Contacts of the strand formed by residues 252 - 256 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213G LYS* 5.2 0.8 - - - +
246G LEU* 3.2 7.2 - - - -
247G TYR* 2.8 76.1 + - + +
250G ASP* 3.4 21.2 - - - +
251G HIS* 1.3 73.7 - - - +
253G ILE* 1.3 63.9 + - - +
254G THR* 3.7 7.1 + - + +
280G ASP* 4.6 2.2 + - - -
282G ILE* 4.2 10.1 - - - +
283G ILE* 6.1 1.0 - - - +
308G TYR* 3.5 37.9 - - - +
309G LEU 3.2 20.0 - - - +
310G THR* 3.9 7.4 - - + +
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Residues in contact with ILE 253 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244G LEU* 3.3 30.3 - - + -
245G TRP 3.9 3.1 - - - -
246G LEU* 3.9 8.1 - - + -
252G GLN* 1.3 73.3 - - - +
254G THR* 1.3 61.1 + - - +
261G LEU* 3.7 27.1 - - + -
263G LEU* 6.4 0.9 - - + -
277G PRO* 3.2 21.1 - - - +
309G LEU* 2.7 24.7 + - + +
310G THR 3.6 23.1 - - - +
311G MET* 3.6 35.4 - - - +
314G LEU* 4.1 19.7 - - + -
326G MET* 5.7 4.0 - - + -
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Residues in contact with THR 254 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210G ARG* 5.3 2.8 + - - +
245G TRP* 2.7 34.3 + - - +
246G LEU 4.9 0.5 - - - -
247G TYR* 3.8 18.1 - - + +
252G GLN* 3.8 11.2 - - + +
253G ILE* 1.3 78.5 - - - +
255G GLU* 1.3 73.7 + - - +
260G ASN* 5.1 0.2 - - - -
261G LEU* 3.6 19.4 + - - +
277G PRO* 3.6 14.6 - - + +
282G ILE* 3.7 32.3 + - + -
283G ILE* 4.1 18.2 - - + +
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Residues in contact with GLU 255 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210G ARG* 3.6 14.8 + - - +
244G LEU* 3.7 4.3 - - - +
245G TRP* 2.9 34.3 + - + -
254G THR* 1.3 91.5 + - - +
256G VAL* 1.3 64.7 + - - +
257G GLY 3.8 9.4 - - - +
259G MET 2.9 13.8 + - - +
260G ASN* 3.4 10.3 - - - +
261G LEU* 4.4 3.1 - - - +
282G ILE 4.7 0.7 - - - +
283G ILE* 3.4 12.1 - - + -
284G LEU* 2.7 34.0 + - - +
420G PLP 2.4 37.9 + - - +
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Residues in contact with VAL 256 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202G LEU* 3.7 34.8 - - + -
242G GLN* 4.5 2.5 - - - -
243G VAL 3.5 4.3 - - - -
244G LEU* 3.8 7.0 - - + -
255G GLU* 1.3 73.0 - - - +
257G GLY* 1.3 59.6 + - - +
258G THR 3.2 0.2 + - - -
259G MET* 2.9 41.4 + - + +
260G ASN 4.0 2.0 - - - +
261G LEU* 3.3 30.9 - - + +
328G SER* 2.6 43.7 - - - +
338G VAL* 4.9 3.8 - - + -
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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