Contacts of the helix formed by residues 286 - 300 (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 GLY 286 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117J ARG* 3.7 0.4 - - - -
260J ASN* 3.2 21.5 - - - +
284J LEU 2.9 10.9 + - - -
285J PRO* 1.3 74.9 - - - +
287J VAL* 1.3 61.3 + - - -
288J THR 3.4 1.1 - - - -
289J ARG* 3.6 6.0 + - - +
290J ARG* 3.1 26.2 + - - +
420J PLP 3.4 20.9 - - - -
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Residues in contact with VAL 287 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109J PHE* 4.3 9.9 - - + +
110J GLN* 3.8 27.8 - - + +
113J LEU* 4.0 31.4 - - + +
114J ASN* 4.2 21.5 - - - +
117J ARG* 4.1 9.4 - - - +
285J PRO 3.7 0.6 + - - +
286J GLY* 1.3 69.0 - - - -
288J THR* 1.3 62.6 + - - +
290J ARG* 3.2 6.4 + - - +
291J CYS* 2.9 41.4 + - - -
331J THR* 5.3 4.0 - - - +
420J PLP 2.9 20.1 + - - +
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Residues in contact with THR 288 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109J PHE* 5.8 2.6 - - - -
287J VAL* 1.3 77.2 - - - +
289J ARG* 1.3 57.0 + - - +
291J CYS* 3.2 7.8 + - - +
292J ILE* 2.9 37.0 + - + +
329J SER* 3.9 7.4 - - - -
330J GLY 3.4 21.6 + - - +
331J THR* 3.7 5.9 + - - -
334J VAL* 3.3 31.9 - - + +
367J LEU* 3.9 21.8 - - + -
420J PLP 2.8 16.6 + - - -
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Residues in contact with ARG 289 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260J ASN* 3.3 42.3 - - + +
262J PHE* 3.6 30.6 - - + -
276J THR* 3.8 11.9 + - - +
277J PRO 3.0 27.5 + - - -
279J LEU* 3.6 31.9 - - - +
283J ILE* 4.3 3.2 - - - +
284J LEU 4.4 2.9 - - - -
285J PRO* 5.4 0.8 - - - +
286J GLY 3.6 13.8 + - - +
288J THR* 1.3 78.5 - - - +
290J ARG* 1.3 90.6 + - - +
292J ILE 3.5 0.2 + - - -
293J LEU* 3.1 31.9 + - + +
306J GLU* 2.9 25.0 + - - +
329J SER* 3.7 2.6 + - - -
420J PLP 4.3 0.4 + - - -
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Residues in contact with ARG 290 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110J GLN* 6.1 0.7 - - - +
113J LEU* 5.2 12.6 - - + -
279J LEU* 4.4 8.7 - - - +
286J GLY 3.1 14.8 + - - +
287J VAL* 3.2 6.3 + - - +
289J ARG* 1.3 99.8 - - - +
291J CYS* 1.3 62.8 + - - +
293J LEU* 3.4 24.9 + - - +
294J ASP* 2.9 57.4 + - - +
297J HIS* 5.2 5.9 - - - -
306J GLU* 3.6 23.4 + - - -
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Residues in contact with CYS 291 (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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109J PHE* 3.7 32.5 - - - -
110J GLN* 3.8 20.4 - - - -
113J LEU* 5.8 0.4 - - - -
287J VAL* 2.9 21.2 + - - +
288J THR* 3.2 10.1 + - - +
290J ARG* 1.3 77.7 - - - +
292J ILE* 1.3 56.2 + - - +
294J ASP* 3.4 1.4 + - - -
295J LEU* 2.9 32.0 + - - +
367J LEU* 4.0 11.9 - - + -
379J TRP* 3.5 30.9 - - + -
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Residues in contact with ILE 292 (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* 3.7 28.5 - - + -
274J LEU* 4.0 14.6 - - + -
288J THR* 2.9 22.2 + - + +
289J ARG 3.8 3.8 - - - +
291J CYS* 1.3 72.7 - - - +
293J LEU* 1.3 61.8 + - - +
295J LEU* 3.4 8.4 + - - +
296J ALA* 2.9 29.3 + - + +
299J TRP* 5.6 0.4 - - + -
327J PHE* 4.4 3.8 - - + -
329J SER* 3.7 29.8 - - - -
335J VAL* 4.0 10.3 - - + -
363J ILE* 3.7 42.0 - - + -
