Contacts of the helix formed by residues 282 - 296 (chain B) in PDB entry 1J0B
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 TYR 282 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B HIS* 4.8 4.9 - + - -
82B ASN* 3.6 13.2 - - - -
131B PHE* 5.6 0.2 - - - -
188B ALA* 3.8 12.1 - - + +
190B GLY* 4.7 4.5 - - - -
216B VAL* 4.0 20.8 - - + +
256B TYR* 2.5 35.8 + + - -
279B ASP* 2.9 12.1 + - - +
281B VAL* 1.3 113.1 - - + +
283B THR* 1.3 66.0 + - - +
284B GLY 3.2 2.4 + - - -
285B LYS* 3.3 14.7 + - - +
286B ALA 3.4 8.3 + - - -
1021B 5PA 3.0 92.5 + + + +
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Residues in contact with THR 283 (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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188B ALA* 5.0 1.1 - - - -
278B LEU* 3.1 15.0 - - - +
279B ASP* 2.3 48.7 + - - +
282B TYR* 1.3 79.5 - - - +
284B GLY* 1.3 56.4 + - - +
286B ALA* 3.6 3.1 + - - -
287B PHE* 3.2 24.6 + - - +
305B PHE* 3.5 19.5 - - + -
307B HIS* 3.8 7.6 - - - +
308B THR* 3.1 38.4 - - - +
309B GLY 3.4 13.7 - - - +
1021B 5PA 4.3 1.6 - - + -
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Residues in contact with GLY 284 (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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263B VAL* 4.1 8.3 - - - -
266B ILE* 3.2 31.5 - - - +
267B ILE* 4.8 1.1 - - - -
278B LEU* 4.0 13.9 - - - -
279B ASP 2.7 27.7 + - - -
283B THR* 1.3 73.1 + - - +
285B LYS* 1.3 62.3 + - - +
287B PHE* 3.6 0.5 + - - +
288B TYR* 3.2 10.7 + - - +
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Residues in contact with LYS 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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214B ILE* 3.8 6.5 - - - +
216B VAL* 4.1 16.8 + - + -
251B TYR* 3.5 29.3 - - + +
252B SER* 3.1 25.5 + - - -
253B PHE* 4.2 3.1 - - + -
255B GLU 3.7 3.8 + - - -
257B GLY* 3.9 7.9 - - - +
258B LYS 3.0 40.7 + - - +
263B VAL* 3.6 24.2 - - + -
279B ASP 4.2 0.2 + - - -
280B PRO 3.6 13.2 - - - +
281B VAL 4.0 15.5 + - - +
282B TYR 3.3 8.4 + - - +
284B GLY* 1.3 77.4 - - - +
286B ALA* 1.3 58.1 + - - +
287B PHE 3.4 0.2 - - - -
288B TYR* 3.5 7.3 - - - +
289B GLY* 2.9 22.9 + - - -
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Residues in contact with ALA 286 (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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186B VAL* 4.0 1.6 - - - +
188B ALA* 3.6 37.2 - - + +
214B ILE* 3.7 26.2 - - + +
282B TYR 3.4 5.3 + - - +
283B THR 4.0 2.2 - - - +
284B GLY 3.3 0.6 - - - -
285B LYS* 1.3 77.2 - - - +
287B PHE* 1.3 62.9 + - - +
288B TYR 3.2 0.9 - - - -
289B GLY 3.6 2.9 - - - -
290B LEU* 3.3 17.8 + - - +
305B PHE* 3.8 17.9 - - + -
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Residues in contact with PHE 287 (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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27B LEU* 4.0 20.4 - - + -
30B ILE* 3.4 46.9 - - + -
38B VAL* 4.5 2.2 - - + -
40B ILE* 5.6 0.7 - - + -
266B ILE* 3.9 9.2 - - + -
270B VAL* 3.2 34.5 - - + -
278B LEU* 3.8 15.5 - - + -
283B THR 3.2 17.0 + - - +
284B GLY 3.6 2.2 + - - +
286B ALA* 1.3 76.9 - - - +
288B TYR* 1.3 61.1 + - - +
290B LEU* 2.8 39.8 + - + +
291B VAL* 3.1 14.9 + - + +
305B PHE* 3.6 34.5 - + + -
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Residues in contact with TYR 288 (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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251B TYR* 4.0 21.8 - + - -
253B PHE* 3.4 37.9 - + - -
262B GLU* 4.2 30.8 - - + +
263B VAL* 5.3 0.4 - - - -
266B ILE* 3.9 25.9 - - + +
284B GLY 3.2 17.2 + - - +
285B LYS* 3.5 5.8 - - - +
287B PHE* 1.3 76.6 - - - +
289B GLY* 1.3 57.8 + - - +
290B LEU 3.0 7.6 + - - -
291B VAL* 3.6 4.4 + - + +
