Contacts of the strand formed by residues 1442 - 1447 (chain A) in PDB entry 4C8D
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 ASP1442 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1440A ASP 3.9 0.7 + - - +
1441A GLN* 1.3 74.5 - - - +
1443A VAL* 1.3 64.3 + - - +
1456A ASP* 4.2 18.3 - - - +
1457A VAL 3.5 11.2 - - - +
1458A LYS* 2.8 26.8 + - - +
1488A TRP* 5.8 1.6 - - - -
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Residues in contact with VAL1443 (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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1442A ASP* 1.3 76.0 - - - +
1444A ASP* 1.3 73.9 + - - +
1445A LEU* 3.7 12.1 - - + -
1456A ASP* 3.6 1.4 - - - +
1457A VAL* 2.7 49.1 + - - +
1458A LYS 4.1 16.8 - - - +
1459A VAL* 4.1 9.0 - - + +
1485A LEU* 3.5 29.2 - - + -
1486A LYS 3.5 23.1 - - - +
1487A ASP 5.3 1.3 - - - +
1488A TRP* 4.4 13.5 - - + -
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Residues in contact with ASP1444 (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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1443A VAL* 1.3 80.6 - - - +
1445A LEU* 1.3 65.9 + - - +
1453A ILE* 4.3 15.0 - - + +
1454A ILE 3.4 6.5 - - - +
1455A SER* 3.5 9.4 - - - -
1456A ASP* 2.9 25.7 + - - -
1486A LYS* 3.2 32.6 + - + +
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Residues in contact with LEU1445 (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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1443A VAL* 3.7 9.9 - - + -
1444A ASP* 1.3 78.1 - - - +
1446A VAL* 1.3 65.3 + - - +
1453A ILE* 3.4 8.0 - - - +
1454A ILE* 2.9 42.3 + - + -
1457A VAL* 4.7 11.4 - - + -
1458A LYS 5.4 0.2 - - - +
1461A ASP* 4.9 0.7 - - + -
1462A PHE* 4.1 23.3 - - + +
1473A LEU* 4.1 20.9 - - + -
1483A LEU* 4.0 29.4 - - + -
1484A LYS 3.4 6.3 - - - +
1485A LEU* 3.3 40.2 - - + -
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Residues in contact with VAL1446 (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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1445A LEU* 1.3 79.6 - - - +
1447A ASN* 1.3 76.2 + - - +
1448A CYS* 3.3 4.1 + - - +
1451A CYS* 4.1 15.5 - - + +
1452A ALA 3.5 8.7 - - - +
1453A ILE* 4.7 11.2 - - + -
1483A LEU* 3.3 7.4 - - - -
1484A LYS* 2.9 57.6 + - - +
1486A LYS* 4.0 20.4 - - + -
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Residues in contact with ASN1447 (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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1446A VAL* 1.3 70.8 - - - +
1448A CYS* 1.3 55.1 + - - +
1449A ARG* 2.9 25.6 + - - +
1450A ASN* 3.1 38.5 + - - +
1451A CYS* 2.7 36.6 + - - -
1452A ALA* 2.8 15.9 + - + +
1454A ILE* 3.7 13.3 - - + +
1475A SER* 5.5 2.8 - - - -
1481A MET* 3.8 26.9 - - - +
1482A VAL 3.6 11.2 + - - +
1483A LEU* 4.1 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