Contacts of the helix formed by residues 282 - 297 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80I HIS* 6.0 0.7 - + - -
81I SER* 4.8 1.4 - - - -
82I ASN* 3.8 11.2 - - - -
188I ALA* 4.3 3.8 - - + -
190I GLY* 5.2 3.4 - - - -
216I VAL* 3.8 25.3 - - + +
256I TYR* 3.1 33.4 + + - -
279I ASP* 2.8 12.6 + - - +
281I VAL* 1.3 113.0 - - + +
283I THR* 1.3 70.1 + - - +
284I GLY 3.0 1.1 - - - -
285I LYS* 2.9 17.0 + - - +
286I ALA* 3.0 9.5 + - - +
1091I 5PA 3.0 96.2 + + + +
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Residues in contact with THR 283 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188I ALA* 4.5 1.5 - - + +
278I LEU* 2.9 23.6 - - - +
279I ASP* 2.5 46.0 + - - +
282I TYR* 1.3 76.9 - - + +
284I GLY* 1.3 62.7 + - - +
286I ALA* 3.9 10.3 - - - -
287I PHE* 3.0 26.0 + - - +
305I PHE* 4.2 5.1 - - + -
307I HIS* 4.0 15.0 - - + +
308I THR* 3.5 37.5 - - - +
309I GLY 4.2 4.5 - - - +
1091I 5PA 4.5 0.7 - - + -
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Residues in contact with GLY 284 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263I VAL* 4.0 17.3 - - - -
266I ILE* 3.3 26.5 - - - +
267I ILE* 4.5 0.9 - - - -
278I LEU* 4.4 5.6 - - - -
279I ASP 2.5 29.5 + - - -
282I TYR 2.9 0.2 + - - -
283I THR* 1.3 76.5 + - - +
285I LYS* 1.3 60.7 + - - +
287I PHE* 4.2 0.2 - - - +
288I TYR* 3.4 11.3 + - - +
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Residues in contact with LYS 285 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214I ILE* 2.6 25.6 - - + +
216I VAL* 2.5 37.4 + - + +
251I TYR* 3.1 26.1 - - - +
252I SER 2.5 24.5 + - - -
253I PHE* 3.4 22.4 - - + -
255I GLU 3.6 12.3 + - - -
256I TYR* 4.3 3.4 - - - +
257I GLY 4.5 2.4 - - - +
258I LYS 4.1 12.7 + - - -
263I VAL* 4.3 7.9 - - + -
280I PRO 4.2 10.1 - - - +
281I VAL* 3.9 13.4 + - - +
282I TYR 2.9 8.9 + - - +
284I GLY* 1.3 71.3 - - - -
286I ALA* 1.3 51.9 + - - +
288I TYR* 3.2 8.3 + - - +
289I GLY 2.7 19.9 + - - -
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Residues in contact with ALA 286 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186I VAL* 5.1 1.6 - - - +
188I ALA* 3.4 32.8 - - + -
214I ILE* 3.3 25.0 - - + +
216I VAL* 4.9 0.6 - - - +
282I TYR 3.0 7.0 + - - +
283I THR* 3.5 6.7 - - - +
285I LYS* 1.3 75.6 - - - +
287I PHE* 1.3 63.0 + - - +
289I GLY 3.3 0.7 + - - -
290I LEU* 3.0 21.5 + - - +
305I PHE* 3.5 23.7 - - + -
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Residues in contact with PHE 287 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I LEU* 3.7 24.9 - - + -
30I ILE* 3.7 40.8 - - + -
38I VAL* 4.6 2.0 - - + -
40I ILE* 5.1 2.0 - - + -
266I ILE* 4.0 5.8 - - + -
270I VAL* 3.1 40.4 - - + -
278I LEU* 3.5 23.3 - - + -
283I THR 3.0 5.9 + - - +
284I GLY 4.2 1.3 - - - +
286I ALA* 1.3 75.6 - - - +
288I TYR* 1.3 51.4 + - - +
290I LEU* 3.0 20.2 + - + +
291I VAL* 2.6 51.7 + - + +
305I PHE* 3.5 34.7 - + + -
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Residues in contact with TYR 288 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251I TYR* 3.5 28.5 - + - -
253I PHE* 4.2 19.0 - + + -
262I GLU* 3.6 49.4 + - + +
263I VAL* 5.0 0.7 - - - -
266I ILE* 4.3 16.5 - - + +
269I LYS* 5.4 3.4 - - - -
284I GLY 3.4 14.5 + - - +
285I LYS* 3.3 11.4 - - - +
287I PHE* 1.3 75.4 - - - +
289I GLY* 1.3 66.8 + - - +
291I VAL* 3.0 22.1 + - + +
292I ASP* 3.0 21.5 + - - +
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Residues in contact with GLY 289 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214I ILE* 3.4 15.5 - - - -
251I TYR* 3.4 28.3 - - - -
