Contacts of the helix formed by residues 1558 - 1564 (chain A) in PDB entry 4W8F
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 VAL1558 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1548A ILE* 4.0 27.8 - - + +
1551A SER* 4.3 12.3 - - - +
1552A GLY* 5.6 1.1 - - - -
1555A HIS* 3.9 15.7 - - - +
1556A ASP 3.2 0.4 - - - -
1557A GLN* 1.3 78.6 - - - +
1559A SER* 1.3 64.6 + - - +
1560A LYS 3.2 0.7 - - - -
1561A PHE* 3.1 21.5 + - - +
1562A MET* 3.7 11.9 - - + +
1565A MET* 4.2 9.6 - - + -
1572A ILE* 5.5 1.1 - - + -
1604A ALA* 4.7 4.0 - - + -
1607A TRP* 3.6 36.3 - - + -
1608A LEU* 4.0 17.9 - - + -
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Residues in contact with SER1559 (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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1555A HIS 4.5 0.6 + - - -
1556A ASP 2.9 23.3 + - - -
1558A VAL* 1.3 80.0 - - - +
1560A LYS* 1.3 67.4 + - - +
1561A PHE 3.2 0.9 + - - -
1562A MET* 3.3 11.9 + - - +
1570A GLU 3.4 14.6 - - - +
1571A SER* 4.0 10.4 + - - -
1572A ILE* 3.2 40.6 - - - +
1574A PHE* 4.7 4.3 - - - -
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Residues in contact with LYS1560 (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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1556A ASP 5.1 0.9 - - - +
1557A GLN* 4.0 23.1 - - + +
1558A VAL 3.2 0.8 - - - -
1559A SER* 1.3 89.3 + - - +
1561A PHE* 1.3 73.9 + - + +
1562A MET 3.5 0.7 + - - -
1563A LYS* 4.1 9.5 + - - +
1564A LYS* 5.5 3.3 - - - +
1570A GLU 4.7 1.6 - - - +
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Residues in contact with PHE1561 (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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1540A LEU* 3.8 31.4 - - + -
1544A ASP* 3.1 43.1 - - + -
1547A LYS* 4.2 19.5 - - + -
1548A ILE* 3.5 34.8 - - + -
1557A GLN* 3.4 26.5 - - + -
1558A VAL 3.1 6.7 + - - +
1559A SER 3.1 1.0 - - - -
1560A LYS* 1.3 87.5 - - + +
1562A MET* 1.3 58.0 + - - +
1563A LYS 3.1 5.6 - - - -
1564A LYS* 2.8 34.9 + - - +
1565A MET* 3.2 15.6 + - + +
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Residues in contact with MET1562 (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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1558A VAL* 3.7 17.5 - - + +
1559A SER* 3.3 8.3 + - - +
1560A LYS 3.3 2.2 - - - -
1561A PHE* 1.3 74.9 - - - +
1563A LYS* 1.3 58.4 + - - +
1565A MET* 4.2 15.9 - - + -
1566A PHE* 3.1 67.1 - - + +
1569A ILE* 2.7 42.6 - - + +
1570A GLU 3.6 12.6 - - - +
1571A SER* 4.8 1.1 - - - -
1572A ILE* 4.2 19.1 - - + -
1582A VAL* 4.9 1.1 - - - -
1608A LEU* 5.0 3.8 - - + -
1611A LEU* 3.9 27.6 - - + -
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Residues in contact with LYS1563 (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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1560A LYS 4.1 7.5 + - - +
1561A PHE 3.1 0.8 - - - -
1562A MET* 1.3 80.2 - - - +
1564A LYS* 1.3 64.2 + - + +
1567A GLY* 2.8 34.4 + - - +
1569A ILE 3.2 9.1 + - - +
1570A GLU* 3.6 17.2 + - + +
1585A VAL* 3.9 29.4 - - + -
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Residues in contact with LYS1564 (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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1539A PHE* 3.5 28.5 - - - +
1540A LEU* 3.8 24.5 - - + +
1544A ASP* 3.6 27.7 + - - -
1560A LYS 5.5 2.5 - - - +
1561A PHE* 2.8 22.9 + - + +
1563A LYS* 1.3 86.2 - - + +
1565A MET* 1.3 58.2 + - - +
1566A PHE 5.1 0.3 - - - -
1567A GLY 5.0 0.2 + - - -
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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