Contacts of the helix formed by residues 283 - 307 (chain A) in PDB entry 2YWB
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 ASP 283 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A VAL* 3.8 1.4 - - + +
282A GLU* 1.3 77.1 - - - +
284A PRO* 1.3 72.4 - - - +
285A GLU* 3.4 12.2 + - - +
286A GLU* 2.8 41.4 + - + +
287A LYS* 2.8 28.5 + - - +
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Residues in contact with PRO 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A GLU 3.2 8.9 - - - +
283A ASP* 1.3 90.8 - - - +
285A GLU* 1.3 69.1 + - + +
287A LYS* 3.2 14.9 + - + +
288A ARG* 3.0 29.2 + - - +
388A VAL* 5.0 0.8 - - + +
503A GLU* 3.4 46.2 - - + +
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Residues in contact with GLU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ASP* 3.4 11.4 + - - +
284A PRO* 1.3 83.8 - - + +
286A GLU* 1.3 61.9 + - - +
288A ARG* 3.5 9.4 + - + +
289A LYS* 3.0 54.9 + - + +
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Residues in contact with GLU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A VAL* 3.3 23.8 - - + -
283A ASP* 2.8 29.8 + - + +
285A GLU* 1.3 76.4 - - - +
287A LYS* 1.3 66.2 + - - +
289A LYS* 3.0 10.8 + - - +
290A ILE* 2.9 52.5 + - + +
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Residues in contact with LYS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU* 4.1 18.6 - - + -
281A VAL* 3.6 25.1 - - + +
282A GLU 3.7 10.3 - - - -
283A ASP 2.8 16.5 + - - +
284A PRO* 3.4 9.4 - - + +
286A GLU* 1.3 76.6 - - - +
288A ARG* 1.3 53.2 + - - +
290A ILE* 3.8 0.9 - - - +
291A ILE* 2.7 42.8 + - + +
387A ALA* 3.0 19.6 + - + +
388A VAL* 5.0 7.2 - - + -
390A VAL 2.7 30.3 + - - -
392A GLY 2.8 21.0 + - - +
394A VAL* 3.9 10.5 - - + +
503A GLU* 2.8 22.1 + - - +
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Residues in contact with ARG 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PRO 3.0 18.2 + - - +
285A GLU* 3.9 9.0 - - + +
287A LYS* 1.3 74.3 - - - +
289A LYS* 1.3 62.8 + - + +
291A ILE* 3.9 6.3 - - - +
292A GLY* 3.0 23.9 + - - -
382A PRO* 5.1 5.1 - - - +
384A PRO* 3.6 25.1 - - + +
388A VAL* 3.9 24.7 - - + +
501A GLU* 4.7 9.1 - - - +
503A GLU* 2.6 42.4 + - - -
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Residues in contact with LYS 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A GLU* 3.0 45.5 + - + +
286A GLU* 3.0 15.3 + - - +
288A ARG* 1.3 76.7 - - - +
290A ILE* 1.3 61.8 + - - +
292A GLY* 3.3 1.4 + - - -
293A ARG* 2.9 31.2 + - - +
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A PHE* 6.3 0.2 - - - -
277A ALA* 3.5 42.4 - - + +
278A LEU* 4.0 12.3 - - + -
281A VAL* 3.7 23.8 - - + -
286A GLU* 2.9 39.1 + - + +
287A LYS 3.8 3.1 - - - +
289A LYS* 1.3 76.4 - - - +
291A ILE* 1.3 56.8 + - + +
293A ARG* 3.2 29.8 + - - +
294A GLU* 2.8 30.9 + - + +
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Residues in contact with ILE 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243A HIS* 4.7 4.9 - - - +
245A LEU* 3.6 15.0 - - + -
274A PHE* 3.4 25.1 - - + -
278A LEU* 3.4 38.6 - - + -
287A LYS 2.7 30.2 + - - +
