Contacts of the strand formed by residues 284 - 296 (chain B) in PDB entry 2ON3
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 PHE 284 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B TYR* 3.3 33.9 - + + -
42B VAL 3.4 3.4 - - - -
43B ALA* 3.5 18.4 - - + -
71B ASN* 3.6 24.9 - - - -
76B ILE* 3.5 31.2 - - + -
280B VAL* 4.2 3.4 - - + -
281B ALA 3.8 1.8 + - - -
282B SER 3.2 2.3 + - - +
283B ALA* 1.3 89.4 - - + +
285B THR* 1.3 61.6 + - - +
385B ASN 3.6 7.8 + - - -
386B MET* 2.9 27.5 + - - -
387B GLY* 3.6 25.1 - - - +
391B VAL* 4.7 3.6 - - + -
405B ILE* 3.7 30.1 - - + -
407B TYR* 4.0 9.6 - + - -
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Residues in contact with THR 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LYS* 6.1 2.5 - - + +
24B LEU* 4.0 30.0 - - + +
40B PHE 3.9 0.2 - - - +
41B TYR* 3.2 7.9 - - - -
42B VAL* 2.8 38.3 + - - +
282B SER 5.0 3.1 + - - -
283B ALA 5.6 0.2 - - - -
284B PHE* 1.3 75.5 + - - +
286B LEU* 1.3 67.6 + - - +
287B ALA 4.2 0.2 + - - -
382B LEU* 4.4 6.7 - - + -
383B PHE 3.4 20.9 - - - +
384B GLU* 4.4 16.4 - - + +
385B ASN 5.0 0.9 + - - -
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Residues in contact with LEU 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA* 4.3 7.0 - - + -
40B PHE 3.6 7.0 - - - +
41B TYR* 3.8 30.1 - - + +
285B THR* 1.3 76.4 - - - +
287B ALA* 1.3 64.0 + - - +
288B VAL* 3.7 16.6 - - + -
320B ASP* 3.8 22.7 - - - +
325B SER* 4.0 2.7 - - - -
326B PHE* 3.5 32.5 - - + -
381B MET 3.5 1.7 - - - +
382B LEU* 3.4 5.7 - - - +
383B PHE* 2.9 43.2 + - + +
386B MET* 3.7 20.2 - - + -
403B PRO* 4.4 2.9 - - + -
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Residues in contact with ALA 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B LEU* 3.7 14.8 - - + +
28B ILE* 4.7 1.3 - - + -
39B ALA* 2.9 26.0 - - - +
40B PHE* 2.8 45.4 + - + +
285B THR 4.2 0.4 - - - -
286B LEU* 1.3 73.6 - - - +
288B VAL* 1.3 61.0 + - - +
380B TRP* 3.5 10.7 - - + -
381B MET 3.6 4.9 - - - -
382B LEU* 3.9 9.2 - - + -
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Residues in contact with VAL 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ALA* 3.8 4.0 - - + -
286B LEU* 3.7 27.8 + - + -
287B ALA* 1.3 73.9 - - - +
289B ASN* 1.3 60.4 + - - +
318B VAL* 3.9 20.4 - - + -
319B ASN* 3.7 7.9 - - - +
320B ASP* 3.7 29.6 - - + +
326B PHE* 4.3 4.9 - - + -
380B TRP* 3.3 8.9 - - - -
381B MET* 3.0 44.5 + - + +
383B PHE* 3.6 22.7 - - + -
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Residues in contact with ASN 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLN* 5.5 0.3 - - - +
37B LYS* 3.3 44.7 - - + +
288B VAL* 1.3 74.1 - - - +
290B ILE* 1.3 77.5 + - - +
291B ILE* 3.1 20.8 + - + +
318B VAL* 3.3 4.1 - - - -
319B ASN* 2.6 26.9 + - - +
377B VAL* 5.7 0.5 - - - +
378B GLY* 2.8 30.7 + - - -
379B ASP 2.8 16.3 + - - -
380B TRP* 3.6 19.1 - - + -
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Residues in contact with ILE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ASN* 1.3 70.8 - - - +
