Contacts of the helix formed by residues 282 - 299 (chain B) in PDB entry 2XAR
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 HIS 282 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B SER* 3.6 18.7 + - - +
280B ASP* 2.8 46.4 + - + +
281B GLY* 1.3 78.3 + - - +
283B ARG* 1.3 64.2 + - - +
284B THR 3.3 2.5 - - - -
285B GLU* 2.8 36.6 + - + +
286B CYS* 3.3 27.4 + - - +
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Residues in contact with ARG 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B GLU* 2.5 54.9 + - - +
270B ASP* 5.3 1.4 - - - +
272B LEU* 3.3 38.1 - - + -
273B LYS* 3.3 28.9 + - - +
276B ILE* 3.4 23.8 + - + +
278B SER* 3.5 35.4 + - - +
279B GLU* 3.4 31.1 + - - +
282B HIS* 1.3 78.3 - - - +
284B THR* 1.3 57.5 + - - +
286B CYS 3.5 0.9 + - - -
287B PHE* 2.8 30.5 + - - +
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Residues in contact with THR 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B TYR* 3.7 42.0 + - + +
265B GLY 4.4 1.0 + - - -
268B PHE* 3.8 17.6 - - + -
269B GLU* 2.8 30.5 + - - +
272B LEU* 4.0 7.4 - - - -
281B GLY 5.2 3.4 - - - -
282B HIS 3.3 0.4 - - - -
283B ARG* 1.3 76.5 - - - +
285B GLU* 1.3 57.4 + - - +
287B PHE* 3.2 4.1 + - - +
288B LEU* 2.9 41.2 + - + +
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Residues in contact with GLU 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LEU* 5.7 0.7 - - - +
230B LYS* 6.3 3.4 - - - -
281B GLY 5.0 2.3 - - - +
282B HIS* 2.8 45.8 + - + +
284B THR* 1.3 79.7 - - - +
286B CYS* 1.3 63.2 + - - +
288B LEU* 3.5 12.8 + - + +
289B GLN* 3.0 25.6 + - - +
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Residues in contact with CYS 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ILE* 4.5 7.9 - - + -
278B SER* 5.3 4.0 - - - -
282B HIS* 3.3 22.7 + - - +
283B ARG 3.9 2.9 - - - +
284B THR 3.3 0.6 - - - -
285B GLU* 1.3 78.8 - - - +
287B PHE* 1.3 57.9 + - - +
289B GLN* 3.3 9.1 + - - +
290B LEU* 2.9 27.9 + - - +
392B LEU* 3.5 30.0 - - + +
394B PRO* 4.0 29.2 - - - -
395B THR* 5.6 2.9 - - - -
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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
----------------------------------------------------------
163B ILE* 3.6 25.4 - - + -
165B VAL* 3.5 25.8 - - + -
240B PHE* 4.3 5.6 - + - -
242B VAL* 3.7 20.4 - - + -
250B LEU* 5.7 0.2 - - + -
268B PHE* 3.6 25.8 - + - -
272B LEU* 3.8 17.9 - - + -
275B PHE* 4.6 3.1 - + - -
276B ILE* 3.6 13.8 - - + +
283B ARG 2.8 18.7 + - - +
284B THR 3.4 3.4 - - - +
286B CYS* 1.3 74.7 - - - +
288B LEU* 1.3 77.3 + - + +
290B LEU* 3.0 19.0 + - + +
291B VAL* 2.9 44.7 + - + +
375B PHE* 5.3 1.6 - + - -
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Residues in contact with LEU 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LEU* 4.3 5.1 - - + +
229B ILE* 3.8 25.7 - - + +
230B LYS* 4.3 27.1 - - + -
233B TYR* 3.6 46.7 - - + -
240B PHE* 4.8 2.5 - - + -
284B THR* 2.9 25.7 + - + +
285B GLU* 3.6 13.5 - - + +
286B CYS 3.3 0.2 - - - -
287B PHE* 1.3 93.6 - - + +
289B GLN* 1.3 56.4 + - - +
291B VAL* 3.4 3.2 + - - +
292B SER* 2.9 30.2 + - - -
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Residues in contact with GLN 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LYS* 4.1 8.7 - - - +
226B LEU* 3.9 33.9 - - + +
285B GLU 3.0 14.3 + - - +
286B CYS* 3.4 12.3 - - - +
288B LEU* 1.3 75.1 - - - +
290B LEU* 1.3 58.6 + - - +
292B SER* 3.3 6.2 + - - -
293B ASP* 2.9 66.1 + - - +
392B LEU* 4.7 9.4 - - + -
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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
----------------------------------------------------------
275B PHE* 3.8 30.5 - - + -
276B ILE* 5.1 1.8 - - + -
286B CYS 2.9 14.1 + - - +
287B PHE* 3.0 20.2 + - + +
289B GLN* 1.3 76.9 - - - +
291B VAL* 1.3 63.0 + - - +
293B ASP* 3.3 3.8 + - - +
294B ALA* 3.1 22.2 + - - +
375B PHE* 3.7 29.8 - - + -
390B VAL* 3.6 33.2 - - + +
392B LEU* 4.5 8.7 - - + +
399B PHE* 3.6 32.3 - - + -
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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
