Contacts of the helix formed by residues 332 - 355 (chain H) in PDB entry 4E2I
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 332 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339G GLN* 4.0 0.2 - - - +
270H TRP* 5.1 7.2 - - + -
330H SER* 3.2 10.0 + - - +
331H LYS* 1.3 94.1 - - - +
333H GLN* 1.3 64.1 + - - +
334H LYS 3.2 3.8 - - - +
335H THR* 3.6 28.8 + - + -
336H ILE* 3.0 29.2 + - + +
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Residues in contact with GLN 333 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274G THR* 5.1 7.3 + - - +
339G GLN* 3.0 35.0 + - + +
343G THR* 3.5 23.4 + - - +
289H LEU* 3.2 26.4 - - + +
293H LEU* 3.8 24.9 - - - +
296H GLN* 4.9 0.2 - - - +
327H PHE* 3.3 39.5 - - + +
328H ALA* 3.0 27.7 - - - +
330H SER* 3.6 6.5 - - - +
332H ASN* 1.3 76.2 - - - +
334H LYS* 1.3 60.7 + - - +
337H CYS* 3.6 10.0 + - - -
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Residues in contact with LYS 334 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338G GLN* 5.3 3.6 + - - +
339G GLN* 4.7 5.8 - - + +
342G ASP* 3.8 35.4 + - + +
512G LYS* 4.6 11.7 - - - +
514G LEU* 5.6 4.3 - - - +
516G LYS* 4.5 19.6 - - - +
285H VAL* 4.1 25.0 - - + +
286H LEU* 4.6 7.2 - - + -
289H LEU* 4.5 16.2 - - + -
332H ASN 3.2 0.4 - - - -
333H GLN* 1.3 77.8 - - - +
335H THR* 1.3 60.6 + - - +
337H CYS* 4.0 2.4 - - - -
338H GLN* 3.0 33.5 + - + +
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Residues in contact with THR 335 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270H TRP* 3.6 23.7 - - + -
332H ASN* 3.1 31.4 + - + +
334H LYS* 1.3 77.5 - - - +
336H ILE* 1.3 65.6 + - - +
338H GLN* 3.1 16.2 + - + +
339H GLN* 3.2 11.6 + - - +
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Residues in contact with ILE 336 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268H VAL* 3.9 20.6 - - + -
269H SER 4.6 0.4 - - - +
270H TRP* 3.6 45.7 - - + +
273H VAL* 3.6 33.5 - - + +
274H THR* 5.3 1.6 + - - -
327H PHE* 3.5 25.6 - - + -
330H SER* 3.3 26.5 - - - +
332H ASN* 3.0 13.6 + - + +
335H THR* 1.3 76.6 - - - +
337H CYS* 1.3 62.5 + - - +
338H GLN 3.4 0.3 + - - -
339H GLN* 3.6 4.9 + - - +
340H ALA* 3.5 16.3 + - - +
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Residues in contact with CYS 337 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273H VAL* 4.2 15.3 - - - -
285H VAL* 4.3 8.7 - - + +
288H LEU* 3.4 16.0 - - + +
289H LEU* 3.6 29.8 - - + -
292H TYR* 4.7 1.6 - - - -
327H PHE* 3.5 28.7 - - - -
333H GLN 3.6 10.1 + - - +
334H LYS* 4.3 3.1 - - - +
335H THR 3.3 0.4 - - - -
336H ILE* 1.3 77.9 - - - +
338H GLN* 1.3 64.9 + - - +
340H ALA* 3.3 9.6 + - - +
341H VAL* 3.0 28.4 + - - +
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Residues in contact with GLN 338 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514G LEU* 4.9 10.3 - - - +
285H VAL* 3.2 38.0 - - + +
334H LYS* 3.0 27.4 + - + +
335H THR* 3.1 13.2 + - + +
337H CYS* 1.3 76.8 - - - +
339H GLN* 1.3 62.6 + - - +
341H VAL* 3.1 21.1 + - - +
342H ASP* 3.0 38.3 + - - +
334I LYS* 5.2 3.1 + - - +
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Residues in contact with GLN 339 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270H TRP* 3.2 29.9 - - + +
274H THR* 4.2 9.9 + - - +
335H THR 3.2 7.5 + - - +
336H ILE 3.9 7.0 - - - +
338H GLN* 1.3 79.0 - - - +
340H ALA* 1.3 62.2 + - - +
342H ASP* 3.2 13.0 + - + +
343H THR* 2.9 24.6 + - - +
289I LEU* 6.4 0.7 - - + -
330I SER 3.4 11.4 + - - +
331I LYS 3.0 24.4 + - - -