292B ASP* 3.4 27.2 + - + +
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Residues in contact with GLY 289 (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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186B VAL* 5.1 0.2 - - - +
214B ILE* 3.6 19.0 - - - +
251B TYR* 3.7 31.6 - - - -
285B LYS 2.9 15.0 + - - -
286B ALA 3.6 5.8 + - - -
287B PHE 3.2 0.6 - - - -
288B TYR* 1.3 75.4 - - - +
290B LEU* 1.3 57.6 + - - +
291B VAL 3.6 0.2 - - - -
292B ASP 4.2 2.7 - - - -
293B LEU* 3.7 21.6 - - - +
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Residues in contact with LEU 290 (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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34B ILE* 3.5 22.9 - - + -
38B VAL* 4.2 18.2 - - + -
186B VAL* 3.4 31.4 - - + -
286B ALA 3.3 13.3 + - - +
287B PHE* 2.8 43.7 + - + +
289B GLY* 1.3 80.1 - - - +
291B VAL* 1.3 63.4 + - - +
293B LEU 3.6 0.6 + - - -
294B ALA* 3.0 28.2 + - + +
299B LEU* 3.4 19.7 - - + +
303B ILE* 3.8 11.0 - - + -
305B PHE* 4.9 5.4 - - + -
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Residues in contact with VAL 291 (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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30B ILE* 4.8 3.1 - - + -
33B GLU* 5.2 3.6 - - - +
34B ILE* 3.2 36.1 - - + -
266B ILE* 3.8 24.2 - - + -
287B PHE* 3.1 21.3 + - + +
288B TYR* 4.1 7.6 - - + +
290B LEU* 1.3 73.4 - - - +
292B ASP* 1.3 68.6 + - - +
294B ALA* 3.0 2.6 + - - +
295B ARG* 2.9 59.6 + - - +
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Residues in contact with ASP 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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251B TYR* 2.5 44.9 + - + +
288B TYR* 3.4 18.6 + - + +
289B GLY* 4.3 1.1 - - - -
290B LEU 3.4 0.2 - - - -
291B VAL* 1.3 80.2 - - - +
293B LEU* 1.3 65.5 + - - +
295B ARG* 3.5 8.5 + - - +
296B LYS* 3.2 50.0 + - - +
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Residues in contact with LEU 293 (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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186B VAL* 6.1 0.4 - - + -
212B VAL* 4.1 5.2 - - + -
214B ILE* 4.4 2.7 - - + -
249B TYR* 3.6 43.1 - - + -
251B TYR* 3.0 37.5 - - + +
289B GLY 3.7 16.9 + - - +
290B LEU 3.6 1.7 + - - +
291B VAL 3.2 0.6 - - - -
292B ASP* 1.3 78.8 + - - +
294B ALA* 1.3 61.0 + - - +
295B ARG 3.1 4.5 - - - -
296B LYS* 3.1 10.9 + - + +
298B GLU* 2.9 47.1 + - + +
299B LEU* 3.7 30.1 - - + -
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Residues in contact with ALA 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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34B ILE* 2.9 42.5 - - + +
35B GLY 5.6 0.3 - - - -
36B ALA* 4.6 6.2 - - + +
290B LEU* 3.0 18.8 + - + +
291B VAL 3.0 2.9 + - - +
293B LEU* 1.3 76.6 - - - +
295B ARG* 1.3 58.7 + - - +
297B GLY* 3.8 8.1 + - - -
298B GLU 4.9 0.2 - - - +
299B LEU* 4.3 9.5 - - - +
300B GLY 6.0 0.7 - - - -
303B ILE* 4.0 22.0 - - + -
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Residues in contact with ARG 295 (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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33B GLU* 3.8 23.8 + - - +
34B ILE* 4.2 22.4 - - - +
291B VAL* 2.9 41.7 + - + +
292B ASP* 3.8 6.6 - - - +
294B ALA* 1.3 75.4 - - - +
296B LYS* 1.3 60.9 + - + +
297B GLY 3.0 8.1 + - - -
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Residues in contact with LYS 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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292B ASP* 3.2 41.8 + - - +
293B LEU* 3.1 7.6 + - + +
295B ARG* 1.3 76.9 - - + +
297B GLY* 1.3 63.8 + - - +
298B GLU* 3.2 31.5 + - + +
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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