Contacts of the helix formed by residues 346 - 369 (chain A) in PDB entry 4DM8
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 GLU 346 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A LEU* 5.9 0.4 - - + +
255A THR* 4.8 17.2 + - + -
258A ASP* 3.3 17.0 + - - +
344A LEU* 4.7 0.4 - - - -
345A GLU* 1.3 92.5 - - + +
347A PRO* 1.3 57.7 - - - +
348A THR 3.3 2.9 - - - -
349A LYS* 2.9 57.0 + - + +
350A VAL* 3.2 10.1 + - - +
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Residues in contact with PRO 347 (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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339A GLY* 3.7 17.8 - - - +
341A ARG 5.4 1.1 - - - +
344A LEU* 3.5 35.4 - - + +
345A GLU 3.4 7.6 - - - +
346A GLU* 1.3 90.9 - - - +
348A THR* 1.3 52.8 + - - +
350A VAL* 2.9 5.0 + - - +
351A ASP* 2.7 41.9 + - - +
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Residues in contact with THR 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A GLU 3.3 0.8 - - - -
347A PRO* 1.3 81.1 - - - +
349A LYS* 1.3 56.5 + - - +
351A ASP* 3.4 12.5 + - + +
352A LYS* 3.0 32.2 + - + +
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Residues in contact with LYS 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A GLY* 3.7 24.2 + - - -
254A LEU* 4.0 22.8 - - + +
346A GLU* 2.9 45.1 + - + +
348A THR* 1.3 77.6 - - - +
350A VAL* 1.3 60.9 + - - +
352A LYS* 3.4 8.7 + - - +
353A LEU* 3.4 25.1 + - + +
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Residues in contact with VAL 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LEU* 4.0 22.7 - - + -
258A ASP* 4.5 2.7 - - - +
262A LEU* 4.2 8.7 - - + -
337A ILE* 3.4 27.0 - - + +
338A CYS 3.6 32.8 - - - +
339A GLY* 4.1 2.9 - - - -
344A LEU* 3.8 22.0 - - + -
346A GLU 3.5 13.2 - - - +
347A PRO 2.9 7.3 + - - +
349A LYS* 1.3 76.2 - - - +
351A ASP* 1.3 64.7 + - - +
353A LEU* 3.0 14.8 + - - -
354A GLN* 3.1 10.2 + - - +
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Residues in contact with ASP 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A GLY* 3.6 20.8 + - - +
340A ASP* 4.4 7.0 - - - +
347A PRO* 2.7 31.0 + - - +
348A THR* 3.6 13.1 + - + +
350A VAL* 1.3 73.6 - - - +
352A LYS* 1.3 62.7 + - - +
354A GLN* 3.2 23.9 + - - +
355A GLU* 3.2 20.7 + - + +
1378B LYS* 4.3 24.7 + - - +
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Residues in contact with LYS 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A THR* 3.0 19.4 + - + +
349A LYS* 3.6 12.1 - - - +
351A ASP* 1.3 76.9 - - - +
353A LEU* 1.3 61.2 + - + +
355A GLU* 3.6 23.1 + - - +
356A PRO* 3.1 24.1 - - - +
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Residues in contact with LEU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A PRO 4.1 17.0 - - - +
250A GLY* 3.6 22.9 - - - +
251A PHE* 4.2 2.7 - - - +
254A LEU* 3.2 40.8 - - + -
337A ILE* 3.6 19.1 - - + -
349A LYS* 3.4 14.1 + - + +
350A VAL* 3.0 8.1 + - - +
352A LYS* 1.3 80.5 - - + +
354A GLN* 1.3 61.8 + - - +
356A PRO* 3.3 12.6 - - - +
357A LEU* 3.5 15.9 - - + +
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Residues in contact with GLN 354 (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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334A ILE* 3.0 43.2 + - + +
337A ILE* 3.2 21.9 + - - +
338A CYS* 4.4 11.4 - - - +
339A GLY 4.9 0.7 + - - +
350A VAL 3.1 9.6 + - - +
351A ASP* 3.2 19.5 + - - +
353A LEU* 1.3 77.0 - - - +
355A GLU* 1.3 64.5 + - - +
