Contacts of the helix formed by residues 322 - 345 (chain H) in PDB entry 6MZL
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 322 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321H PRO* 1.3 90.5 - - + +
323H VAL* 1.3 60.0 + - + +
325H ASN* 3.0 34.6 + - - +
326H HIS* 3.0 28.7 + - + +
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Residues in contact with VAL 323 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276H LEU* 3.9 22.7 - - + -
318H CYS* 3.8 22.9 - - + -
319H LEU* 3.2 23.6 - - + +
320H ARG 3.0 12.5 + - - +
321H PRO* 5.2 0.9 - - + -
322H ASP* 1.3 78.5 - - + +
324H ASP* 1.3 48.9 + - - +
326H HIS* 2.9 11.0 + - + +
327H TRP* 2.3 58.3 + - - +
330H ARG* 3.5 19.3 - - - +
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Residues in contact with ASP 324 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320H ARG* 3.5 8.7 + - - +
321H PRO* 3.1 20.0 + - - +
323H VAL* 1.3 76.1 - - - +
325H ASN* 1.3 59.7 + - - +
327H TRP* 2.9 22.3 + - - +
328H ALA 2.8 21.5 + - - -
415H ILE* 4.7 18.0 - - - +
418H ILE* 4.3 19.6 - - + +
419H GLY* 5.0 3.0 - - - -
422H HIS* 3.3 39.1 + - + +
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Residues in contact with ASN 325 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321H PRO 5.1 1.6 + - - -
322H ASP* 3.0 21.4 + - + +
324H ASP* 1.3 74.8 - - - +
326H HIS* 1.3 56.2 + - + +
328H ALA* 2.8 14.8 - - + +
329H LEU* 2.6 38.9 + - + +
422H HIS* 4.6 11.8 - - - +
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Residues in contact with HIS 326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276H LEU* 4.5 26.6 - - + +
322H ASP* 3.0 44.7 + - + +
323H VAL* 2.9 20.5 + - + +
325H ASN* 1.3 74.3 - - + +
327H TRP* 1.3 52.2 + - - +
329H LEU* 2.9 29.5 + - + +
330H ARG* 2.7 51.2 + - - +
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Residues in contact with TRP 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311H CYS 4.2 8.1 - - - -
312H ILE* 5.0 2.7 - - - -
313H VAL 4.3 2.0 - - - -
314H SER* 3.1 50.9 - - - -
316H GLN* 4.1 19.9 - - - +
317H LEU 5.0 0.7 - - - -
318H CYS* 5.1 5.1 - - - +
320H ARG 5.5 0.4 + - - -
323H VAL* 2.3 58.4 + - + +
324H ASP* 2.9 25.4 + - - +
326H HIS* 1.3 68.6 - - - +
328H ALA* 1.3 53.8 + - - +
330H ARG* 3.0 57.6 + - + +
331H ASP* 2.9 20.5 + - - +
371H THR* 3.2 27.8 - - - -
374H TYR* 3.9 17.4 - + + -
375H GLY* 6.5 0.2 - - - -
422H HIS* 5.0 1.1 - - - +
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Residues in contact with ALA 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324H ASP 2.8 6.5 + - - -
325H ASN* 2.8 24.7 - - + +
327H TRP* 1.3 76.2 - - - +
329H LEU* 1.3 57.1 + - + +
331H ASP* 2.8 36.1 + - - +
332H PHE* 3.4 2.9 + - - +
374H TYR* 3.3 17.3 - - - +
422H HIS* 4.9 1.1 - - + -
426H LEU* 6.0 0.4 - - + -
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Residues in contact with LEU 329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280H ILE* 5.1 21.6 - - + +
325H ASN* 2.6 19.5 + - + +
326H HIS* 2.9 41.9 + - + +
328H ALA* 1.3 72.5 - - + +
330H ARG* 1.3 59.4 + - - +
332H PHE* 2.7 38.1 - - + +
333H ALA* 3.6 1.2 + - - +
