Contacts of the helix formed by residues 331 - 353 (chain A) in PDB entry 3SN6
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 331 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A LEU* 3.6 24.7 - - + +
329A GLY 4.0 3.2 + - - -
330A GLU* 1.3 72.9 - - - +
332A PRO* 1.3 86.1 - - - +
333A ARG* 2.8 50.2 + - - +
334A VAL* 2.8 27.1 + - + +
335A THR* 3.1 8.5 + - - -
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Residues in contact with PRO 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A THR* 4.1 4.3 + - - +
326A PRO* 6.1 0.9 - - + -
330A GLU 3.2 6.2 - - - +
331A ASP* 1.3 91.7 - - - +
333A ARG* 1.3 57.9 + - + +
335A THR* 3.5 11.0 + - - +
336A ARG* 2.9 29.8 + - - +
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Residues in contact with ARG 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A VAL* 3.7 27.2 + - + +
302A LEU* 3.7 33.0 + - + +
304A GLY* 5.3 4.0 - - - -
307A LYS* 5.5 8.9 - - - +
315A PHE* 5.1 0.3 - - - -
331A ASP* 2.8 33.1 + - - +
332A PRO* 1.3 77.5 - - + +
334A VAL* 1.3 60.1 + - - +
336A ARG* 3.2 19.1 + - - +
337A ALA* 2.9 29.6 + - - +
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Residues in contact with VAL 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLN 5.6 1.3 - - - +
297A LEU* 4.8 5.8 - - + +
298A ALA* 3.6 48.9 - - + +
301A VAL* 4.1 12.6 - - + -
302A LEU* 3.9 21.1 - - + -
330A GLU* 4.0 20.4 - - + +
331A ASP* 2.8 12.8 + - + +
333A ARG* 1.3 77.9 - - - +
335A THR* 1.3 58.8 + - - +
337A ALA* 3.4 3.1 + - - +
338A LYS* 2.9 35.9 + - + +
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Residues in contact with THR 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A THR* 4.2 9.4 - - + -
324A ALA* 4.7 2.0 - - + -
326A PRO* 3.6 27.1 - - + +
330A GLU* 2.6 37.3 + - - +
331A ASP 3.1 7.1 + - - -
332A PRO* 3.7 11.5 - - - +
333A ARG 3.3 0.2 - - - -
334A VAL* 1.3 76.9 - - - +
336A ARG* 1.3 57.3 + - - +
338A LYS* 3.5 2.6 - - - +
339A TYR* 2.9 63.4 + - + -
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Residues in contact with ARG 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A LYS* 5.6 3.8 - - - +
309A GLU* 5.5 2.0 + - - -
315A PHE* 3.4 54.8 + - + -
316A ALA* 4.3 10.3 + - - +
318A TYR* 2.9 35.4 + - + -
319A THR* 4.4 2.0 - - - +
320A THR* 3.0 40.1 + - - +
332A PRO 2.9 16.3 + - - +
333A ARG* 3.4 18.3 + - - +
335A THR* 1.3 77.3 - - - +
337A ALA* 1.3 56.1 + - - +
339A TYR* 3.8 0.5 - - - -
340A PHE 2.9 22.7 + - - -
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A LEU* 4.8 4.0 - - + -
301A VAL* 4.1 18.4 - - + -
308A ILE* 3.3 28.5 - - + -
315A PHE* 3.7 14.8 - - + -
333A ARG 2.9 15.6 + - - +
334A VAL 3.8 3.6 - - - +
336A ARG* 1.3 72.9 - - - +
338A LYS* 1.3 68.2 + - - +
340A PHE* 2.9 12.8 + - - +
341A ILE* 2.9 19.2 + - - +
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Residues in contact with LYS 338 (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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250A SER* 5.8 0.4 - - - +
294A GLN* 3.0 26.2 - - - +
297A LEU* 4.1 15.1 - - + +
325A THR 5.9 0.6 + - - -
326A PRO* 5.6 1.4 - - - +
327A GLU* 4.2 13.9 + - - +
330A GLU* 3.1 37.5 + - - +
334A VAL* 2.9 21.9 + - + +
335A THR 3.5 1.8 - - - +
337A ALA* 1.3 77.3 - - - +
339A TYR* 1.3 70.5 + - - +
341A ILE* 3.3 6.1 + - - +
342A ARG* 3.0 27.0 + - - +