332I ASN* 3.6 0.8 - - - +
333I GLN* 2.9 50.8 - - + +
334I LYS* 4.5 8.0 - - + +
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Residues in contact with ALA 340 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273H VAL 4.1 4.0 - - - +
274H THR* 3.9 20.6 + - - +
277H ALA* 3.6 14.4 - - + +
288H LEU* 3.4 17.5 - - + -
336H ILE 3.5 10.5 + - - +
337H CYS* 3.4 11.4 - - - +
339H GLN* 1.3 79.7 - - - +
341H VAL* 1.3 62.3 + - - +
343H THR* 3.0 11.2 + - - -
344H VAL* 2.9 26.8 + - - +
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Residues in contact with VAL 341 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282H CYS 4.3 1.1 - - - -
283H ASP* 3.5 30.7 - - - +
284H ASP 3.1 28.9 - - - +
285H VAL* 3.7 21.5 - - + -
288H LEU* 3.9 6.0 - - + +
337H CYS 3.0 16.8 - - - +
338H GLN* 3.1 10.0 + - - +
340H ALA* 1.3 76.9 - - - +
342H ASP* 1.3 57.5 + - - +
344H VAL* 3.0 11.2 + - - +
345H LEU* 2.9 39.2 + - + +
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Residues in contact with ASP 342 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338H GLN* 3.0 34.3 + - - +
339H GLN* 3.2 12.4 + - + +
341H VAL* 1.3 77.6 - - - +
343H THR* 1.3 57.4 + - - +
345H LEU* 4.5 9.5 - - - +
346H ALA* 2.8 30.0 + - - +
516H LYS* 5.9 0.3 - - - -
286I LEU* 3.8 22.0 - - + +
289I LEU* 4.3 8.1 - - + -
334I LYS* 3.4 41.1 + - + +
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Residues in contact with THR 343 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274H THR* 3.6 23.3 - - + +
278H MET* 3.5 29.1 - - + +
339H GLN* 2.9 15.3 + - - +
340H ALA 3.0 9.5 + - - -
342H ASP* 1.3 75.8 - - - +
344H VAL* 1.3 62.2 + - - +
346H ALA* 3.4 6.6 - - - +
347H LYS* 3.1 17.2 + - - +
289I LEU* 4.5 5.1 - - - +
293I LEU* 3.7 23.5 - - + +
333I GLN* 3.4 18.9 + - - +
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Residues in contact with VAL 344 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277H ALA* 3.7 28.0 - - + +
278H MET* 4.3 9.0 - - - +
281H LYS* 3.6 22.9 - - - +
282H CYS 3.1 24.2 - - - +
283H ASP* 4.0 5.4 - - + +
340H ALA 2.9 16.5 + - - +
341H VAL 3.0 6.7 + - - +
343H THR* 1.3 74.5 - - - +
345H LEU* 1.3 65.6 + - - +
347H LYS* 3.1 18.9 + - - +
348H LYS* 3.3 32.3 + - - +
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Residues in contact with LEU 345 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283H ASP* 3.9 28.7 - - + +
341H VAL* 2.9 31.1 + - + +
342H ASP* 4.0 10.3 - - - +
344H VAL* 1.3 76.7 - - - +
346H ALA* 1.3 51.8 + - - +
348H LYS* 3.4 14.9 + - + +
349H ARG* 2.8 36.1 + - - +
466H ASP* 4.9 1.6 - - - +
511H LYS* 4.3 25.1 - - + +
286I LEU* 4.0 22.9 - - + -
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Residues in contact with ALA 346 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342H ASP 2.8 19.8 + - - +
343H THR* 3.4 12.3 - - - +
344H VAL 3.1 0.2 - - - -
345H LEU* 1.3 75.7 - - - +
347H LYS* 1.3 65.0 + - - +
349H ARG* 3.1 5.7 + - - +
350H VAL* 3.0 29.0 + - - +
286I LEU* 3.4 26.3 - - + +
289I LEU* 4.0 8.7 - - + -
290I GLY* 3.8 15.3 - - - +
293I LEU* 4.9 1.1 - - + -
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Residues in contact with LYS 347 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278H MET* 3.9 26.7 - - + +
343H THR 3.1 11.5 + - - +
344H VAL* 3.1 12.2 + - + +
346H ALA* 1.3 76.7 - - - +
348H LYS* 1.3 57.5 + - + +
350H VAL* 3.0 10.0 + - + +
351H ASP* 2.7 57.2 + - - +
290I GLY* 5.1 1.8 - - - -
294I GLU* 4.5 18.0 + - - +
297I TYR* 5.8 1.8 + - - -
304I LYS* 6.0 2.4 - - - +