285I LYS 2.7 14.8 + - - -
287I PHE 3.2 0.2 - - - -
288I TYR* 1.3 71.0 - - - +
290I LEU* 1.3 52.7 + - - +
292I ASP* 2.7 15.6 + - - +
293I LEU* 2.7 30.8 - - - +
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Residues in contact with LEU 290 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I ILE* 6.2 0.7 - - + -
34I ILE* 4.5 6.1 - - + -
38I VAL* 3.4 35.7 - - + -
186I VAL* 3.7 22.6 - - + +
214I ILE* 5.6 0.6 - - - +
286I ALA 3.0 12.2 + - - +
287I PHE* 3.0 19.3 + - + +
289I GLY* 1.3 73.4 - - - +
291I VAL* 1.3 65.0 + - + +
292I ASP 3.1 1.2 + - - -
293I LEU* 4.7 0.7 - - - -
294I ALA* 2.9 32.6 + - + +
299I LEU* 3.1 27.1 - - + +
303I ILE* 4.0 13.0 - - + -
305I PHE* 3.6 28.9 - - + -
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Residues in contact with VAL 291 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I ILE* 5.0 7.4 - - + -
34I ILE* 4.6 13.5 - - + +
266I ILE* 3.9 15.9 - - + -
269I LYS* 6.1 1.6 - - + +
287I PHE* 2.6 55.5 + - + +
288I TYR* 3.0 16.6 + - + +
290I LEU* 1.3 78.5 - - + +
292I ASP* 1.3 57.4 + - - +
294I ALA* 4.4 2.5 - - - +
295I ARG* 3.5 48.9 + - - +
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Residues in contact with ASP 292 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251I TYR* 2.8 39.5 + - + +
288I TYR* 3.0 16.6 + - - +
289I GLY 2.7 14.1 + - - +
291I VAL* 1.3 69.2 - - - +
293I LEU* 1.3 65.4 + - - +
294I ALA 3.2 1.1 - - - -
295I ARG* 3.3 10.2 + - - +
296I LYS* 3.1 44.8 + - - +
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Residues in contact with LEU 293 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212I VAL* 4.2 3.4 - - + -
249I TYR* 3.6 43.7 - - + +
251I TYR* 2.7 34.3 - - + +
289I GLY 2.7 20.2 - - - +
290I LEU* 5.3 0.4 - - - -
292I ASP* 1.3 69.5 - - - +
294I ALA* 1.3 54.9 + - - +
296I LYS* 2.8 14.1 + - + +
297I GLY 2.4 33.8 + - - -
298I GLU* 2.9 23.1 + - + +
299I LEU* 3.1 34.3 - - + -
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Residues in contact with ALA 294 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I ILE* 4.3 20.9 - - + +
35I GLY 4.8 5.0 - - - +
36I ALA* 5.1 5.8 - - + +
290I LEU* 2.9 26.2 + - + +
291I VAL 4.4 2.2 - - - +
293I LEU* 1.3 79.0 - - - +
295I ARG* 1.3 56.1 + - - +
297I GLY* 2.7 24.6 + - - +
299I LEU* 3.5 19.0 - - + +
300I GLY 5.9 0.9 - - - -
303I ILE* 3.8 15.7 - - + -
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Residues in contact with ARG 295 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I GLU* 4.2 35.2 + - - +
34I ILE* 4.2 25.1 - - + +
269I LYS* 6.0 3.8 - - - +
291I VAL* 3.5 34.2 + - - +
292I ASP* 3.3 13.7 + - - +
293I LEU 3.2 0.4 - - - -
294I ALA* 1.3 78.5 - - - +
296I LYS* 1.3 62.2 + - + +
297I GLY* 3.5 0.3 + - - -
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Residues in contact with LYS 296 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251I TYR* 4.6 4.4 + - - -
292I ASP* 3.1 37.8 + - - +
293I LEU* 2.8 12.2 + - + +
295I ARG* 1.3 77.7 - - + +
297I GLY* 1.3 59.5 + - - +
298I GLU* 3.2 30.4 - - - +
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Residues in contact with GLY 297 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293I LEU 2.4 16.0 + - - -
294I ALA 2.7 15.0 + - - -
295I ARG 3.1 0.4 - - - -
296I LYS* 1.3 74.3 - - - +
298I GLU* 1.3 58.4 + - - +
299I LEU 3.5 3.3 + - - -
300I GLY* 4.5 12.6 + - - +
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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
------------------------------------------------------------
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