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Residues in contact with ARG 330 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276H LEU* 3.4 33.1 - - - +
279H LEU* 4.3 21.8 - - + +
283H MET* 6.1 2.5 - - + -
311H CYS* 3.8 24.0 - - + +
312H ILE* 4.9 8.9 - - + +
318H CYS* 4.2 10.9 - - - -
323H VAL* 3.3 24.0 + - - +
326H HIS* 2.7 22.2 + - - +
327H TRP* 3.0 71.8 + - + +
329H LEU* 1.3 73.0 - - - +
331H ASP* 1.3 58.7 + - - +
332H PHE 3.2 0.2 - - - -
333H ALA* 2.8 33.0 + - + +
334H ALA* 3.1 4.5 + - - +
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Residues in contact with ASP 331 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312H ILE* 5.4 2.6 - - - +
327H TRP 2.9 12.7 - - - +
328H ALA* 2.8 20.1 + - - +
330H ARG* 1.3 76.4 - - - +
332H PHE* 1.3 58.8 + - - +
334H ALA* 2.9 24.3 + - - +
335H ARG* 3.0 10.2 + - - -
374H TYR* 3.2 30.2 + - - -
375H GLY* 4.5 5.0 - - - -
378H ALA* 3.5 27.8 - - + +
382H GLU* 4.1 9.0 - - + +
426H LEU* 4.0 8.3 - - + +
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Residues in contact with PHE 332 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280H ILE* 5.3 11.9 - - + -
283H MET* 4.7 20.2 - - + -
284H ARG* 4.8 17.5 - - + -
287H LYS* 4.5 31.2 - - + -
328H ALA 3.4 3.0 + - - -
329H LEU* 2.7 25.6 + - + +
331H ASP* 1.3 76.2 - - - +
333H ALA* 1.3 60.1 + - + -
335H ARG* 2.9 51.5 + - - +
336H LEU* 3.4 12.8 + - + +
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Residues in contact with ALA 333 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283H MET* 3.7 35.2 - - + -
308H VAL* 4.6 4.3 - - + +
311H CYS* 5.5 3.8 - - + -
312H ILE* 5.1 9.4 - - + -
329H LEU 3.6 0.6 + - - +
330H ARG* 2.8 21.8 + - + +
332H PHE* 1.3 81.6 - - + +
334H ALA* 1.3 56.0 + - - +
336H LEU* 2.8 38.9 + - - +
337H VAL* 3.4 6.3 + - - +
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Residues in contact with ALA 334 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312H ILE* 4.5 11.6 - - + +
330H ARG 3.1 6.1 + - - +
331H ASP* 2.9 22.7 + - - +
333H ALA* 1.3 72.5 - - - +
335H ARG* 1.3 63.1 + - - +
337H VAL* 2.9 30.7 + - + +
338H ALA 3.6 0.2 + - - -
375H GLY 5.2 1.1 - - - +
378H ALA* 4.1 7.2 - - + +
379H GLY* 4.1 19.7 - - - +
382H GLU* 3.5 21.5 - - + +
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Residues in contact with ARG 335 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287H LYS* 5.2 8.2 - - - +
331H ASP 3.0 6.0 + - - +
332H PHE* 2.9 40.7 + - - +
334H ALA* 1.3 75.4 - - - +
336H LEU* 1.3 59.7 + - + +
338H ALA* 3.1 8.5 + - - +
339H GLN* 3.0 48.7 + - + +
382H GLU* 3.3 30.7 - - - +
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Residues in contact with LEU 336 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283H MET* 3.7 32.8 - - + +
286H VAL* 4.5 14.6 - - + +
287H LYS* 3.7 41.5 - - + +
290H MET* 4.9 8.0 - - + +
308H VAL* 5.4 3.6 - - + -
332H PHE* 3.4 11.9 + - + +
333H ALA* 2.8 30.9 + - + +
335H ARG* 1.3 77.3 - - + +
337H VAL* 1.3 48.4 + - + +
339H GLN* 2.9 16.7 + - + +
340H ILE* 2.5 45.7 + - + +
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Residues in contact with VAL 337 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308H VAL* 3.6 28.5 - - + -
