Contacts of the helix formed by residues 1724 - 1733 (chain A) in PDB entry 4C6C
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 SER1724 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1718A VAL* 3.9 4.2 - - - +
1723A LEU* 1.3 77.2 - - - +
1725A LEU* 1.3 65.0 + - - +
1726A ASP* 3.4 9.4 + - - +
1727A ASP* 2.9 36.3 + - - +
1728A LEU* 3.1 21.5 + - - +
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Residues in contact with LEU1725 (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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1462A VAL* 4.4 21.5 - - + -
1464A LEU* 4.0 20.2 - - + -
1715A LEU* 5.0 9.0 - - + -
1718A VAL* 4.0 18.0 - - + +
1724A SER* 1.3 73.2 - - - +
1726A ASP* 1.3 63.3 + - - +
1728A LEU* 3.1 20.9 + - + +
1729A LEU* 2.9 37.6 + - + +
1752A VAL* 6.5 0.2 - - + -
1754A LEU* 5.9 7.6 - - + -
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Residues in contact with ASP1726 (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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1724A SER* 3.2 8.3 + - - +
1725A LEU* 1.3 79.6 - - - +
1727A ASP* 1.3 67.5 + - - +
1729A LEU* 4.3 8.1 - - - +
1730A GLN* 2.8 55.7 + - - +
1734A HIS* 5.5 0.3 - - - -
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Residues in contact with ASP1727 (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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1677A MET* 5.1 6.0 - - + +
1723A LEU* 3.6 20.1 - - + +
1724A SER* 2.9 44.4 + - - +
1726A ASP* 1.3 81.7 - - - +
1728A LEU* 1.3 63.8 + - - +
1730A GLN* 4.7 1.3 - - - +
1731A ARG* 3.0 52.1 + - - +
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Residues in contact with LEU1728 (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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1464A LEU* 5.7 1.1 - - + -
1467A LEU* 6.0 0.4 - - + -
1683A PHE* 3.9 9.6 - - + -
1711A LEU* 3.9 12.6 - - + -
1714A LEU* 3.7 27.8 - - + -
1715A LEU* 3.9 28.7 - - + -
1718A VAL* 4.1 16.4 - - + -
1723A LEU* 4.1 6.9 - - + +
1724A SER 3.1 11.9 + - - +
1725A LEU* 3.4 15.9 - - + +
1727A ASP* 1.3 76.8 - - - +
1729A LEU* 1.3 65.6 + - + +
1731A ARG* 3.1 3.5 + - - +
1732A LEU* 2.9 50.3 + - + +
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Residues in contact with LEU1729 (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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1463A ARG 5.9 0.2 - - - +
1464A LEU* 4.3 20.2 - - + -
1465A PRO* 4.0 26.5 - - + -
1467A LEU* 3.7 28.3 - - + -
1725A LEU* 2.9 40.3 + - + +
1726A ASP* 3.9 8.3 - - - +
1728A LEU* 1.3 79.4 - - + +
1730A GLN* 1.3 65.2 + - - +
1732A LEU 4.4 0.9 - - - +
1733A HIS* 3.0 23.4 + - + +
1734A HIS* 3.2 18.8 + - + +
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Residues in contact with GLN1730 (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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1726A ASP* 2.8 52.1 + - - +
1727A ASP* 3.9 7.2 - - - +
1729A LEU* 1.3 73.6 - - - +
1731A ARG* 1.3 68.2 + - - +
1734A HIS* 3.5 34.4 + - - +
1735A ASN* 2.8 51.6 + - - +
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Residues in contact with ARG1731 (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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1677A MET* 2.9 42.4 + - - +
1678A ALA* 3.9 11.5 + - - +
1680A ILE* 2.8 20.2 + - - +
1681A ASP* 3.4 20.2 - - - +
1682A CYS* 3.3 6.0 - - - +
1683A PHE* 3.0 69.0 + - + +
1727A ASP* 3.0 46.4 + - - +
1728A LEU 3.1 2.4 + - - +
1730A GLN* 1.3 90.1 - - + +
1732A LEU* 1.3 57.8 + - - +
1733A HIS 3.6 0.2 - - - -
1735A ASN* 4.7 1.8 - - - +
1736A PRO* 3.5 10.7 - - - +
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Residues in contact with LEU1732 (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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1467A LEU* 3.4 31.0 - - + -
1468A ILE 2.8 40.5 + - - +
1497A ILE* 4.8 4.3 - - + -
1683A PHE* 3.4 32.1 - - + +
1684A ALA* 5.2 0.2 - - - -
1710A MET* 3.8 26.0 - - + -
1711A LEU* 4.3 8.1 - - + -
1714A LEU* 4.0 13.0 - - + -
1728A LEU* 2.9 36.0 + - + +
1731A ARG* 1.3 76.2 - - - +
1733A HIS* 1.3 62.2 + - - +
1736A PRO* 3.9 7.0 - - - -
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Residues in contact with HIS1733 (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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1465A PRO* 3.4 37.7 - - + +
1466A GLY* 2.8 25.5 + - - -
1467A LEU* 4.2 10.5 - - + -
1468A ILE* 3.9 8.3 - - + +
1729A LEU* 3.0 12.5 + - + +
1731A ARG 3.6 1.2 - - - -
1732A LEU* 1.3 82.0 - - - +
1734A HIS* 1.3 92.5 + + - +
1735A ASN 3.5 1.1 - - - -
1736A PRO* 3.5 4.4 - - - +
1737A ARG* 3.1 69.4 + - + +
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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