288A ARG* 3.9 5.6 - - - +
290A ILE* 1.3 76.3 - - + +
292A GLY* 1.3 65.0 + - - +
294A GLU 3.4 0.2 + - - -
295A PHE* 3.0 23.4 + - + +
383A GLY 4.4 6.7 - - - +
384A PRO* 3.9 34.3 - - + -
387A ALA* 4.6 3.8 - - + -
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Residues in contact with GLY 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A ARG 3.0 16.8 + - - -
289A LYS* 3.7 2.9 - - - -
291A ILE* 1.3 79.3 - - - +
293A ARG* 1.3 62.2 + - - +
295A PHE* 3.1 14.8 + - - +
296A VAL* 3.1 21.2 + - - +
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Residues in contact with ARG 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A ALA* 4.6 4.6 + - - +
289A LYS 2.9 17.5 + - - +
290A ILE* 3.5 35.2 - - - +
292A GLY* 1.3 75.0 - - - +
294A GLU* 1.3 94.7 + - - +
296A VAL* 3.0 29.0 - - + +
297A ALA* 3.2 8.7 + - + +
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Residues in contact with GLU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ARG* 3.1 37.1 + - - +
274A PHE* 3.3 35.2 - - + -
277A ALA* 3.6 28.2 - - + +
290A ILE* 2.8 23.9 + - + +
293A ARG* 1.3 103.5 + - - +
295A PHE* 1.3 61.8 + - - +
297A ALA* 3.6 5.9 + - - +
298A ALA* 3.1 23.9 + - - +
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Residues in contact with PHE 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ALA* 3.9 26.0 - - + -
216A VAL 5.8 2.5 - - - -
239A VAL 5.5 0.4 - - - -
241A VAL* 3.3 46.2 - - + +
243A HIS* 5.7 5.4 - - - -
274A PHE* 3.5 10.1 - + + -
291A ILE* 3.0 16.1 + - + +
292A GLY* 3.1 10.7 + - - +
294A GLU* 1.3 75.6 - - - +
296A VAL* 1.3 74.5 + - + +
298A ALA* 3.3 3.1 + - - +
299A PHE* 2.9 42.4 + + + +
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A GLY 3.1 12.3 + - - +
293A ARG* 3.0 23.1 - - + +
295A PHE* 1.3 84.0 - - + +
297A ALA* 1.3 60.8 + - + +
299A PHE* 3.8 5.1 - - - +
300A SER* 2.6 39.8 + - - +
341A GLY 4.5 24.0 - - - +
342A LEU* 4.5 17.9 - - + +
343A PRO* 5.5 4.5 - - + -
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ARG* 2.9 25.6 + - - +
293A ARG* 3.2 15.0 + - + +
294A GLU* 3.7 7.6 - - - +
295A PHE 3.1 0.4 - - - -
296A VAL* 1.3 82.1 - - + +
298A ALA* 1.3 63.8 + - - +
300A SER* 3.5 5.6 + - - -
301A GLN* 3.2 20.6 + - - +
304A ARG* 4.7 3.4 + - - +
343A PRO* 5.9 1.6 - - - -
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Residues in contact with ALA 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A VAL* 4.4 21.1 - - + -
268A VAL* 4.7 13.1 - - + +
270A ALA* 4.7 4.0 - - + -
273A ARG* 3.3 28.4 - - - +
274A PHE* 4.9 0.2 - - + -
294A GLU 3.1 14.1 + - - +
295A PHE 4.0 2.9 - - - +
297A ALA* 1.3 78.1 - - - +
299A PHE* 1.3 64.0 + - - +
301A GLN* 3.4 5.6 + - - +
302A VAL* 3.3 25.1 + - - +
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Residues in contact with PHE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LEU* 3.6 31.6 - - + -
214A LEU 3.9 6.7 - - - -
215A ALA* 3.9 28.5 - - + -
239A VAL* 3.7 38.1 - - + -
241A VAL* 4.9 4.2 - - + +
295A PHE* 2.9 36.8 + + + +
296A VAL* 3.8 4.0 - - - +
298A ALA* 1.3 76.8 - - - +
300A SER* 1.3 60.9 + - - +
302A VAL* 3.1 9.6 + - - +
