.1 + - - -
1565B THR* 3.1 13.2 + - - -
1567B LEU* 1.3 73.7 - - - +
1569B GLN* 1.3 64.7 + - - +
1570B LYS* 3.3 4.9 + - - +
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Residues in contact with GLN1569 (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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1565B THR 2.9 12.4 + - - +
1566B LEU* 3.3 16.4 - - - +
1568B SER* 1.3 78.1 - - - +
1570B LYS* 1.3 63.6 + - - +
1571B ASP* 3.4 13.4 + - + +
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Residues in contact with LYS1570 (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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1566B LEU 3.6 1.6 + - - -
1567B LEU 3.2 8.5 + - - +
1568B SER 3.2 8.0 - - - +
1569B GLN* 1.3 79.5 - - - +
1571B ASP* 1.3 64.0 + - - +
1574B PHE* 3.6 13.7 - - - -
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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