291B ILE* 1.3 61.2 + - - +
292B ALA 3.6 19.1 - - - +
293B LYS* 5.2 0.7 - - + -
316B TYR* 4.1 18.8 - - + -
317B TYR 3.4 7.2 - - - +
318B VAL* 4.3 2.5 - - + -
375B MET* 3.7 47.8 - - + -
376B HIS 3.6 15.0 - - - +
377B VAL* 3.4 4.6 - - + +
378B GLY 3.0 23.4 + - - -
379B ASP* 2.9 25.3 + - + +
381B MET* 3.7 25.4 - - + -
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Residues in contact with ILE 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A CYS 4.0 13.7 - - - +
115A LYS 4.0 0.3 - - - +
116A GLN* 3.4 58.1 - - + +
117A VAL* 5.0 0.6 - - - +
141A LYS* 3.2 25.6 + - - -
289B ASN* 3.1 28.0 - - - +
290B ILE* 1.3 75.7 - - - +
292B ALA* 1.3 59.7 + - - +
317B TYR* 2.7 26.1 + - + +
318B VAL 4.1 6.5 - - - +
319B ASN* 4.1 13.9 - - + -
358B PRO* 4.4 14.4 - - + -
377B VAL* 3.5 14.2 - - - +
400B PHE* 6.1 1.6 - - + -
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Residues in contact with ALA 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A CYS* 3.6 39.9 - - + -
135A SER* 5.3 1.1 - - - +
137A VAL* 4.9 1.3 - - + -
138A GLU* 4.1 2.0 - - - +
141A LYS* 3.8 12.1 - - - +
290B ILE* 3.6 10.8 - - - +
291B ILE* 1.3 79.9 - - + +
293B LYS* 1.3 65.9 + - - +
316B TYR* 3.8 0.5 - - - -
317B TYR* 3.0 33.7 + - + -
377B VAL* 3.7 8.1 - - - -
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Residues in contact with LYS 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A SER* 3.6 8.1 + - - -
137A VAL* 3.5 39.4 - - + +
290B ILE* 5.2 0.7 - - + -
292B ALA* 1.3 80.3 - - - +
294B LYS* 1.3 75.8 + - - +
295B ILE* 4.8 7.7 - - + +
314B PHE* 3.6 25.0 - - + -
315B MET 3.3 7.6 - - - +
316B TYR* 3.7 19.3 - - + -
317B TYR* 4.1 1.1 - - - -
374B GLU* 2.8 30.9 + - - -
375B MET 3.0 27.7 + - - +
376B HIS* 3.5 12.5 + - - -
377B VAL* 4.2 10.2 - - + +
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Residues in contact with LYS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A CYS* 4.2 9.6 - - - -
134A ASP* 2.6 47.3 + - - +
135A SER* 3.6 15.9 - - - -
137A VAL* 5.5 0.2 - - - -
169A LYS 3.3 18.4 + - - +
170A PHE* 4.0 4.0 - - - +
171A GLY 4.4 1.4 - - - +
293B LYS* 1.3 79.5 - - - +
295B ILE* 1.3 67.9 + - - +
296B VAL* 4.2 0.4 + - + -
313B THR 4.1 0.2 - - - +
314B PHE* 3.6 7.4 - - - -
315B MET* 3.0 56.6 + - + +
317B TYR* 3.4 26.7 - - + +
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Residues in contact with ILE 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLU* 4.4 24.7 - - + +
137A VAL* 5.1 5.4 - - + -
293B LYS* 4.8 13.7 - - + +
294B LYS* 1.3 79.1 - - - +
296B VAL* 1.3 67.8 + - - +
297B LEU* 4.2 16.7 - - + +
311B GLU* 3.7 37.9 - - + -
313B THR 3.9 3.8 - - - +
314B PHE* 3.7 24.9 - - + -
374B GLU* 5.6 1.3 - - - +
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294B LYS* 5.1 0.4 - - + +
295B ILE* 1.3 79.0 - - - +
297B LEU* 1.3 66.0 + - - +
312B GLN 3.5 5.6 + - - -
313B THR* 3.0 61.4 + - - +
315B MET* 4.0 33.4 - - + -
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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