367J LEU* 4.1 6.7 - - + -
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Residues in contact with LEU 293 (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* 3.7 24.2 - - + -
274J LEU* 5.0 3.4 - - + +
276J THR* 3.9 12.6 - - + -
289J ARG* 3.1 53.4 + - + +
290J ARG* 3.6 28.5 - - - +
292J ILE* 1.3 74.2 - - - +
294J ASP* 1.3 63.8 + - - +
296J ALA* 3.4 3.2 + - - +
297J HIS* 3.0 35.7 + - + +
304J VAL* 3.6 25.8 - - + -
305J SER 5.3 1.1 - - - +
306J GLU* 4.0 15.0 - - + +
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Residues in contact with ASP 294 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290J ARG* 2.9 49.8 + - - +
291J CYS* 3.5 5.6 - - - +
293J LEU* 1.3 76.0 - - - +
295J LEU* 1.3 56.9 + - + +
297J HIS* 4.6 3.2 + - - -
298J GLN* 2.8 50.7 + - + +
379J TRP* 3.9 24.3 + - + -
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Residues in contact with LEU 295 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291J CYS 2.9 22.5 + - - +
292J ILE* 3.5 9.0 - - - +
294J ASP* 1.3 71.6 - - - +
296J ALA* 1.3 58.4 + - - +
298J GLN* 3.2 9.3 + - + +
299J TRP* 3.0 55.7 + - + +
363J ILE* 5.2 4.5 - - + -
366J LYS* 4.0 31.6 - - + -
367J LEU* 3.8 31.9 - - + -
370J ILE* 4.9 3.4 - - + -
379J TRP* 3.6 22.4 - - + -
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Residues in contact with ALA 296 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274J LEU* 3.8 22.0 - - + -
292J ILE 2.9 21.1 + - - +
293J LEU 3.9 2.5 - - - +
295J LEU* 1.3 70.8 - - - +
297J HIS* 1.3 66.9 + - - +
299J TRP* 3.5 16.3 + - + +
300J GLY* 3.4 17.0 + - - -
301J GLU 4.8 1.7 + - - -
302J PHE* 4.0 13.1 - - + +
304J VAL* 3.5 27.3 - - + +
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Residues in contact with HIS 297 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290J ARG* 5.2 6.7 + - - -
293J LEU* 3.0 35.4 + - + +
294J ASP* 3.6 8.6 + - - +
296J ALA* 1.3 76.3 - - - +
298J GLN* 1.3 72.8 + - - +
300J GLY* 3.4 13.4 + - - -
304J VAL* 3.6 39.9 + - + +
306J GLU* 5.2 6.1 - - + -
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Residues in contact with GLN 298 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294J ASP* 2.8 41.5 + - + +
295J LEU* 3.2 8.9 + - + +
297J HIS* 1.3 88.8 + - - +
299J TRP* 1.3 69.4 + - + +
300J GLY* 3.5 0.7 + - - -
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Residues in contact with TRP 299 (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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274J LEU* 6.4 0.2 - - + -
292J ILE* 5.6 0.4 - - + -
295J LEU* 3.0 38.3 + - + +
296J ALA* 3.8 25.4 - - + +
297J HIS 3.4 0.2 - - - -
298J GLN* 1.3 80.6 - - + +
300J GLY* 1.3 62.3 + - - +
301J GLU* 3.3 24.9 + - + +
302J PHE* 4.3 10.5 - + + -
359J LEU* 3.8 22.7 - - + -
362J ARG* 3.5 53.2 - - + +
363J ILE* 4.1 21.5 - - + -
366J LYS* 4.2 26.9 - - + +
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Residues in contact with GLY 300 (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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296J ALA 3.4 8.7 + - - -
297J HIS 3.4 10.3 + - - -
298J GLN 3.3 3.1 - - - -
299J TRP* 1.3 78.6 - - - +
301J GLU* 1.3 60.2 + - - +
302J PHE 3.6 6.3 - - - -
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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