Contacts of the helix formed by residues 283 - 306 (chain E) in PDB entry 4Q9U
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 VAL 283 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212E GLU* 4.0 2.9 - - + +
213E LYS* 3.8 39.7 - - + +
216E MET* 4.3 4.9 - - + -
281E LYS* 3.2 20.8 - - + +
282E ARG* 1.3 79.8 - - + +
284E PRO* 1.4 72.6 - - + +
285E ARG* 3.5 17.3 - - + +
286E ASP* 3.0 37.2 - - - +
287E LYS* 3.1 27.5 + - - +
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Residues in contact with PRO 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212E GLU* 3.3 26.9 - - + +
216E MET* 3.5 26.5 - - + -
282E ARG 4.0 1.8 - - - +
283E VAL* 1.4 91.1 - - + +
285E ARG* 1.3 58.4 + - - +
287E LYS* 3.8 10.5 - - + -
288E LEU* 2.9 35.1 + - + +
337E TYR* 4.4 11.7 - - + +
338E ILE* 6.0 4.9 - - + -
341E PHE* 3.6 21.1 - - + +
342E CYS* 4.7 7.4 - - + -
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Residues in contact with ARG 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209E ASP* 4.0 45.1 + - + +
210E GLN* 5.6 2.5 - - - +
212E GLU* 4.8 4.6 + - + -
213E LYS* 3.1 36.7 - - - +
283E VAL* 3.2 12.5 - - + +
284E PRO* 1.3 76.1 - - - +
286E ASP* 1.3 78.9 + - - +
288E LEU* 3.9 1.7 - - - +
289E ALA* 2.9 31.2 + - + +
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Residues in contact with ASP 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626D GLU* 5.5 0.9 - - - +
213E LYS* 4.5 1.6 + - - -
281E LYS* 2.9 43.2 + - + +
283E VAL* 3.0 19.1 - - - +
285E ARG* 1.3 100.5 + - - +
287E LYS* 1.3 57.4 + - - +
289E ALA* 3.3 9.4 + - - +
290E CYS* 2.9 35.1 + - - -
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Residues in contact with LYS 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E TYR* 6.2 0.8 - - - -
224E PHE* 5.7 1.9 - - - -
278E MET* 2.5 44.4 + - + +
279E ASP* 3.8 4.2 + - - +
281E LYS* 2.4 30.7 + - - +
282E ARG* 3.7 16.2 + - - +
283E VAL 3.1 12.2 + - - +
284E PRO* 3.8 6.7 - - + +
285E ARG 3.2 0.2 - - - -
286E ASP* 1.3 74.8 - - - +
288E LEU* 1.3 62.5 + - - +
290E CYS* 2.7 26.9 + - - +
291E ILE* 2.9 11.1 + - - +
334E ASN* 3.8 25.5 + - - +
337E TYR* 4.3 14.4 - - + -
338E ILE* 4.3 27.8 - - + -
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Residues in contact with LEU 288 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284E PRO* 2.9 23.6 + - + +
285E ARG* 4.3 1.6 - - - +
287E LYS* 1.3 75.5 - - + +
289E ALA* 1.3 57.1 + - - +
291E ILE* 2.8 43.0 - - + +
292E THR* 3.0 16.6 + - - -
338E ILE* 3.9 30.1 - - + -
342E CYS* 3.4 31.9 - - + -
346E ARG* 3.7 24.0 - - + -
347E LEU* 4.9 2.0 - - + -
352E ASP* 3.8 21.4 - - + +
356E PHE* 4.6 8.1 - - + -
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Residues in contact with ALA 289 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285E ARG* 2.9 21.2 + - + +
286E ASP* 3.4 10.5 - - - +
287E LYS 3.0 0.2 - - - -
288E LEU* 1.3 76.5 - - - +
290E CYS* 1.3 58.9 + - - +
292E THR* 4.1 4.9 - - - -
293E LYS* 3.0 42.2 + - + +
352E ASP* 6.1 0.4 - - - -
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Residues in contact with CYS 290 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E ASP* 3.5 18.5 - - - +
275E ILE* 5.3 1.1 - - - -
277E GLU* 4.0 15.0 - - - -
278E MET* 3.4 38.1 - - + -
281E LYS* 5.7 2.2 - - - -
286E ASP* 2.9 27.7 + - - -
