Contacts of the strand formed by residues 5340 - 5344 (chain b) in PDB entry 3A0B
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 HIS5340 (chain b).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5281b ILE* 5.5 3.6 - - + -
5282b ASN* 6.2 0.2 + - - -
5299b TRP* 3.3 62.0 + + + -
5337b TRP* 2.9 10.8 - - + -
5339b GLY* 1.3 72.1 - - - +
5341b ALA* 1.3 66.5 + - - +
5342b VAL* 3.3 34.7 + - + +
5352b PHE* 5.5 5.2 - + - -
5355b ARG* 5.5 6.3 + - - -
5397b SER 4.0 0.2 - - - +
5398b PHE* 3.4 0.9 - - - -
5399b TYR* 2.9 29.7 + - - +
5425b GLU* 2.8 39.0 - - - +
5426b ILE* 6.2 0.7 - - - -
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Residues in contact with ALA5341 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5339b GLY 3.5 0.6 + - - +
5340b HIS* 1.3 85.8 + - - +
5342b VAL* 1.3 59.1 + - - +
5343b PHE* 3.4 24.5 - - + -
5353b VAL* 5.7 3.1 - - - +
5396b VAL* 4.5 1.1 - - + -
5397b SER 3.3 14.1 - - - +
5398b PHE* 3.6 36.8 - - + -
5425b GLU* 4.8 1.0 + - - -
5426b ILE* 5.7 8.8 - - + +
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Residues in contact with VAL5342 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5295b LEU* 5.7 3.6 - - + -
5299b TRP* 5.5 1.8 - - + +
5340b HIS* 3.3 27.1 + - + +
5341b ALA* 1.3 69.9 - - - +
5343b PHE* 1.3 64.4 + - - +
5344b ARG* 4.0 17.3 + - - +
5350b GLU* 3.5 38.4 - - + +
5351b LEU 4.8 1.3 - - - -
5352b PHE* 4.1 13.0 - - + -
5395b THR 4.0 0.2 - - - +
5396b VAL* 3.9 0.3 - - - -
5397b SER* 3.4 20.3 + - - -
5399b TYR* 4.1 27.8 - - + -
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Residues in contact with PHE5343 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5341b ALA* 3.4 24.9 - - + -
5342b VAL* 1.3 78.3 - - - +
5344b ARG* 1.3 56.8 + - - +
5350b GLU 3.5 1.9 - - - -
5351b LEU* 2.6 40.5 + - - +
5353b VAL* 3.1 28.0 - - + -
5367b LEU* 3.9 30.7 - - + -
5394b VAL* 4.7 6.3 - - + -
5395b THR 3.1 10.5 - - - +
5396b VAL* 3.1 32.5 - - + -
5414b VAL 5.0 0.2 - - - -
5417b TYR* 4.0 3.8 - - + -
5418b ALA* 3.1 46.7 - - + -
5421b ALA* 3.9 10.8 - - + -
5426b ILE* 6.2 0.2 - - + -
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Residues in contact with ARG5344 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5295b LEU* 4.4 11.5 - - - +
5342b VAL* 4.0 17.9 + - - +
5343b PHE* 1.3 73.0 - - - +
5345b ASN* 1.3 63.6 + - - +
5348b GLY* 2.8 30.4 + - - +
5349b GLU 3.0 24.9 - - - +
5350b GLU* 3.5 22.9 + - + +
5351b LEU* 3.5 5.6 - - - +
5394b VAL* 3.3 7.8 - - - +
5395b THR* 2.8 38.9 + - - +
5397b SER* 5.3 4.8 + - - -
5399b TYR* 3.8 29.7 + - - -
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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