Contacts of the helix formed by residues 308 - 331 (chain A) in PDB entry 6MBZ
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 PRO 308 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A GLN* 4.3 5.6 - - + +
227A VAL* 4.4 17.3 - - + -
307A GLY* 1.3 85.5 - - - +
309A VAL* 1.3 61.0 + - - +
310A GLU 3.5 2.5 - - - -
311A GLU* 3.9 9.8 + - + +
312A MET* 3.2 29.7 + - + +
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Residues in contact with VAL 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A GLN* 3.5 26.5 - - - +
226A ARG* 4.6 21.8 - - + +
227A VAL* 4.5 5.6 - - + -
230A ALA* 5.0 6.7 - - + -
300A CYS* 4.3 24.9 - - - -
305A ILE 4.2 6.7 - - - +
306A PRO 3.9 14.1 - - - +
307A GLY 3.5 1.0 - - - -
308A PRO* 1.3 75.9 - - - +
310A GLU* 1.3 71.4 + - + +
312A MET* 3.2 10.9 + - - +
313A LEU* 2.9 35.4 + - + +
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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
----------------------------------------------------------
300A CYS* 5.6 9.7 - - + +
301A GLN* 5.7 1.6 - - - +
304A PRO* 5.6 5.9 - - - +
305A ILE 5.6 1.8 - - - +
306A PRO 5.2 6.5 + - - +
307A GLY 5.3 0.4 + - - -
308A PRO 3.5 0.4 - - - -
309A VAL* 1.3 85.7 - - + +
311A GLU* 1.3 57.6 + - - +
313A LEU* 3.3 9.1 + - - +
314A ALA* 2.9 28.6 + - - +
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Residues in contact with GLU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A PRO* 3.9 10.6 + - + +
309A VAL 3.3 0.4 - - - -
310A GLU* 1.3 75.5 - - - +
312A MET* 1.3 60.8 + - + +
314A ALA* 3.3 6.8 + - - +
315A GLU* 2.9 31.5 + - - +
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Residues in contact with MET 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A VAL* 4.1 16.4 - - + +
230A ALA* 3.6 29.2 - - + -
231A GLU* 4.1 21.8 - - + +
234A GLN* 3.3 32.5 + - - +
308A PRO* 3.2 26.0 - - + +
309A VAL* 3.2 12.7 + - - +
311A GLU* 1.3 78.4 - - + +
313A LEU* 1.3 57.6 + - - +
315A GLU* 3.8 5.1 - - - +
316A VAL* 2.9 35.0 + - + +
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Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ALA* 4.5 18.6 - - + -
233A HIS* 5.5 0.4 - - - +
293A ILE* 4.0 30.1 - - + +
296A ALA* 4.3 14.4 - - + +
297A GLU* 3.8 46.7 - - + +
300A CYS* 4.7 8.1 - - + -
309A VAL* 2.9 30.4 + - + +
310A GLU* 3.8 7.2 - - - +
312A MET* 1.3 77.0 - - - +
314A ALA* 1.3 57.0 + - - +
316A VAL* 3.4 4.3 + - + +
317A ASN* 2.9 34.3 + - - +
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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
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297A GLU* 6.1 0.7 - - - -
310A GLU 2.9 17.8 + - - +
311A GLU* 3.7 7.2 - - - +
313A LEU* 1.3 77.9 - - - +
315A GLU* 1.3 62.5 + - - +
317A ASN* 3.4 5.8 + - - +
318A ALA* 3.2 23.0 + - - +
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Residues in contact with GLU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A GLN* 6.6 0.2 - - - -
311A GLU 2.9 17.4 + - - +
312A MET* 3.8 5.4 - - - +
314A ALA* 1.3 76.9 - - - +
316A VAL* 1.3 63.5 + - + +
318A ALA* 3.5 5.9 + - - +
319A THR* 3.2 24.3 + - - -
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Residues in contact with VAL 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A ALA* 4.8 3.4 - - - +
233A HIS* 4.9 1.8 - - + -
234A GLN* 3.4 41.5 - - + +
237A LEU* 3.5 19.9 - - + +
293A ILE* 3.5 34.1 - - + -
312A MET* 2.9 19.7 + - + +
