Contacts of the strand formed by residues 252 - 256 (chain J) in PDB entry 2ABJ
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 GLN 252 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213J LYS* 6.0 0.8 - - - +
246J LEU* 3.2 9.4 - - - -
247J TYR* 2.9 56.9 + - - +
248J GLY* 5.7 0.9 - - - -
250J ASP* 3.5 9.9 - - + +
251J HIS* 1.3 71.8 - - - +
253J ILE* 1.3 62.7 + - - +
254J THR* 3.6 9.0 - - + +
280J ASP* 4.8 1.4 + - - -
282J ILE* 4.2 10.3 - - - +
308J TYR* 3.4 45.5 - - + +
309J LEU 3.3 10.1 - - - +
310J THR* 4.0 15.7 - - + +
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Residues in contact with ILE 253 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244J LEU* 4.0 17.3 - - + -
245J TRP 4.0 3.8 - - - -
246J LEU* 3.8 9.2 - - + -
252J GLN* 1.3 72.4 - - - +
254J THR* 1.3 60.9 + - - +
261J LEU* 3.9 14.1 - - + -
263J LEU* 4.9 3.6 - - + -
277J PRO* 3.3 16.8 - - - +
309J LEU* 2.7 43.7 + - + +
310J THR 4.6 2.2 - - - +
311J MET* 3.5 40.6 - - + +
314J LEU* 4.4 14.1 - - + -
326J MET* 3.7 26.2 - - + -
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Residues in contact with THR 254 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210J ARG* 5.2 2.8 + - - +
244J LEU* 4.9 0.4 - - - +
245J TRP* 2.9 28.7 + - - +
247J TYR* 3.7 23.6 - - + -
252J GLN* 3.6 22.9 - - + +
253J ILE* 1.3 75.4 - - - +
255J GLU* 1.3 79.8 + - - +
261J LEU* 3.6 10.6 + - - +
277J PRO* 3.4 23.0 - - + +
282J ILE* 3.7 18.0 + - + -
283J ILE* 3.5 19.4 - - + +
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Residues in contact with GLU 255 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210J ARG* 3.2 24.2 + - - +
244J LEU* 3.7 5.5 - - - +
245J TRP* 3.0 38.6 + - + -
254J THR* 1.3 91.2 + - - +
256J VAL* 1.3 63.5 + - - +
257J GLY 3.9 3.1 - - - +
259J MET 3.2 10.8 + - - +
260J ASN* 3.8 12.3 - - - +
261J LEU* 4.2 5.1 - - - +
283J ILE* 3.4 11.7 - - + -
284J LEU* 2.7 30.5 + - - +
420J PLP 2.4 34.1 + - - +
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Residues in contact with VAL 256 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200J VAL* 5.0 0.9 - - + -
202J LEU* 3.4 46.7 - - + -
242J GLN* 4.3 2.2 - - + -
243J VAL 3.6 2.7 - - - -
244J LEU* 4.2 2.2 - - + -
255J GLU* 1.3 73.8 - - - +
257J GLY* 1.3 60.7 + - - +
258J THR 3.1 0.7 + - - -
259J MET* 2.8 45.2 + - + +
261J LEU* 3.2 35.8 - - + +
328J SER* 2.9 31.2 - - - +
338J VAL* 4.7 1.3 - - + -
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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