Contacts of the strand formed by residues 1530 - 1533 (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 ASP1530 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1498A THR 3.1 3.6 + - - -
1499A MET* 3.2 7.0 - - + -
1500A VAL 3.0 20.6 + - - -
1529A CYS* 1.3 81.5 - - - +
1531A PHE* 1.3 62.9 + - - +
1745A GLN* 2.8 31.0 + - - +
1788A LEU* 3.6 3.8 - - - +
1789A ARG* 2.8 46.1 + - - -
1806A GLY* 3.5 0.5 - - - -
1807A GLN* 2.9 20.7 + - - +
1809A VAL* 3.7 12.6 - - + -
1812A TRP* 3.4 14.1 - - - -
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Residues in contact with PHE1531 (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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1474A LEU* 6.1 0.7 - - + -
1485A PHE* 5.8 3.1 - + + -
1489A THR* 5.9 0.2 - - + -
1499A MET* 4.5 1.8 - - - -
1500A VAL* 3.1 23.3 - - + +
1502A ALA* 5.8 0.9 - - + +
1520A GLN* 4.7 2.0 - - - -
1523A ALA* 3.4 40.2 - - + -
1524A GLU* 3.8 14.1 - - + -
1527A ALA* 3.6 20.4 - - + -
1529A CYS 3.8 4.0 - - - +
1530A ASP* 1.3 77.0 - - - +
1532A ALA* 1.3 65.4 + - - +
1533A LEU* 3.9 25.8 - - + -
1806A GLY 4.0 2.0 - - - -
1807A GLN* 3.0 25.1 + - - -
1808A ASP* 3.4 33.3 - - + -
1809A VAL* 2.9 31.6 + - - +
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Residues in contact with ALA1532 (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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1499A MET* 5.3 0.2 - - - +
1500A VAL 3.0 5.9 + - - +
1501A CYS* 3.2 13.5 - - - -
1502A ALA* 3.0 24.1 + - - +
1531A PHE* 1.3 77.6 - - - +
1533A LEU* 1.3 67.3 + - - +
1553A ALA* 3.7 26.2 - - + +
1742A LEU* 4.4 4.0 - - + -
1808A ASP* 4.3 4.7 - - - -
1809A VAL* 4.1 16.4 - - + -
1810A ARG* 4.4 9.9 - - + -
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Residues in contact with LEU1533 (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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1485A PHE* 4.2 17.3 - - + -
1502A ALA* 3.8 22.0 - - + +
1510A ILE* 5.7 2.0 - - + -
1516A LEU* 4.2 14.6 - - + +
1519A ALA* 3.7 19.3 - - + +
1520A GLN* 3.6 44.0 - - + +
1523A ALA* 4.6 1.8 - - + -
1531A PHE* 3.9 20.9 - - + -
1532A ALA* 1.3 81.1 - - - +
1534A PHE* 1.3 60.3 + - - +
1551A SER 5.3 1.9 + - - +
1552A ALA* 3.2 12.5 - - - +
1553A ALA* 2.8 26.0 + - - +
1808A ASP* 5.1 3.4 + - - +
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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