Contacts of the strand formed by residues 259 - 266 (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 MET 259 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200G VAL* 5.6 1.8 - - + -
242G GLN* 3.9 16.6 - - + +
255G GLU* 2.9 14.3 - - - +
256G VAL* 2.9 44.0 + - + +
257G GLY 3.2 0.2 - - - -
258G THR* 1.3 77.6 - - - +
260G ASN* 1.3 59.8 + - - +
328G SER* 2.8 42.2 - - - +
329G SER 3.3 14.6 - - - +
333G CYS* 3.6 12.6 - - - -
336G CYS* 3.8 5.6 - - - -
420G PLP 3.7 0.4 - - - -
3401G CBC 3.3 64.4 - - + +
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Residues in contact with ASN 260 (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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255G GLU* 3.4 13.3 - - - +
256G VAL* 4.6 0.4 - - - -
259G MET* 1.3 73.5 - - - +
261G LEU* 1.3 60.6 + - - +
262G PHE* 4.0 2.6 + - + -
276G THR* 5.1 1.1 - - - +
283G ILE* 3.5 12.4 - - + +
284G LEU 2.8 18.7 + - - +
286G GLY* 3.2 35.2 - - - +
289G ARG* 3.4 26.5 - - + +
327G PHE 3.9 0.2 - - - +
328G SER* 3.0 9.4 - - - -
329G SER* 3.0 42.9 + - - +
420G PLP 3.5 14.3 + - - -
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Residues in contact with LEU 261 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253G ILE* 3.7 27.6 - - + -
254G THR 3.6 23.5 + - - +
255G GLU* 4.4 0.4 - - - -
256G VAL* 3.3 30.1 - - + -
259G MET 4.0 0.2 + - - -
260G ASN* 1.3 74.7 - - - +
262G PHE* 1.3 74.1 + - - +
263G LEU* 4.4 4.0 - - + +
276G THR* 2.6 29.8 + - - -
277G PRO* 3.4 13.0 - - + +
309G LEU* 4.3 20.6 - - + -
326G MET* 3.7 32.1 - - + -
327G PHE 3.9 5.6 - - - +
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Residues in contact with PHE 262 (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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260G ASN* 4.4 3.8 - - + -
261G LEU* 1.3 77.9 - - - +
263G LEU* 1.3 59.7 + - - +
264G TYR 4.2 0.7 - - - -
274G LEU* 4.0 22.7 - - + -
275G ALA 3.5 1.6 - - - -
276G THR* 3.7 23.1 - - - -
289G ARG* 3.7 39.5 - - + -
292G ILE* 3.8 21.1 - - + -
293G LEU* 3.7 20.0 - - + -
326G MET* 3.5 9.7 - - - +
327G PHE* 2.8 71.3 + + + +
329G SER* 3.3 28.0 - - - -
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Residues in contact with LEU 263 (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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253G ILE* 6.4 0.7 - - + -
261G LEU* 4.4 3.3 - - + +
262G PHE* 1.3 72.8 - - - +
264G TYR* 1.3 68.2 + - - +
265G TRP* 3.6 38.5 + - + -
273G GLU 3.5 3.6 - - - +
274G LEU* 3.5 3.6 - - - -
275G ALA* 2.8 44.6 + - + +
309G LEU* 3.9 29.8 - - + -
313G ASP* 6.2 0.9 - - + -
314G LEU* 4.5 14.1 - - + -
323G VAL* 3.8 25.8 - - + -
325G GLU 3.6 10.5 - - - +
326G MET* 4.4 20.0 - - + -
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Residues in contact with TYR 264 (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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262G PHE 4.2 0.4 - - - -
263G LEU* 1.3 71.0 - - - +
265G TRP* 1.3 61.5 + - - +
272G GLU* 3.0 43.3 + - + -
273G GLU 3.4 15.7 - - - -
274G LEU* 4.3 4.9 - - + +
302G PHE* 3.9 25.1 - + - -
324G ARG* 2.8 61.3 + - + -
325G GLU* 2.8 46.8 + - + +
327G PHE* 4.8 2.2 - - + -
358G LYS* 5.8 0.7 - - + -
359G LEU* 3.7 38.1 - - + -
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Residues in contact with TRP 265 (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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263G LEU* 3.6 35.0 - - + -
264G TYR* 1.3 78.3 - - - +
266G ILE* 1.3 62.6 + - - +
267G ASN* 3.8 6.3 - - + +
268G GLU* 3.7 22.0 - - - -
272G GLU* 3.5 4.1 - - - +
273G GLU* 2.8 71.0 + - + +
275G ALA* 4.0 5.3 - - - +
307G ARG* 3.7 28.5 - - - -
309G LEU* 3.9 10.5 - - + -
313G ASP* 3.7 21.5 - - + -
314G LEU 4.8 0.2 - - - -
317G ALA* 3.5 26.9 - - + -
322G ARG* 3.3 32.1 - - - +
323G VAL* 3.9 8.5 - - + -
324G ARG* 4.1 6.3 - - - +
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Residues in contact with ILE 266 (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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265G TRP* 1.3 77.2 - - - +
267G ASN* 1.3 65.7 + - - +
270G GLY* 3.6 28.3 - - - +
271G GLU 3.4 3.6 - - - -
272G GLU* 4.6 15.9 - - + +
321G ASN 5.5 1.8 - - - +
322G ARG* 2.7 70.2 + - + +
324G ARG* 5.6 7.0 - - + +
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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