Contacts of the strand formed by residues 4293 - 4298 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4242D LYS* 5.3 1.0 + - - +
4254D LEU* 3.5 25.9 - - + +
4255D THR 4.9 0.5 - - - +
4258D GLY* 3.0 35.3 + - - +
4260D VAL* 4.0 14.1 - - + -
4288D LEU* 4.4 13.2 - - + -
4291D VAL* 3.9 19.5 - - + +
4292D ILE* 1.3 72.0 - - - +
4294D GLU* 1.3 63.7 + - - +
4295D ASP 3.4 23.8 - - - +
4296D VAL* 4.0 9.9 - - + -
4305D ALA* 4.0 15.5 - - + -
4306D LEU 3.6 11.2 - - - +
4307D ALA* 3.8 15.3 - - + +
4313D TYR* 4.6 8.3 - - + -
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Residues in contact with GLU4294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4242D LYS* 2.9 35.7 + - - +
4254D LEU* 3.6 7.0 - - - +
4292D ILE* 3.5 18.2 - - - +
4293D ILE* 1.3 73.9 - - - +
4295D ASP* 1.3 63.3 + - + +
4306D LEU* 2.8 17.7 + - + +
4307D ALA 4.0 1.6 - - - +
4308D SER* 3.3 44.7 - - - +
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Residues in contact with ASP4295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4243D LYS* 2.9 32.1 + - - +
4254D LEU* 3.8 5.1 - - - +
4293D ILE* 3.4 8.8 - - - +
4294D GLU* 1.3 81.2 - - + +
4296D VAL* 1.3 80.3 + - - +
4297D ALA* 5.4 0.2 - - - +
4305D ALA* 3.4 0.7 - - - -
4306D LEU* 2.9 38.0 + - + +
4347D GLN* 5.9 1.0 - - - -
4348D ILE* 4.2 24.5 + - + +
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Residues in contact with VAL4296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4243D LYS* 2.8 46.4 + - + +
4245D ALA* 4.6 10.5 - - + -
4252D VAL* 4.1 28.3 - - + +
4254D LEU* 4.3 16.7 - - + +
4260D VAL* 4.4 14.1 - - + -
4293D ILE* 4.0 15.0 - - + -
4295D ASP* 1.3 83.9 + - - +
4297D ALA* 1.3 59.8 + - - +
4298D VAL* 5.0 1.1 - - + -
4303D THR* 4.6 5.8 - - + -
4304D LEU 3.3 7.9 - - - +
4305D ALA* 4.1 11.0 - - + -
4315D TRP* 5.4 0.2 - - + -
4348D ILE* 3.9 2.5 - - - -
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Residues in contact with ALA4297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4243D LYS* 4.8 2.9 - - - +
4295D ASP* 5.4 0.4 - - - +
4296D VAL* 1.3 75.7 - - - +
4298D VAL* 1.3 62.8 + - - +
4303D THR* 3.4 2.3 - - - -
4304D LEU* 2.8 33.2 + - + +
4348D ILE* 3.7 33.4 - - + +
4349D SER* 4.0 16.2 - - - -
4350D ALA* 3.8 10.3 - - + +
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Residues in contact with VAL4298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4088D CYS* 4.8 3.5 - - - -
4245D ALA* 3.7 27.5 - - + +
4246D CYS 3.4 25.4 - - - +
4250D PHE* 3.6 27.1 - - + -
4252D VAL* 3.7 24.7 - - + -
4296D VAL* 5.0 1.1 - - + -
4297D ALA* 1.3 79.1 - - - +
4299D GLY* 1.3 72.9 + - - +
4302D HIS 3.6 2.7 - - - +
4303D THR* 3.8 11.0 - - + +
4350D ALA* 3.5 11.3 - - - +
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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