313A LEU* 3.9 5.2 - - + +
315A GLU* 1.3 74.6 - - + +
317A ASN* 1.3 62.7 + - - +
319A THR* 3.3 9.0 + - - -
320A ILE* 3.0 26.9 + - + +
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Residues in contact with ASN 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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290A ARG* 4.5 10.9 + - - +
293A ILE* 3.7 20.3 - - + +
294A ARG* 4.4 11.5 - - - +
297A GLU* 3.1 30.5 + - - -
313A LEU 2.9 16.6 + - - +
314A ALA* 3.9 4.7 - - - +
315A GLU 3.3 0.2 - - - -
316A VAL* 1.3 79.8 - - - +
318A ALA* 1.3 61.7 + - - +
320A ILE* 3.0 17.7 + - - +
321A THR* 3.0 35.0 + - + +
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Residues in contact with ALA 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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314A ALA 3.2 17.2 + - - +
315A GLU* 3.8 7.0 - - - +
317A ASN* 1.3 76.1 - - - +
319A THR* 1.3 62.0 + - - +
321A THR* 3.1 12.3 + - - -
322A ASP* 2.9 23.7 + - - +
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Residues in contact with THR 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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237A LEU* 4.2 20.9 - - + -
241A ARG* 4.7 15.9 - - + +
315A GLU 3.2 12.5 + - - -
316A VAL* 3.5 10.9 - - - -
318A ALA* 1.3 78.1 - - - +
320A ILE* 1.3 58.2 + - - +
322A ASP* 3.3 7.9 + - - +
323A ILE* 2.9 43.9 + - + +
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Residues in contact with ILE 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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237A LEU* 3.6 27.4 - - + -
286A ILE* 3.7 13.6 - - + +
289A ASN* 4.1 7.2 - - + +
290A ARG* 3.6 61.0 - - + +
293A ILE* 4.3 13.9 - - + -
316A VAL* 3.0 17.6 + - + +
317A ASN* 3.0 16.3 + - - +
319A THR* 1.3 76.8 - - - +
321A THR* 1.3 64.7 + - + +
323A ILE* 3.2 4.0 + - - +
324A ILE* 2.9 34.0 + - + +
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Residues in contact with THR 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ARG* 5.8 4.5 - - - +
317A ASN* 3.0 25.0 + - - +
318A ALA* 3.1 10.8 + - - -
320A ILE* 1.3 79.3 - - + +
322A ASP* 1.3 60.6 + - - +
324A ILE* 3.7 7.6 - - - +
325A SER* 2.9 30.7 + - - -
455A LEU* 6.1 9.6 - - + -
457A PHE* 5.6 0.7 - - - -
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Residues in contact with ASP 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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241A ARG* 3.8 22.2 + - - -
318A ALA 2.9 13.7 + - - +
319A THR* 3.5 8.5 - - - +
320A ILE 3.2 0.2 - - - -
321A THR* 1.3 82.5 + - - +
323A ILE* 1.3 62.9 + - - +
325A SER* 3.3 6.9 + - - -
326A ALA* 3.0 26.2 + - - +
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Residues in contact with ILE 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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237A LEU* 4.4 7.4 - - + +
240A LEU* 4.2 22.7 - - + -
241A ARG* 3.3 45.5 - - + +
244A GLN* 3.2 33.7 + - + +
286A ILE* 3.4 24.0 - - + -
319A THR* 2.9 28.0 + - + +
322A ASP* 1.3 76.7 - - + +
324A ILE* 1.3 59.1 + - - +
326A ALA* 3.3 1.4 + - - -
327A LEU* 2.9 27.5 + - + +
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Residues in contact with ILE 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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286A ILE* 3.5 24.9 - - + -
287A TRP* 3.5 39.5 - - + -
