Contacts of the strand formed by residues 323 - 330 (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 323 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263J LEU* 4.2 20.4 - - + -
265J TRP* 4.1 7.0 - - + -
314J LEU* 3.9 13.7 - - + -
317J ALA* 3.7 25.3 + - + -
318J LEU* 3.7 28.7 - - + +
321J ASN* 3.5 5.6 - - - +
322J ARG* 1.3 78.0 - - - +
324J ARG* 1.3 67.8 + - - +
325J GLU 4.2 0.4 - - - +
350J ILE* 3.8 28.7 - - + -
351J PRO* 3.4 21.1 - - + +
355J ASN* 4.0 2.8 + - - -
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Residues in contact with ARG 324 (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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264J TYR* 2.9 60.2 + - + +
265J TRP* 4.7 3.8 - - - +
266J ILE* 5.2 13.6 - - + +
272J GLU* 3.7 12.7 + - - +
322J ARG 3.7 6.9 + - - +
323J VAL* 1.3 79.2 - - - +
325J GLU* 1.3 67.7 + - + +
351J PRO 3.5 1.4 - - - +
352J THR* 3.5 11.3 + - - -
355J ASN* 3.0 37.2 + - - +
358J LYS* 3.5 43.8 - - - +
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Residues in contact with GLU 325 (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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262J PHE 4.2 0.2 - - - +
263J LEU* 3.6 5.8 - - - +
264J TYR* 2.8 57.4 + - + +
323J VAL* 4.2 2.4 - - - +
324J ARG* 1.3 85.5 + - + +
326J MET* 1.3 59.7 + - - +
327J PHE* 4.4 7.9 - - + -
352J THR* 3.7 26.0 - - + +
355J ASN* 4.0 4.1 - - + +
357J PRO* 3.4 3.1 - - + +
358J LYS* 3.3 18.2 + - - +
359J LEU* 2.8 27.2 + - - +
360J ALA* 2.8 35.9 + - - +
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Residues in contact with MET 326 (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* 4.9 1.6 - - - -
244J LEU* 4.8 7.4 - - + -
253J ILE* 3.7 26.9 - - + -
261J LEU* 3.5 28.9 - - + -
262J PHE 3.5 12.1 - - - +
263J LEU* 4.3 11.4 - - + -
314J LEU* 4.2 16.6 - - + -
325J GLU* 1.3 74.1 - - - +
327J PHE* 1.3 61.9 + - - +
337J PRO* 3.6 1.7 - - - +
338J VAL* 2.7 55.6 + - + -
341J ILE* 4.0 15.7 - - + -
350J ILE* 3.9 20.1 - - + +
352J THR* 3.0 10.5 + - - +
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Residues in contact with PHE 327 (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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261J LEU* 4.0 3.4 - - - +
262J PHE* 2.9 66.7 + + + +
264J TYR* 4.7 3.4 - - + -
274J LEU* 3.9 17.9 - - + -
292J ILE* 4.4 2.9 - - + -
325J GLU* 4.4 18.4 - - + -
326J MET* 1.3 79.2 - - - +
328J SER* 1.3 64.3 + - - +
335J VAL* 3.7 31.4 - - + -
336J CYS 3.3 19.3 - - - +
337J PRO* 3.9 3.8 - - + -
338J VAL* 4.4 3.4 - - - +
359J LEU* 4.4 9.2 - - + -
360J ALA* 4.2 13.7 - - + -
363J ILE* 3.6 31.0 - - + -
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Residues in contact with SER 328 (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* 5.1 0.7 - - - +
256J VAL* 2.9 35.0 - - - +
259J MET* 3.2 39.5 - - - +
260J ASN 3.1 6.3 - - - -
327J PHE* 1.3 76.2 - - - +
329J SER* 1.3 60.6 + - - +
335J VAL* 3.3 6.4 - - - +
336J CYS* 2.8 35.6 + - - +
338J VAL* 4.0 3.8 - - - +
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Residues in contact with SER 329 (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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259J MET* 3.1 10.0 - - - -
260J ASN* 2.8 46.6 + - - +
262J PHE* 3.4 22.2 - - - -
288J THR* 3.9 5.6 - - - -
289J ARG 3.7 9.2 + - - -
292J ILE* 3.7 22.4 - - - -
328J SER* 1.3 74.8 - - - +
330J GLY* 1.3 58.8 + - - +
334J VAL 3.3 14.6 - - - -
335J VAL* 4.4 0.7 - - - -
420J PLP 3.9 4.8 - - - +
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Residues in contact with GLY 330 (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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259J MET* 4.1 0.4 - - - +
288J THR* 3.4 12.8 + - - -
329J SER* 1.3 76.1 - - - +
331J THR* 1.3 60.8 + - - -
332J ALA 3.3 2.7 - - - -
333J CYS* 3.7 1.4 + - - -
334J VAL* 2.9 33.7 + - - -
420J PLP 3.8 14.8 - - - -
4401J CBC 3.4 16.9 + - - -
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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