Contacts of the helix formed by residues 309 - 333 (chain A) in PDB entry 4KPD
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 309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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305A TYR 3.3 2.0 + - - -
306A GLU 3.4 12.5 + - - +
307A GLU 3.2 7.3 - - - +
308A LEU* 1.4 78.0 - - - +
310A LEU* 1.3 58.7 + - - +
311A PRO* 3.4 6.1 - - - +
312A ALA* 3.1 25.1 + - - +
313A VAL* 3.0 28.4 + - + +
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Residues in contact with LEU 310 (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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245A TYR* 5.0 1.8 - - - -
249A PHE* 5.0 0.2 - - + -
269A TRP* 4.8 3.6 - - + -
270A LEU* 3.4 40.6 - - + +
273A GLN* 4.1 13.7 - - + -
274A CYS* 3.8 10.8 - - + +
277A ARG* 4.1 26.5 - - - -
305A TYR* 3.1 48.5 + - + +
308A LEU* 4.1 13.5 - - + +
309A ASP* 1.3 75.9 - - - +
311A PRO* 1.4 66.1 - - + +
313A VAL* 3.0 10.2 + - + +
314A PHE* 2.9 23.4 + - - +
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Residues in contact with PRO 311 (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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245A TYR* 3.5 30.1 + - + +
249A PHE* 3.8 33.0 - - + -
305A TYR 4.1 6.5 - - - +
306A GLU* 4.4 10.1 - - + +
309A ASP* 3.5 7.6 - - - +
310A LEU* 1.4 90.9 - - + +
312A ALA* 1.4 58.4 + - - +
314A PHE* 3.5 5.9 + - - +
315A LEU* 3.3 19.2 + - - +
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Residues in contact with ALA 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A ASP* 3.1 30.9 + - - +
311A PRO* 1.4 75.6 - - - +
313A VAL* 1.3 65.9 + - + +
314A PHE 3.2 0.4 - - - -
315A LEU* 3.2 19.2 + - - +
316A GLN* 3.2 13.9 + - - +
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Residues in contact with VAL 313 (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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269A TRP* 4.1 15.9 - - + -
273A GLN* 4.6 4.5 - - + +
277A ARG* 3.4 46.4 - - - +
308A LEU 4.4 4.7 - - - +
309A ASP* 3.0 24.2 + - + +
310A LEU* 3.0 17.9 + - + +
312A ALA* 1.3 75.0 - - + +
314A PHE* 1.4 57.1 + - - +
316A GLN* 3.6 7.1 + - - +
317A TYR* 3.1 25.7 + - + +
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Residues in contact with PHE 314 (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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238A PHE* 5.8 0.2 - + - -
241A ILE* 3.9 22.2 - - + -
242A GLN* 3.8 36.8 - - + -
245A TYR* 3.5 61.0 - + + -
269A TRP* 3.7 17.7 - + + -
310A LEU 2.9 9.6 + - - +
311A PRO 3.5 8.5 - - - +
313A VAL* 1.4 74.8 - - - +
315A LEU* 1.4 62.3 + - + +
317A TYR* 3.3 2.9 + + - +
318A GLU* 2.9 59.0 + - + +
351A ARG 5.9 5.2 - - - -
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Residues in contact with LEU 315 (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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311A PRO 3.3 9.7 + - - +
312A ALA* 3.2 14.2 + - - +
314A PHE* 1.4 82.5 - - + +
316A GLN* 1.4 60.1 + - - +
318A GLU* 3.6 8.8 + - - +
319A GLU* 3.2 22.1 + - - +
350A LYS* 4.9 7.8 + - - +
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Residues in contact with GLN 316 (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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312A ALA 3.2 9.3 + - - +
313A VAL* 3.9 9.6 - - - +
314A PHE 3.3 0.2 - - - -
315A LEU* 1.4 75.9 - - - +
317A TYR* 1.4 64.4 + - - +
319A GLU* 3.3 27.4 + - - +
320A ASP* 3.0 60.3 + - - +
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Residues in contact with TYR 317 (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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194A LYS* 6.2 0.9 - - - -
