Contacts of the strand formed by residues 334 - 343 (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 VAL 334 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97J LYS* 5.8 1.6 - - - +
288J THR* 3.3 16.4 - - + +
329J SER* 3.3 16.8 - - - -
330J GLY 2.9 17.0 + - - -
331J THR* 3.8 6.3 + - - +
332J ALA 3.6 2.7 - - - +
333J CYS* 1.3 80.7 - - - +
335J VAL* 1.3 71.1 + - + +
364J LEU* 3.7 33.9 - - + -
367J LEU* 3.7 29.8 - - + -
368J THR* 4.6 4.0 - - + -
371J GLN* 4.6 22.7 - - - +
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Residues in contact with VAL 335 (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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191J TYR* 6.0 0.5 - - - +
197J PHE* 3.4 27.2 - - + -
292J ILE* 4.0 7.2 - - + -
327J PHE* 3.7 28.0 - - + -
328J SER 3.3 5.2 - - - +
329J SER* 4.4 0.2 - - - -
333J CYS* 2.6 21.4 + - - +
334J VAL* 1.3 88.1 - - + +
336J CYS* 1.3 63.8 + - - +
360J ALA* 3.8 39.0 - - + +
363J ILE* 3.9 24.7 - - + -
364J LEU* 4.9 1.8 - - + +
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Residues in contact with CYS 336 (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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191J TYR* 6.4 0.7 - - - -
197J PHE* 5.2 0.2 - - - -
198J ASN 4.5 7.2 - - - -
200J VAL* 3.8 35.9 - - - -
259J MET* 3.8 15.9 - - + -
327J PHE* 3.3 3.5 - - - -
328J SER* 2.8 35.4 + - - -
333J CYS* 3.6 18.4 - - + -
335J VAL* 1.3 75.1 - - - +
337J PRO* 1.4 71.8 - - - +
338J VAL* 3.7 0.7 + - - +
4401J CBC 3.9 17.5 - - - -
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Residues in contact with PRO 337 (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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197J PHE* 3.5 49.1 - - + -
198J ASN 5.0 1.8 - - - +
199J PRO* 3.3 12.1 - - + +
200J VAL* 3.0 25.3 + - - +
326J MET 3.6 6.3 - - - +
327J PHE* 3.9 5.3 - - + -
335J VAL* 4.0 2.5 - - + +
336J CYS* 1.4 90.3 - - + +
338J VAL* 1.3 59.4 + - - +
352J THR* 3.6 20.9 - - + -
353J MET* 3.8 15.9 - - - -
357J PRO* 4.6 4.7 - - + -
360J ALA* 5.2 1.1 - - + -
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Residues in contact with VAL 338 (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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199J PRO* 4.8 0.7 - - - -
200J VAL* 3.6 11.4 - - + +
202J LEU* 3.8 31.4 - - + -
256J VAL* 4.7 1.6 - - + -
326J MET* 2.7 43.7 + - + +
327J PHE* 4.4 0.9 - - - -
328J SER* 4.0 18.6 - - - +
336J CYS 4.1 1.1 - - - +
337J PRO* 1.3 75.2 - - - +
339J SER* 1.3 61.6 + - - +
340J ASP 3.8 21.1 - - - +
341J ILE* 4.3 1.8 - - + -
350J ILE* 3.6 13.5 - - + +
352J THR* 2.6 28.3 + - - -
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Residues in contact with SER 339 (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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199J PRO* 3.7 26.3 - - - +
200J VAL 3.0 15.4 + - - -
201J SER* 4.0 2.1 + - - -
337J PRO 4.1 1.4 + - - -
338J VAL* 1.3 74.1 - - - +
340J ASP* 1.3 83.8 + - - +
349J HIS* 3.2 9.5 + - - -
350J ILE* 2.7 38.4 + - - +
352J THR* 5.1 1.1 - - - -
353J MET* 4.9 7.0 - - - -
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Residues in contact with ASP 340 (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 3.7 0.8 + - - -
201J SER* 3.3 19.4 + - - +
202J LEU 2.8 29.3 + - - -
338J VAL* 3.8 5.4 - - - +
339J SER* 1.3 101.1 + - - +
341J ILE* 1.3 63.3 + - - +
342J LEU* 4.3 3.8 - - + -
347J THR* 4.1 20.9 - - + +
348J ILE 3.3 7.1 - - - +
349J HIS* 2.9 32.9 + - - +
350J ILE* 4.3 0.9 - - - +
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Residues in contact with ILE 341 (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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202J LEU* 3.3 11.0 - - + +
204J ALA* 3.8 27.6 - - + -
244J LEU* 3.8 22.2 - - + -
311J MET* 4.4 5.6 - - + -
314J LEU* 3.6 31.2 - - + -
326J MET* 4.0 13.2 - - - -
338J VAL* 4.3 7.0 - - + -
340J ASP* 1.3 78.8 - - - +
342J LEU* 1.3 67.8 + - - +
343J TYR* 3.6 9.5 + - + -
348J ILE* 2.8 46.6 + - + +
350J ILE* 4.0 15.9 - - + -
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Residues in contact with LEU 342 (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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201J SER* 4.9 3.6 - - - -
202J LEU 2.7 13.1 + - - +
203J TRP* 3.6 32.2 - - + -
204J ALA* 2.9 32.4 + - - +
238J ASN* 4.7 9.9 - - + +
240J CYS* 3.7 22.9 - - - -
340J ASP* 4.9 7.0 - - + -
341J ILE* 1.3 74.8 - - - +
343J TYR* 1.3 59.6 + - - +
345J GLY 5.7 3.8 - - - +
346J GLU 3.5 9.9 - - - +
347J THR* 3.6 34.3 - - + +
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Residues in contact with TYR 343 (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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204J ALA* 3.3 26.0 - - + -
206J PRO* 4.3 11.5 - - + +
246J LEU* 3.8 20.2 - - + -
251J HIS* 3.6 28.9 + - - -
311J MET* 3.5 42.1 - - + +
312J ASP* 5.6 3.3 + - - -
315J THR* 5.4 4.5 - - + -
341J ILE* 3.6 5.3 + - + -
342J LEU* 1.3 74.0 - - - +
344J LYS* 1.3 100.3 + - + +
345J GLY 3.3 1.9 - - - +
346J GLU* 3.0 24.9 + - - +
348J ILE* 3.8 22.3 - - + +
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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