Contacts of the helix formed by residues 1557 - 1566 (chain B) in PDB entry 3ZQK
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 SER1557 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1531B GLY* 4.5 6.1 - - - -
1532B GLN* 3.9 9.1 + - - +
1555B ALA* 4.2 6.4 - - - +
1556B GLN* 1.3 76.8 - - - +
1558B LYS* 1.3 67.3 + - - +
1559B GLY 3.3 1.6 - - - -
1560B ASP* 2.4 34.6 + - - +
1561B ILE* 3.0 20.8 + - - +
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Residues in contact with LYS1558 (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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1525B ILE* 3.3 24.0 - - + +
1526B GLN* 2.8 40.6 + - - +
1527B ARG 4.5 0.4 - - - -
1528B MET 2.9 19.7 + - - -
1529B ASP* 5.0 1.2 - - - +
1530B VAL* 3.9 32.5 + - + +
1531B GLY* 4.7 0.2 - - - -
1556B GLN 3.5 2.8 + - - -
1557B SER* 1.3 72.2 - - - +
1559B GLY* 1.3 63.1 + - - +
1561B ILE* 3.4 2.7 + - - +
1562B LEU* 3.0 38.3 + - + +
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Residues in contact with GLY1559 (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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1557B SER* 3.3 2.0 - - - -
1558B LYS* 1.3 79.0 - - - +
1560B ASP* 1.3 57.9 + - - +
1562B LEU* 3.6 6.9 + - - +
1563B GLN* 3.1 28.5 + - - +
1566B ARG* 5.5 0.9 + - - -
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Residues in contact with ASP1560 (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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1550B TYR* 4.6 0.2 - - - -
1555B ALA* 4.4 7.6 - - + +
1557B SER* 2.4 32.4 + - - +
1559B GLY* 1.3 75.8 - - - +
1561B ILE* 1.3 65.4 + - - +
1563B GLN* 3.4 14.1 + - - +
1564B ARG* 3.1 56.7 + - - +
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Residues in contact with ILE1561 (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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1525B ILE* 4.2 15.7 - - + -
1530B VAL* 3.3 34.1 - - + -
1537B VAL* 4.6 10.3 - - + -
1550B TYR* 3.9 18.8 - - + +
1555B ALA 3.5 16.8 - - - +
1556B GLN* 3.3 33.0 - - - +
1557B SER 3.0 11.3 + - - +
1558B LYS* 3.7 5.6 - - - +
1560B ASP* 1.3 75.4 - - - +
1562B LEU* 1.3 58.5 + - - +
1564B ARG* 3.2 2.4 + - - +
1565B LEU* 2.9 55.1 + - + +
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Residues in contact with LEU1562 (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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1522B GLU* 3.9 37.2 - - + +
1525B ILE* 3.8 26.5 - - + -
1526B GLN* 3.8 22.0 - - + +
1558B LYS* 3.0 37.8 + - + +
1559B GLY* 3.9 6.5 - - - +
1561B ILE* 1.3 76.6 - - - +
1563B GLN* 1.3 64.2 + - - +
1565B LEU* 4.0 3.8 - - + +
1566B ARG* 3.2 51.2 + - - +
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Residues in contact with GLN1563 (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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1559B GLY 3.1 18.2 + - - +
1560B ASP* 3.7 16.7 - - - +
1561B ILE 3.3 0.2 - - - -
1562B LEU* 1.3 79.9 - - - +
1564B ARG* 1.3 71.6 + - + +
1566B ARG* 3.5 27.1 + - - +
1567B GLU* 3.7 13.8 - - + +
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Residues in contact with ARG1564 (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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1550B TYR* 3.3 44.3 + - + -
1554B GLU* 3.8 16.5 + - - -
1555B ALA* 3.6 19.2 - - - +
1560B ASP* 3.1 42.7 + - - +
1561B ILE 3.9 0.2 - - - +
1563B GLN* 1.3 82.9 + - + +
1565B LEU* 1.3 68.7 + - - +
1566B ARG 3.1 1.6 - - - -
1567B GLU* 2.9 22.7 + - - +
1568B ILE* 3.6 6.2 + - - +
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Residues in contact with LEU1565 (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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1518B LYS* 3.5 10.1 - - - +
1521B MET* 3.7 27.8 - - + +
1522B GLU* 4.9 9.2 - - + -
1525B ILE* 3.4 33.7 - - + -
1537B VAL* 4.7 0.4 - - + -
1539B VAL* 3.8 18.6 - - + -
1549B GLU 5.4 0.2 - - - +
1550B TYR* 3.9 24.5 - - + -
1561B ILE* 2.9 28.6 + - + +
1562B LEU* 4.1 6.7 - - + +
1564B ARG* 1.3 77.0 - - - +
1566B ARG* 1.3 61.1 + - - +
1568B ILE* 3.1 40.5 + - + +
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Residues in contact with ARG1566 (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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1518B LYS* 3.0 20.4 + - - +
1522B GLU* 3.7 34.4 + - - +
1559B GLY 5.5 0.6 + - - -
1562B LEU* 3.2 34.7 + - - +
1563B GLN* 3.6 26.9 - - - +
1564B ARG 3.1 0.8 - - - -
1565B LEU* 1.3 76.3 - - - +
1567B GLU* 1.3 64.1 + - + +
1568B ILE 4.2 0.2 - - - +
4676B NAG 3.9 9.2 + - - -
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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