303A ALA* 3.0 26.0 + - + +
312A LEU* 4.0 17.9 - - + -
342A LEU* 4.3 23.1 - - + -
346A LEU* 6.3 0.2 - - + -
348A PHE* 5.7 0.4 - + - -
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Residues in contact with SER 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A VAL 2.6 23.9 + - - -
297A ALA* 3.8 6.3 - - - -
298A ALA 3.3 0.2 - - - -
299A PHE* 1.3 76.0 - - - +
301A GLN* 1.3 59.8 + - - +
303A ALA* 3.2 2.9 + - - +
304A ARG* 2.9 44.0 + - - +
342A LEU* 3.8 4.7 - - - +
343A PRO* 2.9 35.9 - - - +
346A LEU* 3.5 21.0 - - - +
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Residues in contact with GLN 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A ARG* 4.2 17.9 + - - +
297A ALA 3.2 14.0 + - - +
298A ALA* 3.5 11.3 - - - +
299A PHE 3.2 0.2 - - - -
300A SER* 1.3 76.4 - - - +
302A VAL* 1.3 62.6 + - + +
304A ARG* 3.3 17.0 + - - +
305A GLU* 3.0 54.6 + - + +
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Residues in contact with VAL 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LEU* 4.6 1.3 - - + -
237A LEU* 3.8 10.8 - - + -
239A VAL* 3.4 35.2 - - + -
266A LEU* 3.5 20.2 - - + -
268A VAL* 3.7 30.1 - - + -
298A ALA 3.3 13.4 + - - +
299A PHE 3.1 8.9 + - - +
301A GLN* 1.3 78.3 - - + +
303A ALA* 1.3 59.6 + - - +
305A GLU* 4.1 6.9 - - - +
306A ARG* 2.8 33.6 + - - +
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Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LEU* 3.7 25.5 - - + +
299A PHE* 3.0 12.2 + - + +
300A SER 3.2 8.5 + - - +
302A VAL* 1.3 77.1 - - - +
304A ARG* 1.3 57.3 + - - +
307A GLY* 3.0 27.9 + - - -
309A PHE* 3.8 12.8 - - - -
346A LEU* 3.9 15.0 - - + +
348A PHE* 3.8 19.8 - - + -
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Residues in contact with ARG 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297A ALA* 4.7 4.2 + - - +
300A SER* 2.9 32.7 + - - +
301A GLN* 3.7 19.6 - - - +
303A ALA* 1.3 78.8 - - - +
305A GLU* 1.3 67.8 + - + +
306A ARG 3.5 0.3 + - - -
307A GLY* 3.5 6.1 + - - -
343A PRO* 4.1 14.1 - - - +
345A ASP* 2.7 54.1 + - - +
346A LEU* 3.7 11.1 - - + +
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Residues in contact with GLU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A GLN* 3.0 43.6 + - + +
302A VAL* 4.1 5.5 - - - +
304A ARG* 1.3 78.7 - - + +
306A ARG* 1.3 73.5 + - + +
307A GLY 3.8 1.6 + - - +
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Residues in contact with ARG 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ARG* 4.2 12.4 + - - +
237A LEU* 3.4 37.9 - - + +
266A LEU* 3.6 35.0 - - - +
302A VAL* 2.8 20.4 + - - +
305A GLU* 1.3 84.1 + - + +
307A GLY* 1.3 67.8 + - - +
309A PHE* 3.5 14.5 - - + -
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Residues in contact with GLY 307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ARG* 5.7 0.4 - - - -
303A ALA 3.0 21.2 + - - -
304A ARG 3.5 5.8 + - - -
305A GLU 3.4 4.5 - - - +
306A ARG* 1.3 84.7 - - - +
308A PRO* 1.3 75.6 - - - +
309A PHE* 3.8 3.1 - - - -
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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