357A LEU* 3.1 11.4 + - - +
358A LEU* 3.1 39.6 + - + +
1381B MET* 3.9 16.9 - - - +
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Residues in contact with GLU 355 (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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351A ASP* 3.2 17.1 + - + +
352A LYS* 3.6 30.4 - - - +
354A GLN* 1.3 75.3 - - - +
356A PRO* 1.3 71.7 - - + +
358A LEU* 3.2 14.3 + - + +
359A GLU* 3.1 24.0 + - - +
1374B HIS* 3.5 42.3 + - + +
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Residues in contact with PRO 356 (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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186A LEU* 3.8 14.9 - - + +
189A LEU* 3.7 20.9 - - + -
352A LYS 3.1 19.3 - - - +
353A LEU* 3.3 11.7 - - - +
355A GLU* 1.3 93.5 - - + +
357A LEU* 1.3 50.3 + - - +
359A GLU* 3.3 6.4 + - + +
360A ALA* 2.7 37.6 + - - +
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Residues in contact with LEU 357 (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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189A LEU* 4.0 11.7 - - + -
193A ILE* 3.2 35.9 - - + -
248A LEU* 5.8 2.5 - - + -
249A PRO* 6.0 1.1 - - + -
330A LEU* 4.4 4.4 - - + +
333A ALA* 3.8 34.5 - - + +
334A ILE* 3.6 19.0 - - + +
337A ILE* 4.0 13.2 - - + -
353A LEU* 3.5 20.4 - - + +
354A GLN* 3.1 14.8 + - - +
356A PRO* 1.3 74.9 - - - +
358A LEU* 1.3 59.5 + - - +
360A ALA* 3.3 5.3 + - - +
361A LEU* 2.9 29.3 + - - +
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Residues in contact with LEU 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ILE* 3.6 23.6 - - + -
354A GLN* 3.1 35.6 + - + +
355A GLU* 3.2 11.4 + - + +
357A LEU* 1.3 74.7 - - - +
359A GLU* 1.3 58.7 + - - +
361A LEU* 3.2 4.4 + - - +
362A LYS* 2.9 25.1 + - - +
376A PHE* 3.4 15.8 - - + -
380A LEU* 3.9 16.6 - - + -
1374B HIS* 5.7 6.5 - - + +
1377B PRO* 3.9 24.7 - - + -
1378B LYS* 5.3 2.2 - - + +
1381B MET* 3.4 30.1 - - + -
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Residues in contact with GLU 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A THR* 5.9 0.5 - - - +
186A LEU* 3.4 30.4 - - + +
355A GLU 3.1 16.8 + - - +
356A PRO* 3.7 7.0 - - + +
358A LEU* 1.3 75.9 - - - +
360A ALA* 1.3 60.2 + - - +
362A LYS* 3.3 21.7 + - - +
363A ILE* 2.8 44.1 + - + +
1374B HIS* 3.9 26.5 + - + +
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Residues in contact with ALA 360 (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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186A LEU* 4.3 17.7 - - + +
189A LEU* 4.6 6.7 - - + -
190A THR* 3.5 22.4 + - - +
330A LEU* 4.3 12.8 - - + -
356A PRO 2.7 23.0 + - - +
357A LEU* 3.7 5.4 - - - +
359A GLU* 1.3 70.2 - - - +
361A LEU* 1.3 61.0 + - - +
363A ILE* 3.9 5.2 - - - +
364A TYR* 2.8 33.7 + - - +
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Residues in contact with LEU 361 (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 GLU* 4.1 20.0 - - + +
330A LEU* 3.9 22.6 - - + +
331A LEU* 4.4 13.9 - - + -
334A ILE* 3.6 24.0 - - + -
357A LEU 2.9 13.9 + - - +
358A LEU 3.2 7.4 + - - +
360A ALA* 1.3 78.2 - - - +
362A LYS* 1.3 56.8 + - - +
364A TYR* 3.6 0.7 - - - +
365A ILE* 2.8 54.9 + - + +
376A PHE* 3.9 21.1 - - + -
379A ILE* 4.7 11.7 - - + -
380A LEU* 4.1 12.3 - - + -
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Residues in contact with LYS 362 (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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358A LEU 2.9 12.8 + - - +
