Contacts of the strand formed by residues 286 - 292 (chain A) in PDB entry 2JA4
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 GLU 286 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A LEU* 3.7 15.6 - - - +
281A GLY* 3.1 24.9 + - - -
282A SER* 2.5 40.0 + - - -
283A SER* 3.2 21.9 + - - +
284A ILE 3.4 1.9 + - - +
285A CYS* 1.3 80.2 - - - +
287A GLY* 1.3 59.8 + - - +
364A PHE* 3.9 15.9 - - + -
365A VAL 3.2 13.0 - - - +
366A THR* 3.9 25.4 + - + +
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Residues in contact with GLY 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU* 3.7 11.2 - - - +
279A VAL 3.3 12.1 - - - -
281A GLY 4.0 3.1 - - - -
286A GLU* 1.3 79.7 - - - +
288A THR* 1.3 64.4 + - - -
289A VAL 3.7 0.5 + - - -
364A PHE* 3.6 20.6 - - - -
365A VAL 2.9 29.9 + - - +
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Residues in contact with THR 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A LEU* 3.3 3.1 - - - -
279A VAL* 2.8 46.7 + - + +
287A GLY* 1.3 72.2 - - - -
289A VAL* 1.3 72.8 + - - +
290A GLU* 3.4 2.6 + - + -
299A ALA* 5.1 4.5 - - + -
330A LEU* 3.4 25.9 - - + +
362A LYS* 4.5 18.2 - - + -
363A VAL 3.3 11.9 - - - +
364A PHE* 4.0 8.6 - - - +
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Residues in contact with VAL 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A SER* 4.8 2.5 - - - -
277A ARG 3.5 6.3 - - - +
278A LEU* 3.8 11.4 - - + -
288A THR* 1.3 76.2 - - - +
290A GLU* 1.3 71.9 + - - +
291A VAL* 4.5 4.5 - - + -
299A ALA* 3.6 5.2 - - - +
300A LEU* 3.0 48.8 + - + +
312A TRP* 4.1 15.3 - - + -
315A VAL* 4.5 14.4 - - + -
363A VAL* 2.9 20.5 + - + +
365A VAL* 3.6 31.6 - - + -
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Residues in contact with GLU 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A SER* 3.2 5.9 - - - -
277A ARG* 2.7 79.3 + - + +
279A VAL* 3.4 26.9 - - + +
288A THR* 4.4 2.0 - - + +
289A VAL* 1.3 79.1 - - - +
291A VAL* 1.3 65.4 + - - +
297A TRP* 3.9 10.5 - - + +
298A ALA* 3.2 28.8 - - - +
299A ALA* 3.9 7.6 + - + +
300A LEU 4.1 0.4 - - - +
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Residues in contact with VAL 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A VAL* 4.0 5.8 - - + -
275A GLN 3.2 12.1 - - - +
276A SER* 4.3 1.3 - - - -
289A VAL* 4.5 1.1 - - + -
290A GLU* 1.3 79.9 - - - +
292A ARG* 1.3 62.3 + - - +
296A GLN 3.8 0.9 - - - +
297A TRP* 3.5 4.5 - - - -
298A ALA 2.9 32.5 + - - +
300A LEU* 4.0 31.6 - - + -
340A LEU* 4.0 16.4 - - + +
347A LEU* 3.6 31.0 - - + -
353A LEU* 3.6 24.0 - - + -
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Residues in contact with ARG 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A LYS 4.3 0.2 - - - +
274A VAL* 3.8 1.6 - - - +
275A GLN* 2.7 87.3 + - - +
291A VAL* 1.3 77.6 - - - +
293A GLN* 1.3 65.7 + - - +
294A GLY 4.1 2.7 - - - +
295A ALA* 3.5 35.2 - - - +
296A GLN 3.6 14.7 - - - +
297A TRP* 3.2 46.4 - - + +
353A LEU* 3.8 6.7 - - - -
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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