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Residues in contact with LYS 348 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281H LYS* 3.7 24.1 + - - +
283H ASP* 4.4 11.9 - - - +
344H VAL* 3.3 35.9 + - - +
345H LEU* 3.8 17.7 - - + +
347H LYS* 1.3 78.5 - - + +
349H ARG* 1.3 62.8 + - - +
351H ASP* 4.0 8.5 - - - +
352H SER* 3.1 27.9 + - - -
466H ASP* 4.1 17.4 - - + +
467H GLN* 5.5 9.2 - - - +
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Residues in contact with ARG 349 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345H LEU* 2.8 14.6 + - - +
346H ALA* 3.1 16.8 + - - +
348H LYS* 1.3 75.8 - - - +
350H VAL* 1.3 57.1 + - - +
352H SER* 3.0 13.5 + - - -
353H LEU* 4.0 6.1 - - - +
465H ILE* 3.1 17.0 - - - +
466H ASP* 3.0 28.6 + - - -
511H LYS* 3.5 18.2 - - - +
516H LYS* 2.9 37.3 + - - +
517H ARG* 3.1 27.1 + - - +
284I ASP* 4.3 2.6 + - - -
286I LEU* 3.1 35.3 - - - +
287I LEU* 3.5 38.2 - - + +
----------------------------------------------------------
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Residues in contact with VAL 350 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346H ALA 3.0 16.3 + - - +
347H LYS* 3.0 9.8 + - + +
349H ARG* 1.3 77.4 - - + +
351H ASP* 1.3 61.0 + - - +
352H SER 3.1 1.8 - - - -
353H LEU* 2.9 21.5 + - + +
354H GLN* 3.1 44.0 + - + +
287I LEU* 4.2 13.5 - - + +
290I GLY* 3.7 25.4 - - - -
291I MET* 3.5 21.1 - - + +
294I GLU* 4.5 9.9 - - - +
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Residues in contact with ASP 351 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347H LYS* 2.7 52.7 + - - +
348H LYS* 3.4 8.1 + - - +
350H VAL* 1.3 77.3 - - - +
352H SER* 1.3 57.4 + - - +
353H LEU 3.0 5.0 + - - -
354H GLN* 4.5 3.4 - - - +
355H LEU* 3.3 55.6 + - + +
360H MET* 4.0 8.7 - - + +
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Residues in contact with SER 352 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348H LYS 3.1 11.6 + - - -
349H ARG 3.0 18.9 + - - -
351H ASP* 1.3 75.0 - - - +
353H LEU* 1.3 63.8 + - - +
355H LEU 4.9 2.2 - - - -
360H MET* 4.2 19.5 - - - +
466H ASP* 3.1 38.9 + - - -
467H GLN 5.5 1.8 - - - -
517H ARG* 4.1 5.4 + - - -
519H GLN* 4.6 3.3 + - - -
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Residues in contact with LEU 353 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349H ARG 4.0 3.6 - - - +
350H VAL* 2.9 6.0 + - + +
352H SER* 1.3 88.3 - - - +
354H GLN* 1.3 66.9 + - + +
355H LEU 3.9 2.8 - - - +
517H ARG* 3.2 32.5 - - - +
519H GLN* 6.0 2.7 - - + -
287I LEU* 3.6 35.2 - - + -
310I GLN* 5.2 6.0 + - - +
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Residues in contact with GLN 354 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350H VAL* 3.1 38.5 + - + +
351H ASP* 5.0 1.8 - - - +
353H LEU* 1.3 81.5 - - + +
355H LEU* 1.3 68.2 - - + +
356H THR* 3.5 5.7 + - - +
359H GLN* 4.6 1.4 - - - +
291I MET* 3.4 14.4 - - + +
294I GLU* 3.4 21.7 + - - -
304I LYS* 4.1 20.0 - - - +
309I GLU* 5.2 3.5 - - - +
310I GLN* 3.4 45.0 + - + +
313I HIS* 5.6 2.4 - - - +
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Residues in contact with LEU 355 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351H ASP* 3.3 49.0 + - + +
352H SER 4.9 0.7 - - - -
353H LEU 4.6 2.8 - - - -
354H GLN* 1.3 83.9 + - + +
356H THR* 1.3 70.7 + - - +
357H ARG 3.8 0.3 + - - -
359H GLN* 3.4 31.4 - - + +
360H MET* 3.8 15.3 - - + +
363H ASN* 3.6 26.2 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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