287E LYS 2.7 11.0 + - - +
289E ALA* 1.3 75.8 - - - +
291E ILE* 1.3 62.8 + - - +
293E LYS* 4.0 3.8 - - - +
294E CYS* 3.0 24.6 + - - +
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Residues in contact with ILE 291 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275E ILE* 5.2 10.3 - - + -
278E MET* 5.2 1.2 - - + +
287E LYS 2.9 7.6 + - - +
288E LEU* 2.8 49.6 - - + +
290E CYS* 1.3 76.8 - - - +
292E THR* 1.3 58.8 + - - +
294E CYS* 3.0 9.0 + - - +
295E SER* 2.9 25.5 + - - +
338E ILE* 6.4 1.3 - - + -
352E ASP* 3.4 11.9 - - + +
355E TYR* 3.5 12.1 - - + -
356E PHE* 3.2 43.5 - - + +
359E LEU* 3.5 23.6 - - + -
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Residues in contact with THR 292 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288E LEU 3.0 14.1 + - - -
289E ALA* 4.1 4.9 - - - +
291E ILE* 1.3 73.3 - - - +
293E LYS* 1.3 73.3 + - + +
295E SER* 2.8 23.5 + - - -
296E LYS* 3.0 49.2 + - + +
351E GLU* 4.8 0.2 - - + -
352E ASP* 2.7 32.7 + - - +
355E TYR* 3.1 16.2 - - + -
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Residues in contact with LYS 293 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274E ASP* 4.5 14.8 - - - +
289E ALA* 3.0 27.0 + - + +
290E CYS* 4.2 4.0 - - - +
292E THR* 1.3 81.5 - - + +
294E CYS* 1.3 63.1 + - - +
296E LYS* 3.3 8.6 + - + +
297E HIS* 3.0 26.9 + - - +
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Residues in contact with CYS 294 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271E ALA 3.6 12.3 - - - -
274E ASP* 4.1 6.7 - - + +
275E ILE* 3.7 24.9 - - + +
290E CYS 3.0 15.3 + - - +
291E ILE* 3.0 14.5 + - + +
293E LYS* 1.3 72.4 - - - +
295E SER* 1.3 64.2 + - - +
296E LYS 2.9 4.3 + - - -
297E HIS* 2.5 41.5 + - + -
298E ILE* 3.0 29.7 - - - +
322E ILE* 4.2 2.0 - - - -
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Residues in contact with SER 295 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291E ILE* 2.9 12.7 + - - -
292E THR 2.8 18.5 + - - -
294E CYS* 1.3 74.0 - - - +
296E LYS* 1.3 60.5 + - - +
298E ILE* 3.4 19.5 + - - +
299E PHE* 2.8 26.8 - - - -
355E TYR* 3.1 46.8 - - - -
358E ASN* 6.0 0.9 - - - -
359E LEU* 5.4 6.3 - - - -
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Residues in contact with LYS 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292E THR* 3.0 42.8 + - + +
293E LYS* 3.5 8.1 - - + +
294E CYS 2.9 1.4 + - - -
295E SER* 1.3 75.7 - - - +
297E HIS* 1.3 48.0 + - - +
298E ILE 2.9 6.2 + - - -
299E PHE* 3.2 23.3 - - + -
300E ASN* 2.4 28.1 + - - -
351E GLU* 3.1 36.3 + - - -
355E TYR* 3.4 18.8 - - - +
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Residues in contact with HIS 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267E MET* 3.2 20.6 - - + +
270E LYS* 2.8 38.0 + - + -
271E ALA* 3.1 23.1 - - + +
274E ASP* 2.7 28.5 + - - -
293E LYS 3.0 12.1 + - - +
294E CYS* 2.5 54.1 + - - -
296E LYS* 1.3 74.3 - - - +
298E ILE* 1.3 56.6 + - - +
300E ASN* 2.5 30.8 - - - +
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Residues in contact with ILE 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271E ALA* 4.1 13.2 - - + -
294E CYS* 3.0 42.0 - - - +
295E SER* 3.6 13.2 - - - +
296E LYS 2.9 5.3 + - - -
297E HIS* 1.3 82.8 - - - +
299E PHE* 1.3 63.3 + - + +
300E ASN 3.1 5.8 + - - -
301E ALA* 3.4 18.2 + - - +
