Contacts of the helix formed by residues 308 - 332 (chain A) in PDB entry 1P5Q
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 ASN 308 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A PHE 2.7 18.3 + - - -
307A SER* 1.3 73.7 + - - +
309A GLU* 1.3 57.3 + - - +
311A ALA* 3.6 16.7 - - - +
312A GLN* 3.4 19.9 - - - +
377C GLN* 4.2 21.7 + - - +
381C GLN* 3.3 44.3 + - - +
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Residues in contact with GLU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A SER* 2.7 19.2 + - - +
308A ASN* 1.3 70.5 - - - +
310A GLU* 1.3 71.7 + - + +
311A ALA 2.8 1.3 + - - -
312A GLN* 2.9 24.0 + - - +
313A LYS* 3.2 38.5 + - - +
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Residues in contact with GLU 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A SER* 3.4 23.3 + - - -
264A GLU* 3.8 21.9 + - + +
267A LEU* 3.4 24.3 - - + +
305A SER 3.9 2.6 - - - +
306A PHE* 3.7 12.1 - - + -
307A SER* 2.8 42.6 + - - +
309A GLU* 1.3 86.4 + - + +
311A ALA* 1.3 54.6 + - - +
313A LYS* 3.1 8.6 + - + +
314A ALA* 2.8 28.4 + - - +
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Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PHE* 3.7 21.9 - - + +
308A ASN* 3.6 27.8 - - - +
309A GLU 2.8 1.6 + - - +
310A GLU* 1.3 78.2 - - - +
312A GLN* 1.3 59.5 + - + +
314A ALA* 3.0 4.5 + - - +
315A GLN* 2.8 32.6 + - - +
318A ARG* 5.5 0.5 + - - -
377C GLN* 5.2 4.7 - - - +
381C GLN* 4.6 6.5 - - - +
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Residues in contact with GLN 312 (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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308A ASN 3.4 18.7 + - - +
309A GLU* 2.9 17.8 + - - +
311A ALA* 1.3 73.1 - - + +
313A LYS* 1.3 64.9 + - + +
315A GLN* 3.1 9.7 + - - +
316A ALA* 2.8 24.7 + - - +
381C GLN* 4.6 17.1 - - - +
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Residues in contact with LYS 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 3.4 24.9 - - + +
309A GLU* 3.2 35.1 + - - +
310A GLU* 3.1 12.2 + - - +
312A GLN* 1.3 77.8 - - - +
314A ALA* 1.3 58.1 - - - +
316A ALA* 3.2 7.1 + - - +
317A LEU* 3.0 35.5 + - + +
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Residues in contact with ALA 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 3.6 14.9 - - + +
300A LEU* 3.8 10.4 - - + +
306A PHE* 3.2 36.6 - - + -
310A GLU 2.8 8.9 + - - +
311A ALA 3.4 7.0 - - - +
313A LYS* 1.3 72.9 - - - +
315A GLN* 1.3 66.7 + - - +
317A LEU* 3.4 3.0 + - - +
318A ARG* 3.0 37.7 + - - +
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Residues in contact with GLN 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A ALA* 2.8 18.5 + - - +
312A GLN* 3.5 10.9 - - - +
314A ALA* 1.3 75.8 - - - +
316A ALA* 1.3 57.6 + - - +
318A ARG* 3.3 22.5 + - - +
319A LEU* 2.9 27.8 + - + +
348A LEU* 4.0 29.5 - - + +
378C LYS* 2.5 46.2 + - - +
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Residues in contact with ALA 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 GLN 2.8 16.2 + - - +
313A LYS* 3.7 7.0 - - - +
315A GLN* 1.3 73.6 - - - +
317A LEU* 1.3 59.1 + - + +
319A LEU* 3.3 8.7 + - - +
320A ALA* 2.8 37.0 + - - +
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Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LEU* 3.7 24.9 - - + +
270A SER* 3.7 28.5 - - - -
271A THR* 3.8 18.2 - - + +
274A LYS* 4.4 22.2 - - + -
296A ILE* 4.0 10.4 - - + +
