Contacts of the helix formed by residues 1557 - 1568 (chain A) in PDB entry 3PPW
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1530A VAL 5.2 1.1 - - - -
1531A GLY* 5.2 0.9 - - - -
1555A ALA* 3.1 6.0 + - - +
1556A GLN* 1.3 77.9 - - - +
1558A LYS* 1.3 65.5 + - - +
1559A GLY* 4.1 2.0 + - - -
1560A ASP* 3.3 30.8 + - - +
1561A ILE* 3.0 24.8 + - - +
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Residues in contact with LYS1558 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1525A ILE* 3.3 19.5 - - + +
1526A GLN* 2.8 43.1 + - - +
1527A ARG 4.7 0.4 - - - -
1528A MET 2.8 23.8 + - - -
1529A ASP* 4.8 1.6 - - - +
1530A VAL* 4.1 32.5 + - + +
1557A SER* 1.3 71.7 - - - +
1559A GLY* 1.3 57.9 + - - +
1561A ILE* 3.3 4.0 + - - +
1562A LEU* 2.8 49.8 + - + +
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Residues in contact with GLY1559 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1557A SER* 3.3 3.4 + - - -
1558A LYS* 1.3 79.3 - - - +
1560A ASP* 1.3 63.7 + - - +
1562A LEU* 4.1 6.0 - - - +
1563A GLN* 3.2 26.2 + - - +
1566A ARG* 5.1 0.9 + - - -
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Residues in contact with ASP1560 (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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1550A TYR* 3.6 20.9 - - + +
1555A ALA* 3.4 22.3 - - - +
1557A SER* 3.2 21.5 + - - +
1559A GLY* 1.3 77.2 - - - +
1561A ILE* 1.3 62.7 + - - +
1563A GLN* 4.2 3.4 - - - +
1564A ARG* 3.3 22.9 + - - +
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Residues in contact with ILE1561 (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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1525A ILE* 4.1 28.3 - - + -
1530A VAL* 3.6 24.0 - - + -
1537A VAL* 4.0 20.0 - - + -
1539A VAL* 4.8 3.4 - - + -
1550A TYR* 3.6 33.6 - - + -
1555A ALA 4.1 0.9 - - - +
1556A GLN* 3.5 26.7 - - - +
1557A SER 3.0 20.0 + - - +
1558A LYS* 3.8 3.8 - - - +
1560A ASP* 1.3 75.2 - - - +
1562A LEU* 1.3 65.3 + - - +
1564A ARG* 3.3 4.2 + - - +
1565A VAL* 3.0 31.2 + - + +
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Residues in contact with LEU1562 (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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1522A GLU* 3.7 43.8 - - + +
1525A ILE* 3.9 19.7 - - + -
1526A GLN* 3.5 36.3 - - + +
1558A LYS* 2.8 33.0 + - + +
1559A GLY* 4.1 5.4 - - - +
1561A ILE* 1.3 73.9 - - - +
1563A GLN* 1.3 57.2 + - - +
1565A VAL* 3.4 6.9 + - + +
1566A ARG* 3.1 50.9 + - - +
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Residues in contact with GLN1563 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1559A GLY 3.2 18.1 + - - +
1560A ASP* 4.2 4.5 - - - +
1562A LEU* 1.3 73.6 - - - +
1564A ARG* 1.3 65.1 - - - +
1566A ARG* 2.9 42.3 + - - +
1567A GLU* 3.1 52.7 + - - +
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Residues in contact with ARG1564 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1549A GLU* 3.4 28.0 + - + +
1550A TYR* 3.4 28.8 + - + -
1554A GLU* 2.5 38.1 + - - -
1560A ASP 3.3 10.1 + - - +
1561A ILE 3.3 3.2 + - - +
1563A GLN* 1.3 78.1 - - - +
1565A VAL* 1.3 62.6 + - + +
1567A GLU* 3.1 28.3 + - - +
1568A ILE* 3.1 16.4 + - + +
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Residues in contact with VAL1565 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1518A LYS* 3.1 17.8 + - - +
1521A MET* 3.6 33.2 - - + -
1522A GLU* 3.5 32.8 - - + +
1525A ILE* 4.2 16.4 - - + -
1539A VAL* 4.3 12.8 - - + -
1550A TYR* 6.2 0.9 - - + -
1561A ILE* 3.0 22.4 + - + +
1562A LEU* 3.4 10.3 - - - +
1564A ARG* 1.3 74.5 - - + +
1566A ARG* 1.3 64.2 + - - +
1568A ILE* 3.1 21.6 + - + +
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Residues in contact with ARG1566 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1518A LYS* 3.1 19.5 + - - +
1522A GLU* 4.1 22.2 + - - +
1526A GLN* 5.0 4.9 + - - -
1559A GLY 5.1 0.8 + - - -
1562A LEU* 3.1 37.5 + - - +
1563A GLN* 2.9 58.3 + - - +
1565A VAL* 1.3 75.4 - - - +
1567A GLU* 1.3 58.2 + - - +
1568A ILE 4.0 0.5 - - - +
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Residues in contact with GLU1567 (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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1563A GLN* 3.1 41.5 + - - +
1564A ARG* 3.1 27.8 + - - +
1566A ARG* 1.3 75.0 - - - +
1568A ILE* 1.3 63.5 + - - +
1569A ARG* 3.4 16.0 + - - +
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Residues in contact with ILE1568 (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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1503A LEU* 6.0 0.7 - - + -
1514A PHE* 3.8 18.8 - - + -
1518A LYS* 2.9 26.9 + - + +
1521A MET* 4.2 9.6 - - + -
1539A VAL* 3.8 18.4 - - + -
1541A GLN* 3.6 25.1 - - + +
1549A GLU* 3.7 42.0 - - + +
1564A ARG* 3.1 13.2 + - + +
1565A VAL* 3.1 28.3 + - + +
1566A ARG 4.0 0.5 - - - +
1567A GLU* 1.3 76.6 - - - +
1569A ARG* 1.3 63.8 + - - +
1570A TYR 4.1 0.5 + - - -
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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