234A GLU* 5.4 1.2 + - - -
237A GLU* 3.6 12.8 + - - +
238A PHE* 3.8 19.7 + + - -
241A ILE* 3.2 49.6 - - + +
269A TRP* 3.8 23.8 - + + -
313A VAL 3.1 18.6 + - - +
314A PHE* 3.3 5.6 + + - +
316A GLN* 1.4 73.8 - - - +
318A GLU* 1.4 58.2 + - + +
320A ASP* 3.4 6.6 + - + +
321A SER* 2.9 65.2 + - - -
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Residues in contact with GLU 318 (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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238A PHE* 3.7 25.4 - - + -
242A GLN* 3.1 24.6 - - - +
314A PHE* 2.9 45.8 + - + +
315A LEU* 3.6 8.5 - - - +
317A TYR* 1.4 76.6 - - - +
319A GLU* 1.4 60.8 + - - +
322A TYR* 3.2 26.8 + - + +
349A TYR* 5.9 0.2 - - - -
350A LYS* 3.1 48.6 + - + +
351A ARG 5.2 0.3 - - - +
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Residues in contact with GLU 319 (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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315A LEU 3.2 13.6 + - - +
316A GLN* 3.4 33.7 + - - +
317A TYR 3.2 0.4 - - - -
318A GLU* 1.4 77.7 - - - +
320A ASP* 1.3 63.9 + - - +
322A TYR* 3.4 5.0 + - - +
323A SER* 3.2 27.0 + - - +
350A LYS* 5.3 9.6 - - - +
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Residues in contact with ASP 320 (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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316A GLN* 3.0 42.5 + - - +
317A TYR* 3.9 6.6 - - + +
319A GLU* 1.3 76.4 - - - +
321A SER* 1.4 57.6 + - - +
323A SER* 3.5 8.1 + - - -
324A HIS* 3.2 24.3 + - - +
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Residues in contact with SER 321 (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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234A GLU* 5.1 4.5 + - - -
238A PHE* 3.8 15.1 - - - +
317A TYR* 2.9 57.9 + - - -
320A ASP* 1.4 68.7 - - - +
322A TYR* 1.3 60.5 + - - +
324A HIS* 3.1 11.1 + - - +
325A ILE* 2.9 39.7 + - - +
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Residues in contact with TYR 322 (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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238A PHE* 4.9 12.0 - + + -
318A GLU* 3.2 20.0 + - + +
319A GLU* 3.6 5.6 - - - +
321A SER* 1.3 77.4 - - - +
323A SER* 1.4 61.2 + - - +
325A ILE* 3.5 13.1 + - + +
326A MET* 3.0 69.4 + - + +
342A LEU* 5.6 0.5 + - - +
345A ALA* 4.1 13.0 - - + -
346A ARG* 4.6 13.3 + - - +
349A TYR* 3.6 32.0 - - + +
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Residues in contact with SER 323 (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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319A GLU* 3.2 16.1 + - - +
320A ASP* 3.6 11.4 - - - -
321A SER 3.2 0.2 - - - -
322A TYR* 1.4 79.9 - - - +
324A HIS* 1.3 57.2 + - - +
326A MET* 3.4 8.7 + - - +
327A ALA* 3.0 26.5 + - - +
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Residues in contact with HIS 324 (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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234A GLU* 3.7 27.2 + - + +
320A ASP 3.2 12.9 + - - +
321A SER* 3.1 14.9 + - - +
323A SER* 1.3 75.2 - - - +
325A ILE* 1.4 59.1 + - + +
327A ALA* 3.1 11.5 + - + +
328A LEU* 2.9 53.7 + - + +
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Residues in contact with ILE 325 (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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231A ILE* 4.8 2.4 - - + +
234A GLU* 4.0 13.5 - - + +
235A MET* 3.6 43.7 - - + +
238A PHE* 3.8 35.4 - - + -
321A SER* 2.9 27.6 + - - +
322A TYR* 3.7 11.0 - - + +
324A HIS* 1.4 74.9 - - + +