300A LEU* 3.7 21.8 - - + -
313A LYS* 3.0 20.8 + - + +
316A ALA* 1.3 76.7 - - + +
318A ARG* 1.3 52.3 + - - +
320A ALA* 3.3 4.8 + - + +
321A SER* 2.6 36.9 + - - -
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Residues in contact with ARG 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ILE* 4.5 1.1 - - - +
297A VAL* 4.5 20.6 - - + -
300A LEU* 2.5 53.2 + - + +
301A GLU* 4.8 3.8 + - - +
303A GLU 5.0 2.2 + - - -
306A PHE* 4.9 4.9 - - - -
311A ALA 5.5 0.4 + - - -
314A ALA* 3.0 31.2 + - - +
315A GLN* 3.4 29.5 - - - +
317A LEU* 1.3 74.0 - - - +
319A LEU* 1.3 66.7 + - - +
321A SER* 3.2 6.0 + - - -
322A HIS* 2.9 37.1 + - + +
348A LEU* 3.6 20.9 - - + +
374C ALA* 6.1 3.0 - - - +
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Residues in contact with LEU 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 GLN* 2.9 15.0 + - + +
316A ALA* 3.7 10.1 - - - +
318A ARG* 1.3 75.8 - - - +
320A ALA* 1.3 63.5 + - - +
322A HIS* 3.7 1.6 - - - +
323A LEU* 3.0 31.1 + - + +
345A ALA* 3.6 36.3 - - + +
348A LEU* 3.2 16.1 - - + +
349A ASP* 3.7 19.5 - - + +
352A ASN* 3.6 29.2 - - - +
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Residues in contact with ALA 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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274A LYS* 4.2 20.9 - - + +
316A ALA 2.8 21.8 + - - +
317A LEU* 3.5 7.9 - - + +
319A LEU* 1.3 73.1 - - - +
321A SER* 1.3 64.6 + - - +
323A LEU* 4.1 4.9 - - - +
324A ASN* 3.0 35.4 + - - +
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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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274A LYS* 5.6 0.2 - - - -
293A TYR* 2.8 34.6 + - - +
296A ILE* 3.4 22.6 - - - +
297A VAL* 3.4 16.7 - - - +
317A LEU 2.6 20.6 + - - -
318A ARG 3.6 4.9 - - - -
320A ALA* 1.3 71.8 - - - +
322A HIS* 1.3 58.1 + - - +
324A ASN* 3.4 7.2 - - - +
325A LEU* 2.8 34.5 + - - +
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Residues in contact with HIS 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A VAL* 3.9 33.5 - - + +
318A ARG* 2.9 34.1 + - - +
319A LEU 3.7 2.7 - - - +
321A SER* 1.3 74.7 - - - +
323A LEU* 1.3 67.3 + - - +
325A LEU* 3.1 13.7 + - + +
326A ALA* 2.9 19.8 + - - +
341A SER* 3.6 28.8 + - - +
344A LYS* 3.4 39.4 - - + +
345A ALA* 3.7 9.4 - - + -
348A LEU* 4.2 13.2 - - + +
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Residues in contact with LEU 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 LEU* 3.0 27.2 + - + +
320A ALA* 4.2 5.4 - - - +
322A HIS* 1.3 74.2 - - - +
324A ASN* 1.3 63.5 + - - +
326A ALA* 3.3 5.1 + - - +
327A MET 3.2 9.7 + - - -
342A CYS* 5.1 3.8 - - - -
345A ALA* 3.2 26.7 - - + -
352A ASN* 2.8 33.9 - - - +
354A LYS* 3.4 22.2 - - + +
355A GLY* 3.4 26.2 - - - +
358A ARG* 2.9 28.2 + - - +
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Residues in contact with ASN 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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274A LYS* 4.1 21.4 - - - +
278A THR* 4.6 2.0 + - - -
293A TYR* 3.3 46.2 + - + -
320A ALA* 3.0 27.1 + - - +
321A SER 3.4 3.6 - - - +
323A LEU* 1.3 75.9 - - - +
325A LEU* 1.3 66.2 + - - +
327A MET* 3.0 38.5 + - + +
328A CYS* 3.1 15.6 + - - -
354A LYS* 5.8 2.1 + - - -
358A ARG* 4.9 0.9 + - - -
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Residues in contact with LEU 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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290A LEU* 3.9 21.5 - - + +