290A ARG* 3.9 17.0 - - - +
320A ILE* 2.9 23.4 + - + +
321A THR* 3.7 7.2 - - - +
323A ILE* 1.3 75.5 - - - +
325A SER* 1.3 57.1 + - - +
327A LEU* 3.4 8.7 + - + +
328A VAL* 2.9 36.2 + - + +
360A LEU* 5.2 8.3 - - + -
450A VAL* 5.8 0.4 - - + -
455A LEU* 5.4 6.1 - - + -
457A PHE* 3.7 25.6 - - + -
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Residues in contact with SER 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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321A THR 2.9 17.6 + - - -
322A ASP* 3.7 6.9 + - - -
324A ILE* 1.3 76.7 - - - +
326A ALA* 1.3 63.0 + - - +
329A THR* 2.9 38.7 + - - +
457A PHE* 3.9 21.2 - - - -
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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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244A GLN* 3.4 19.7 - - - +
248A LEU* 4.1 4.0 - - + -
322A ASP* 3.0 20.3 + - - +
323A ILE* 4.5 1.1 - - - -
325A SER* 1.3 78.4 + - - +
327A LEU* 1.3 61.0 + - - +
329A THR* 3.3 5.2 + - - -
330A SER* 2.9 31.9 + - - +
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Residues in contact with LEU 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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244A GLN* 3.4 20.3 - - - +
248A LEU* 3.9 20.6 - - + -
279A CYS* 4.9 1.6 - - + +
282A LEU* 3.7 26.5 - - + -
283A ALA* 4.0 25.1 - - + -
286A ILE* 4.9 8.5 - - + -
323A ILE* 2.9 17.4 + - + +
324A ILE* 3.7 8.3 - - + +
326A ALA* 1.3 76.4 - - - +
328A VAL* 1.3 63.8 + - - +
330A SER 3.2 0.7 + - - -
331A THR* 3.1 31.2 + - + +
356A VAL* 3.8 31.9 - - + -
360A LEU* 4.7 7.9 - - + -
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ILE* 2.9 23.8 + - + +
325A SER 4.1 1.3 - - - +
327A LEU* 1.3 76.2 - - + +
329A THR* 1.3 64.3 + - - +
331A THR* 3.8 12.3 + - - -
332A PHE 4.1 2.9 + - - -
354A LEU* 4.4 5.9 - - - +
356A VAL* 4.7 7.0 - - + -
360A LEU* 3.7 30.3 - - + -
362A VAL* 5.8 0.2 - - + -
448A PHE* 3.4 32.9 - - + -
450A VAL* 5.1 1.1 - - + -
457A PHE* 3.5 40.8 - - + -
459A VAL* 4.0 8.6 - - + +
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Residues in contact with THR 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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325A SER* 2.9 30.0 + - - +
326A ALA* 3.3 8.3 + - - -
328A VAL* 1.3 82.2 - - + +
330A SER* 1.3 65.8 + - - +
331A THR 3.7 0.3 + - - -
332A PHE* 3.9 5.4 + - - +
457A PHE* 5.1 6.3 - - + -
458A GLN 4.7 15.0 - - - +
459A VAL* 3.5 24.8 - - + +
460A LYS 4.8 4.2 - - - +
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Residues in contact with SER 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 3.4 26.9 - - - +
252A LEU* 3.6 23.9 - - - +
326A ALA* 2.9 24.3 + - - +
329A THR* 1.3 82.0 + - - +
331A THR* 1.3 58.2 + - - +
332A PHE 3.3 3.8 + - - -
333A ILE* 3.7 7.4 - - - +
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Residues in contact with THR 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A LEU* 4.1 15.5 - - + -
252A LEU* 5.5 2.5 - - + -
279A CYS* 3.9 17.7 - - - -
327A LEU* 3.1 19.6 + - + +
328A VAL 3.8 1.5 + - - -
329A THR 3.5 0.4 - - - -
330A SER* 1.3 77.2 - - - +
332A PHE* 1.3 58.0 + - - +
333A ILE* 3.7 6.4 + - - -
353A ARG 3.3 4.0 - - - +
354A LEU* 3.3 17.7 - - - +
355A LEU* 3.3 35.1 + - + +
356A VAL* 3.4 32.8 + - + +
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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