302E ILE* 4.8 1.0 - - - +
318E THR* 3.9 25.8 - - + +
319E LEU* 5.6 0.7 - - - +
322E ILE* 3.7 37.2 - - + -
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Residues in contact with PHE 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295E SER* 2.8 28.3 - - - -
296E LYS* 3.2 32.3 - - + -
298E ILE* 1.3 71.1 - - + +
300E ASN* 1.3 62.9 + - - +
301E ALA 3.0 3.1 - - - -
302E ILE* 2.8 45.8 + - + +
303E LYS* 3.1 7.7 + - - +
309E PRO 3.7 18.5 - - - +
318E THR* 5.2 2.2 - - + -
355E TYR* 5.0 12.3 - + - -
53F ILE* 3.8 24.0 - - + -
54F GLY* 4.1 22.9 - - - -
55F ALA* 5.4 2.5 - - + +
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Residues in contact with ASN 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267E MET* 3.1 27.4 - - + +
296E LYS 2.4 31.9 + - - -
297E HIS* 2.5 30.8 - - - +
299E PHE* 1.3 76.4 - - - +
301E ALA* 1.3 55.7 + - - +
303E LYS* 3.0 35.4 + - + +
304E ILE* 2.8 30.5 + - - +
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Residues in contact with ALA 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E PRO 4.3 1.1 - - - -
257E VAL* 4.4 16.8 - - + -
264E VAL* 3.5 26.9 - - + +
267E MET* 3.3 18.1 - - - -
268E VAL* 5.2 6.5 - - + -
298E ILE 3.4 12.3 + - - +
299E PHE 3.0 1.0 - - - -
300E ASN* 1.3 72.3 - - - +
302E ILE* 1.3 57.1 + - + +
304E ILE* 3.5 0.5 + - - -
305E THR* 2.4 42.8 + - - +
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Residues in contact with ILE 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E PRO* 3.4 50.5 - - + +
257E VAL* 5.5 1.3 - - + -
298E ILE 4.8 1.6 - - - +
299E PHE* 2.8 37.3 + - + +
301E ALA* 1.3 78.9 - - + +
303E LYS* 1.3 48.4 + - - +
306E LYS* 3.1 15.1 + - + -
307E ASN 2.7 30.8 + - - -
308E GLU* 3.3 28.7 - - + +
309E PRO 3.9 7.0 - - - +
318E THR* 4.4 14.6 - - + +
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Residues in contact with LYS 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299E PHE* 3.1 6.3 + - - -
300E ASN* 3.0 45.3 + - + +
302E ILE* 1.3 79.6 - - - +
304E ILE* 1.3 61.7 + - + +
307E ASN* 3.0 43.5 + - - +
308E GLU 3.5 11.2 + - - +
309E PRO* 5.3 3.6 - - + -
53F ILE* 3.6 44.1 + - - +
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Residues in contact with ILE 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261E ILE* 3.6 17.3 - - + +
263E GLU* 3.1 45.5 - - + +
264E VAL* 3.4 30.5 - - + +
267E MET* 3.6 21.5 - - + -
300E ASN 2.8 17.7 + - - +
302E ILE 3.3 0.2 - - - -
303E LYS* 1.3 84.0 - - + +
305E THR* 1.3 59.8 + - - +
307E ASN* 4.5 3.0 + - - +
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Residues in contact with THR 305 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256E PRO 3.1 17.4 + - - -
257E VAL* 3.6 1.9 - - - -
258E ASN* 3.0 52.9 - - + +
261E ILE* 4.1 7.0 - - + -
264E VAL* 3.5 14.4 - - + -
301E ALA 2.4 23.6 + - - +
302E ILE 3.6 0.2 + - - -
304E ILE* 1.3 78.2 - - - +
306E LYS* 1.3 65.9 + - - +
307E ASN* 5.3 0.2 - - - -
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Residues in contact with LYS 306 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256E PRO* 3.8 28.7 - - - +
302E ILE* 3.1 11.8 + - + +
305E THR* 1.3 81.8 + - - +
307E ASN* 1.3 67.1 + - - +
308E GLU* 3.4 35.0 - - + +
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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