Contacts of the strand formed by residues 4293 - 4298 (chain A) in PDB entry 4O2W
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 ILE4293 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4242A LYS* 5.1 1.2 + - - +
4254A LEU* 3.5 24.8 - - + +
4255A THR 5.0 0.2 - - - +
4258A GLY* 3.1 35.8 + - - +
4260A VAL* 3.9 15.3 - - + -
4288A LEU* 4.4 16.8 - - + -
4291A VAL* 3.8 26.7 - - + +
4292A ILE* 1.3 73.6 - - - +
4294A GLU* 1.3 62.8 + - - +
4295A ASP 3.4 24.5 - - - +
4296A VAL* 4.0 9.9 - - + -
4305A ALA* 3.9 19.7 - - + -
4306A LEU 3.5 12.6 - - - +
4307A ALA* 4.1 1.3 - - + +
4313A TYR* 4.6 2.5 - - + -
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Residues in contact with GLU4294 (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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4242A LYS* 2.7 41.4 + - - +
4254A LEU* 3.5 6.2 - - - +
4292A ILE* 3.7 11.8 - - - +
4293A ILE* 1.3 75.5 - - - +
4295A ASP* 1.3 61.7 + - + +
4306A LEU* 2.7 21.5 + - + +
4307A ALA 4.2 2.0 - - - +
4308A SER* 3.4 41.3 - - - +
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Residues in contact with ASP4295 (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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4242A LYS* 6.0 0.9 - - - -
4243A LYS* 2.8 38.1 + - - +
4254A LEU* 3.7 4.5 - - - -
4293A ILE* 3.4 8.7 - - - +
4294A GLU* 1.3 83.4 - - + +
4296A VAL* 1.3 76.0 + - - +
4306A LEU* 2.9 41.9 + - + -
4347A GLN* 5.8 0.9 - - - -
4348A ILE* 3.9 22.2 + - + +
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Residues in contact with VAL4296 (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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4243A LYS* 3.0 43.6 + - + +
4245A ALA* 4.7 11.9 - - + +
4252A VAL* 4.2 26.5 - - + -
4254A LEU* 4.4 15.7 - - + +
4260A VAL* 4.3 14.6 - - + -
4293A ILE* 4.0 15.3 - - + -
4295A ASP* 1.3 86.3 + - - +
4297A ALA* 1.3 62.5 + - - +
4298A VAL* 5.2 0.4 - - + -
4303A THR* 4.8 6.5 - - + -
4304A LEU 3.3 11.4 - - - +
4305A ALA* 4.3 6.5 - - + -
4348A ILE* 4.1 2.7 - - - -
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Residues in contact with ALA4297 (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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4243A LYS* 5.2 1.1 - - - +
4295A ASP* 5.3 0.4 - - - +
4296A VAL* 1.3 76.2 - - - +
4298A VAL* 1.3 62.1 + - - +
4303A THR* 3.5 2.3 - - - +
4304A LEU* 2.9 34.7 + - + +
4348A ILE* 3.8 21.7 - - + +
4349A SER* 3.9 12.3 - - - -
4350A ALA* 3.9 26.8 - - + +
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Residues in contact with VAL4298 (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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4088A CYS* 4.5 4.3 - - - -
4245A ALA* 3.6 31.5 - - + +
4246A CYS 3.6 21.6 - - - +
4250A PHE* 3.7 26.2 - - + -
4252A VAL* 3.7 25.6 - - + -
4296A VAL* 5.2 0.9 - - + -
4297A ALA* 1.3 79.7 - - - +
4299A GLY* 1.3 74.7 + - - +
4302A HIS 3.6 3.1 - - - +
4303A THR* 4.1 9.2 - - + -
4350A ALA* 3.5 11.9 + - - +
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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