----------------------------------------------------------
165B VAL* 3.7 27.6 - - + -
167B ILE* 4.5 3.1 - - + -
229B ILE* 3.7 30.7 - - + -
240B PHE* 4.8 0.9 - - + -
287B PHE* 2.9 50.1 + - + +
288B LEU 3.7 6.1 - - - +
290B LEU* 1.3 74.6 - - + +
292B SER* 1.3 64.0 + - - +
294B ALA* 3.2 2.1 + - - +
295B VAL* 2.9 29.8 + - + +
373B ILE* 5.0 3.6 - - + -
375B PHE* 3.9 13.9 - - + -
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Residues in contact with SER 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LYS* 4.1 4.5 + - - +
225B VAL* 3.5 6.7 - - - +
226B LEU* 3.1 47.5 + - - +
229B ILE* 3.8 13.4 - - - +
288B LEU 2.9 18.2 + - - -
289B GLN* 3.4 9.1 + - - -
291B VAL* 1.3 76.9 - - - +
293B ASP* 1.3 58.1 + - - +
295B VAL* 3.4 1.7 + - - +
296B TYR* 2.9 31.1 + - - +
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Residues in contact with ASP 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A GLU* 4.9 7.0 - - - +
222B LYS* 2.8 31.1 + - - +
289B GLN* 2.9 39.6 + - - +
290B LEU 3.6 0.2 - - - +
291B VAL 3.2 0.2 - - - -
292B SER* 1.3 77.1 + - - +
294B ALA* 1.3 53.9 + - - +
296B TYR* 4.1 4.4 - - - +
297B GLY* 2.8 31.7 + - - -
390B VAL* 3.6 35.6 - - + +
391B SER 4.5 5.5 - - - +
392B LEU* 5.9 0.3 - - - +
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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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290B LEU 3.1 6.9 + - - +
291B VAL 3.2 1.8 + - - +
293B ASP* 1.3 75.4 - - - +
295B VAL* 1.3 66.1 + - - +
298B SER* 2.9 29.9 + - - -
373B ILE* 4.3 7.0 - - + -
375B PHE* 3.6 38.6 - - + -
390B VAL* 3.8 9.6 - - + +
401B TYR* 4.0 24.0 + - + -
403B VAL* 6.2 0.2 - - - -
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Residues in contact with VAL 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ILE* 4.0 18.4 - - + -
217B LEU* 4.1 4.7 - - + -
225B VAL* 3.7 20.6 - - + -
229B ILE* 4.2 7.6 - - + -
291B VAL* 2.9 21.1 + - + +
292B SER 3.6 3.6 - - - +
294B ALA* 1.3 75.4 - - - +
296B TYR* 1.3 64.1 + - - +
298B SER* 3.0 18.2 + - - -
299B GLY* 3.3 8.1 + - - -
300B VAL* 4.3 3.1 + - - +
301B LEU* 3.5 36.8 + - + +
371B ILE* 6.3 0.4 - - + -
373B ILE* 3.5 25.1 - - + -
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Residues in contact with TYR 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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330A CYS 4.8 0.5 + - - -
331A PRO* 4.0 4.9 + - - +
333A CYS 3.7 14.7 + - - -
334A LYS* 3.5 43.0 + - + +
335A GLU* 3.7 32.3 - - + -
220B GLY* 3.1 31.0 + - - -
222B LYS* 3.7 48.0 + - + +
225B VAL* 4.2 19.5 - - + -
292B SER* 2.9 17.9 + - - +
293B ASP* 4.1 4.3 - - - +
295B VAL* 1.3 77.1 - - - +
297B GLY* 1.3 66.1 + - - +
299B GLY* 3.2 12.4 + - - -
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Residues in contact with GLY 297 (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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334A LYS* 6.0 0.9 - - - +
335A GLU* 4.4 12.6 - - - -
293B ASP 2.8 23.0 + - - -
294B ALA 3.9 0.2 - - - -
296B TYR* 1.3 76.0 - - - +
298B SER* 1.3 61.0 + - - +
299B GLY* 3.2 1.4 + - - -
401B TYR* 4.0 6.3 - - - -
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Residues in contact with SER 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B HIS* 5.8 1.9 + - - -
294B ALA 2.9 15.6 + - - -
295B VAL* 3.0 16.3 + - - -
297B GLY* 1.3 75.9 - - - +
299B GLY* 1.3 61.7 + - - +
300B VAL* 3.1 22.4 + - - +
303B ARG* 5.6 3.8 + - - -
388B ASP* 5.9 0.9 - - - -
401B TYR* 3.4 25.8 + - - -
403B VAL* 4.1 16.3 - - - +
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Residues in contact with GLY 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A LYS* 5.7 2.7 - - - -
295B VAL 3.3 3.9 + - - -
296B TYR 3.2 11.7 + - - -
297B GLY 3.1 4.8 - - - -
298B SER* 1.3 79.1 + - - +
300B VAL* 1.3 62.0 + - - +
301B LEU* 3.2 4.7 + - - -
302B ASP* 3.4 33.9 + - - +
303B ARG* 4.2 8.5 + - - +
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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
------------------------------------------------------------
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