359A GLU* 3.5 29.0 - - - +
361A LEU* 1.3 73.7 - - - +
363A ILE* 1.3 72.8 + - - +
365A ILE* 3.1 14.3 + - - +
366A ARG* 3.1 30.5 + - - +
376A PHE* 3.7 42.9 - - + -
1373B PRO 5.1 4.0 + - - -
1374B HIS* 4.6 16.6 + - - -
1377B PRO* 6.0 2.8 - - - +
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Residues in contact with ILE 363 (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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183A THR* 3.9 31.6 - - + +
186A LEU* 3.8 23.6 - - + -
187A ASP* 4.7 5.6 - - - +
359A GLU* 2.8 33.3 + - + +
360A ALA* 3.9 5.4 - - - +
362A LYS* 1.3 76.1 - - - +
364A TYR* 1.3 65.9 + - - +
366A ARG* 3.1 50.9 - - - +
367A LYS* 3.4 8.2 + - + +
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Residues in contact with TYR 364 (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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190A THR* 3.9 22.9 - - + +
324A ASP* 3.2 28.1 + - - -
326A THR* 3.4 28.3 + - + -
327A GLU* 3.7 22.4 - - + -
330A LEU* 4.6 2.2 - - + -
360A ALA 2.8 23.5 + - - +
361A LEU* 3.6 4.9 - - - +
363A ILE* 1.3 76.3 - - - +
365A ILE* 1.3 63.2 + - - +
366A ARG 3.0 1.0 + - - -
367A LYS* 3.3 44.9 + - - +
368A ARG* 3.1 42.1 + - - +
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Residues in contact with ILE 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A GLU* 2.8 44.6 - - + +
361A LEU* 2.8 43.6 + - + +
362A LYS* 3.1 8.0 + - - +
364A TYR* 1.3 72.8 - - - +
366A ARG* 1.3 56.4 + - - +
368A ARG* 4.6 0.9 - - - -
369A ARG* 2.7 58.2 + - + +
373A PRO* 6.1 1.6 - - + -
374A HIS 5.9 0.2 - - - +
375A MET* 3.6 27.6 - - + +
376A PHE* 4.1 16.2 - - + +
379A ILE* 4.3 7.4 - - + -
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Residues in contact with ARG 366 (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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180A TYR* 3.8 34.0 + - + +
181A GLU* 6.0 4.0 - - - +
362A LYS* 3.1 31.2 + - - +
363A ILE* 3.1 40.1 - - - +
364A TYR 3.0 0.4 - - - -
365A ILE* 1.3 74.6 - - - +
367A LYS* 1.3 66.9 + - - +
369A ARG 3.2 18.1 - - - +
370A PRO* 4.2 4.2 - - - +
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Residues in contact with LYS 367 (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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180A TYR* 3.4 42.4 + - + -
187A ASP* 5.7 6.3 - - - +
363A ILE* 3.4 5.3 + - + +
364A TYR* 3.3 54.0 + - + +
366A ARG* 1.3 80.2 - - - +
368A ARG* 1.3 79.1 + - - +
370A PRO* 5.6 0.3 - - - +
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Residues in contact with ARG 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLU* 2.7 36.7 + - - +
324A ASP* 2.7 39.7 + - - +
327A GLU* 2.7 26.5 + - - -
364A TYR* 3.1 35.7 + - + +
365A ILE* 3.9 2.5 - - - +
367A LYS* 1.3 94.2 - - + +
369A ARG* 1.3 85.1 + - + +
370A PRO* 3.0 14.7 - - - +
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Residues in contact with ARG 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A LEU 2.6 26.8 + - - -
322A GLU 3.6 0.2 + - - -
323A MET* 3.1 19.6 - - - +
327A GLU* 2.7 36.2 + - - +
365A ILE* 2.7 35.0 + - + +
366A ARG* 3.2 9.3 - - - +
368A ARG* 1.3 93.9 - - + +
370A PRO* 1.3 70.2 - - + +
373A PRO* 4.3 8.6 - - - +
375A MET* 3.2 41.1 - - + +
379A ILE* 2.9 31.7 - - - +
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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