293A TYR* 3.7 21.7 - - + -
294A LYS* 3.9 27.4 - - + +
297A VAL* 4.1 20.9 - - + -
321A SER* 2.8 34.5 + - - +
322A HIS* 3.1 14.1 + - + +
324A ASN* 1.3 72.0 - - - +
326A ALA* 1.3 62.7 + - - +
328A CYS* 3.3 8.2 + - - +
329A HIS* 3.0 35.5 + - + +
341A SER* 3.4 16.2 - - - +
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Residues in contact with ALA 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 HIS 2.9 12.6 + - - +
323A LEU* 3.4 12.6 - - - +
324A ASN 3.2 0.2 - - - -
325A LEU* 1.3 75.0 - - - +
327A MET* 1.3 63.6 + - - +
329A HIS* 3.1 2.8 + - - +
330A LEU* 2.7 28.8 + - - +
338A ALA* 3.9 14.8 - - + +
341A SER* 3.8 8.6 - - - -
342A CYS* 3.8 28.7 - - - +
358A ARG* 4.5 9.4 - - + -
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Residues in contact with MET 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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281A PHE* 4.0 38.8 - - + -
293A TYR* 5.0 3.1 - - - +
323A LEU 3.2 3.4 + - - -
324A ASN* 3.0 44.2 + - + +
326A ALA* 1.3 75.6 - - - +
328A CYS* 1.3 65.0 + - - +
330A LEU* 3.1 12.5 + - + +
331A LYS* 2.8 26.8 + - + +
354A LYS* 5.8 1.1 - - - +
358A ARG* 2.9 39.4 - - - +
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Residues in contact with CYS 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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281A PHE* 3.9 25.8 - - - -
286A TYR* 4.2 9.6 - - + +
289A ALA* 3.9 22.2 - - - -
290A LEU* 3.3 30.3 - - + -
293A TYR* 4.0 11.7 - - - -
324A ASN 3.1 12.2 + - - -
325A LEU 3.4 3.1 - - - +
327A MET* 1.3 78.6 - - - +
329A HIS* 1.3 53.7 + - - +
331A LYS* 2.8 6.9 + - - +
332A LEU* 2.7 39.8 + - + +
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Residues in contact with HIS 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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290A LEU* 3.5 33.1 - - + +
294A LYS* 5.1 11.6 - - - -
325A LEU* 3.0 32.8 + - - +
326A ALA* 3.7 3.8 - - - +
328A CYS* 1.3 77.1 - - - +
330A LEU* 1.3 62.6 + - - +
332A LEU* 3.0 5.8 + - - +
333A GLN 2.8 4.9 + - - -
334A ALA* 2.8 51.8 + - + +
337A ALA* 3.8 28.3 - - + +
338A ALA* 3.8 7.9 - - - +
341A SER* 4.0 14.8 + - - -
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Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ALA 2.7 25.4 + - - +
327A MET* 3.5 10.5 - - + +
329A HIS* 1.3 73.0 - - - +
331A LYS* 1.3 59.5 + - + +
333A GLN* 2.7 26.9 + - - +
334A ALA 4.8 0.2 - - - +
335A PHE* 4.0 19.2 - - + -
338A ALA* 3.4 22.2 - - + -
358A ARG* 3.7 38.6 - - + +
361A GLU* 4.8 7.6 - - + -
362A ALA* 3.7 24.0 - - + +
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Residues in contact with LYS 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A PHE* 4.2 14.1 - - + -
286A TYR* 3.6 56.0 + - + +
327A MET* 2.8 19.3 + - + +
328A CYS 2.8 7.4 + - - +
330A LEU* 1.3 72.2 - - + +
332A LEU* 1.3 63.1 + - - +
333A GLN* 3.4 9.5 + - - +
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Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A TYR* 3.6 30.1 - - + -
287A LYS* 4.0 31.0 - - + +
290A LEU* 3.8 28.9 - - + -
328A CYS 2.7 24.8 + - - +
329A HIS* 3.0 10.7 + - - +
331A LYS* 1.3 73.1 - - - +
333A GLN* 1.3 76.1 + - - +
334A ALA* 3.3 7.7 + - + +
222B LYS* 3.3 15.2 + - - -
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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