363A PHE* 3.2 54.0 - - + +
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Residues in contact with TYR 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A TYR* 3.0 17.5 + - - +
320A THR* 4.3 4.3 - - + -
321A PRO* 3.5 27.1 - - + -
323A ASP* 4.9 4.5 - - - -
324A ALA* 4.0 14.3 - - + -
325A THR* 3.4 31.3 + - - -
335A THR* 2.9 51.7 + - + +
336A ARG 3.9 1.8 - - - +
338A LYS* 1.3 90.7 + - - +
340A PHE* 1.3 55.5 + - - +
342A ARG* 3.9 33.4 - - - -
343A ASP* 2.8 34.8 + - - +
363A PHE* 4.7 9.0 - + - -
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Residues in contact with PHE 340 (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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266A LEU* 6.2 0.9 - - + -
308A ILE* 4.0 9.6 - - + -
312A PHE* 3.6 32.3 - + + -
314A GLU* 3.8 15.0 - - + -
315A PHE* 3.3 48.7 - + + -
318A TYR* 3.2 37.7 + + + -
336A ARG 2.9 7.9 + - - +
337A ALA 2.9 10.4 + - - +
339A TYR* 1.3 74.5 - - - +
341A ILE* 1.3 67.8 + - + +
343A ASP* 3.5 3.1 + - + +
344A GLU* 2.9 65.7 + - + +
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Residues in contact with ILE 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A SER* 3.4 34.5 - - - +
253A TYR* 5.5 1.3 - - + -
266A LEU* 4.0 25.6 - - + -
291A LEU* 3.9 14.4 - - + -
297A LEU* 3.8 26.0 - - + -
308A ILE* 5.2 7.4 - - + -
337A ALA 2.9 12.1 + - - +
338A LYS* 3.5 6.1 - - - +
340A PHE* 1.3 79.3 - - + +
342A ARG* 1.3 67.7 + - - +
344A GLU* 2.7 22.1 + - + +
345A PHE* 3.0 34.2 + - + -
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Residues in contact with ARG 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU* 5.2 0.6 - - - +
291A LEU* 3.9 9.8 - - + +
321A PRO* 4.6 7.3 - - - +
323A ASP* 5.6 1.8 + - - -
338A LYS 3.0 16.3 + - - +
339A TYR* 3.6 30.0 - - - +
341A ILE* 1.3 76.3 - - - +
343A ASP* 1.3 82.1 + - - +
345A PHE* 3.1 6.7 + - - +
346A LEU* 2.9 47.0 + - + +
361A PRO* 3.5 38.5 - - + +
363A PHE* 3.8 25.6 - - + -
235R LYS 4.5 14.8 + - - -
236R SER* 4.5 11.3 + - - +
239R ARG* 5.7 0.8 - - - +
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Residues in contact with ASP 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A TYR* 3.9 21.7 + - + +
321A PRO* 4.5 5.6 - - - +
339A TYR* 2.8 23.9 + - - +
340A PHE* 3.8 6.1 - - + +
342A ARG* 1.3 105.0 + - - +
344A GLU* 1.3 61.0 + - - +
346A LEU* 3.5 9.8 - - - +
347A ARG* 2.9 34.6 + - - +
239R ARG* 3.9 13.9 + - - +
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Residues in contact with GLU 344 (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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266A LEU* 6.1 1.6 - - + -
270A LEU* 3.7 31.1 - - + +
312A PHE* 4.4 9.8 - - + -
314A GLU* 4.0 9.3 - - - +
340A PHE* 2.9 59.0 + - + +
341A ILE* 2.7 21.3 + - + +
343A ASP* 1.3 73.9 - - - +
345A PHE* 1.3 55.0 + - + -
347A ARG* 3.0 53.2 + - - +
348A ILE* 4.2 6.8 - - - +
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Residues in contact with PHE 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A PHE* 4.3 4.5 - + - -
248A VAL* 3.5 30.1 - - + -
266A LEU* 3.7 27.8 - - + -
269A ALA* 4.0 7.2 - - + -
270A LEU* 3.4 40.6 - - + -
273A PHE* 3.6 45.3 - + + -
289A LEU* 3.4 32.8 - - + -
291A LEU* 4.0 2.5 - - + -
341A ILE* 3.0 34.2 + - + -
342A ARG 3.7 4.3 - - - +
344A GLU* 1.3 75.8 - - - +
346A LEU* 1.3 64.5 + - - +