326A MET* 1.3 59.5 + - + +
328A LEU* 3.2 10.0 + - + +
329A ILE* 2.8 49.8 + - + +
345A ALA* 4.7 4.7 - - + -
348A ILE* 6.1 0.2 - - + -
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Residues in contact with MET 326 (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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322A TYR* 3.0 63.6 + - + +
323A SER* 3.4 12.1 - - - +
325A ILE* 1.3 77.7 - - + +
327A ALA* 1.4 60.2 + - - +
329A ILE* 3.4 12.4 + - + +
330A GLU* 3.1 34.1 + - - +
342A LEU* 3.7 30.5 - - + +
345A ALA* 3.8 20.9 - - + -
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Residues in contact with ALA 327 (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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323A SER 3.0 14.0 + - - +
324A HIS* 3.1 15.9 + - + +
326A MET* 1.4 74.6 - - - +
328A LEU* 1.3 58.8 + - - +
330A GLU* 3.4 15.5 + - - +
331A GLN* 3.0 28.2 + - - +
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Residues in contact with LEU 328 (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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230A LYS* 4.0 11.9 - - + +
231A ILE* 3.5 21.6 - - + +
234A GLU* 3.5 37.9 - - + -
324A HIS* 2.9 40.1 + - + +
325A ILE* 3.2 11.2 + - - +
327A ALA* 1.3 74.0 - - + +
329A ILE* 1.4 58.6 + - - +
331A GLN* 4.4 7.2 - - - +
332A TYR* 2.8 55.1 + - + +
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Residues in contact with ILE 329 (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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231A ILE* 3.8 16.2 - - + -
235A MET* 5.1 0.7 - - - -
325A ILE* 2.8 33.4 + - + +
326A MET* 3.7 29.4 - - + +
327A ALA 3.4 0.2 - - - -
328A LEU* 1.4 74.2 - - - +
330A GLU* 1.4 61.2 + - + +
333A ALA* 2.8 48.1 + - + +
338A PRO* 4.1 17.7 - - + +
341A PHE* 3.7 32.5 - - + +
342A LEU* 3.8 22.2 - - + -
345A ALA* 4.7 0.7 - - + -
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Residues in contact with GLU 330 (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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326A MET* 3.1 26.7 + - - +
327A ALA* 3.5 13.1 - - - +
328A LEU 3.4 0.2 - - - -
329A ILE* 1.4 78.1 - - + +
331A GLN* 1.3 59.5 + - - +
333A ALA* 4.7 1.8 + - - +
334A ALA* 5.5 2.6 + - - +
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Residues in contact with GLN 331 (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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327A ALA 3.0 17.5 + - - +
328A LEU* 3.8 9.9 - - - +
329A ILE 3.3 0.4 - - - -
330A GLU* 1.3 77.7 - - - +
332A TYR* 1.3 105.3 + - + +
334A ALA* 5.1 4.9 + - - +
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Residues in contact with TYR 332 (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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227A ASN* 3.3 60.1 - - + +
228A ALA 4.8 0.3 + - - -
230A LYS* 3.5 44.4 - - + +
231A ILE* 3.7 7.9 - - + +
328A LEU* 2.8 45.0 + - + +
331A GLN* 1.3 114.1 + - + +
333A ALA* 1.4 64.0 + - - +
334A ALA 3.4 8.0 + - - +
341A PHE* 5.2 0.7 - - - -
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Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A ILE* 3.8 1.4 - - - +
329A ILE* 2.8 42.6 + - + +
330A GLU 4.7 0.4 - - - +
331A GLN 3.8 0.4 - - - -
332A TYR* 1.4 71.1 - - - +
334A ALA* 1.4 60.4 + - - +
335A PRO* 4.4 0.2 - - - +
336A LEU* 2.9 39.3 + - - +
338A PRO* 4.2 12.8 - - + -
341A PHE* 3.9 23.0 - - + -
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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
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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