347A ARG 3.5 0.2 - - - -
348A ILE* 3.8 1.8 + - - +
349A SER* 3.6 7.6 + - - -
359A CYS* 4.7 3.0 - - - -
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Residues in contact with LEU 346 (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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289A LEU* 6.5 0.2 - - + -
342A ARG* 2.9 61.1 + - + +
343A ASP* 3.1 15.0 + - - +
345A PHE* 1.3 75.8 - - - +
347A ARG* 1.3 66.7 + - - +
348A ILE 3.1 2.2 - - - -
349A SER* 3.0 8.0 + - - +
350A THR* 2.9 29.8 + - + +
359A CYS* 4.2 20.2 - - + +
361A PRO* 4.1 19.1 - - + -
236R SER* 3.8 23.3 - - - +
239R ARG* 4.0 13.5 - - - +
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Residues in contact with ARG 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A GLU* 4.3 16.0 + - - +
343A ASP 2.9 16.3 + - - +
344A GLU* 3.0 54.5 + - - +
346A LEU* 1.3 76.3 - - - +
348A ILE* 1.3 60.9 + - + +
350A THR* 3.0 11.1 + - - -
351A ALA* 2.9 28.1 + - - +
239R ARG* 3.7 12.1 - - - +
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Residues in contact with ILE 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU* 4.0 21.3 - - + +
273A PHE* 3.7 28.5 - - + -
274A LYS* 3.8 48.0 - - + -
277A TRP* 3.8 18.2 + - + -
278A ASN* 5.4 1.6 - - - +
344A GLU 4.2 14.8 - - - +
345A PHE 3.8 2.0 + - - +
346A LEU 3.1 0.6 - - - -
347A ARG* 1.3 80.0 - - + +
349A SER* 1.3 64.7 + - - +
351A ALA* 3.0 22.3 + - + +
352A SER* 3.8 1.4 + - - -
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Residues in contact with SER 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A PHE* 3.3 15.4 - - - -
277A TRP* 3.4 33.0 + - - +
345A PHE 3.6 4.0 + - - -
346A LEU* 3.0 12.6 + - - -
348A ILE* 1.3 78.6 - - - +
350A THR* 1.3 63.2 + - - +
351A ALA 3.6 0.3 + - - -
352A SER* 4.1 7.4 + - - -
353A GLY 4.6 2.1 + - - -
354A ASP* 5.2 1.4 - - - +
357A HIS 5.3 1.4 - - - +
358A TYR* 5.6 0.4 - - - -
359A CYS* 2.9 34.7 - - - +
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Residues in contact with THR 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 2.9 22.8 + - + +
347A ARG* 3.0 19.2 + - - -
349A SER* 1.3 78.6 - - - +
351A ALA* 1.3 64.9 + - - +
352A SER 3.4 0.7 - - - -
353A GLY* 3.8 11.2 + - - +
236R SER 5.4 1.3 - - - +
237R GLU* 4.5 18.2 - - + +
239R ARG* 3.5 43.3 + - - +
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Residues in contact with ALA 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ARG 2.9 13.7 + - - +
348A ILE* 3.0 18.1 + - + +
350A THR* 1.3 78.0 - - - +
352A SER* 1.3 67.3 + - - +
353A GLY* 4.4 0.3 - - - -
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Residues in contact with SER 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A TRP* 3.5 29.3 + - - -
278A ASN* 4.5 6.6 + - - -
348A ILE 3.8 1.1 + - - -
349A SER 4.1 2.9 + - - -
350A THR 3.4 0.2 - - - -
351A ALA* 1.3 80.8 - - - +
353A GLY* 1.3 57.5 + - - +
354A ASP* 3.1 31.8 + - - +
357A HIS* 4.5 2.2 + - - -
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Residues in contact with GLY 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A SER 4.6 2.0 + - - -
350A THR* 3.8 12.0 + - - -
351A ALA 3.4 2.6 - - - -
352A SER* 1.3 77.9 - - - +
354A ASP* 1.3 62.1 + - - +
355A GLY 3.5 2.2 - - - -
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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