309H MET* 5.1 4.3 - - + -
312H ILE* 4.2 8.5 - - + -
333H ALA 3.9 0.2 - - - +
334H ALA* 2.9 28.9 + - + +
336H LEU* 1.3 75.2 - - - +
338H ALA* 1.3 56.1 + - - +
340H ILE* 2.9 15.4 + - + +
341H CYS* 2.9 41.9 + - - -
355H ILE* 4.5 22.7 - - + -
359H PHE* 5.0 11.4 - - + -
379H GLY* 5.3 3.6 - - - +
382H GLU* 5.6 0.2 - - + -
383H LEU* 5.3 8.5 - - + -
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Residues in contact with ALA 338 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334H ALA 3.6 1.4 + - - -
335H ARG 3.1 8.3 + - - +
337H VAL* 1.3 79.4 - - - +
339H GLN* 1.3 61.1 + - + +
341H CYS* 2.9 21.5 + - - +
342H LYS* 3.0 32.6 + - + +
382H GLU* 3.3 33.8 - - + +
383H LEU* 4.7 9.8 - - + +
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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
----------------------------------------------------------
287H LYS* 3.9 17.2 - - - +
290H MET* 3.6 21.6 - - + +
335H ARG* 3.0 53.0 + - + +
336H LEU* 2.9 30.0 + - - +
338H ALA* 1.3 78.0 - - + +
340H ILE* 1.3 57.4 + - - +
342H LYS* 5.1 6.1 - - + +
343H HIS* 3.1 29.2 - - + +
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Residues in contact with ILE 340 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286H VAL* 5.7 2.0 - - + -
290H MET* 3.7 20.9 - - + -
301H VAL* 4.5 7.0 - - + -
304H LEU* 5.7 2.9 - - + -
305H ILE* 3.6 35.9 - - + -
308H VAL* 4.0 21.8 - - + -
336H LEU* 2.5 24.0 + - + +
337H VAL* 2.9 18.8 + - + +
339H GLN* 1.3 75.6 - - - +
341H CYS* 1.3 68.7 - - - +
342H LYS 3.3 0.2 - - - -
343H HIS* 2.9 19.1 + - - +
344H PHE* 3.0 38.0 + - + -
351H ILE* 5.2 3.6 - - + -
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Residues in contact with CYS 341 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337H VAL* 2.9 24.5 + - - +
338H ALA* 2.9 6.0 + - - +
340H ILE* 1.3 82.3 - - - +
342H LYS* 1.3 60.6 + - - +
344H PHE 4.1 2.0 - - - +
345H SER* 2.9 36.2 + - - +
351H ILE* 4.0 11.4 - - + -
352H GLN* 4.2 29.1 + - + +
355H ILE* 3.6 31.2 - - - -
383H LEU* 5.0 9.0 - - + -
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Residues in contact with LYS 342 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338H ALA* 3.0 29.3 + - + +
339H GLN* 5.4 5.1 - - + +
341H CYS* 1.3 78.4 - - - +
343H HIS* 1.3 76.2 + - + +
345H SER* 5.0 2.0 + - - -
346H THR* 5.3 0.9 + - - -
352H GLN* 5.3 1.9 - - - +
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Residues in contact with HIS 343 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290H MET* 4.8 10.8 - - + +
339H GLN* 3.1 31.7 + - - +
340H ILE 2.9 2.2 + - - -
342H LYS* 1.3 91.1 + - + +
344H PHE* 1.3 88.6 + - + +
345H SER 3.9 0.4 - - - -
346H THR* 3.5 12.2 + - - -
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Residues in contact with PHE 344 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290H MET* 4.5 15.3 - - - -
295H LEU 5.4 1.1 - - - -
297H LEU* 3.7 31.2 - - + -
298H GLU* 3.6 39.5 - - + -
301H VAL* 4.1 17.5 - - + -
340H ILE* 3.0 40.9 + - + +
341H CYS* 3.0 4.6 + - - -
343H HIS* 1.3 102.5 - - + +
345H SER* 1.3 58.2 + - - +
346H THR* 3.0 12.3 + - - -
347H THR* 3.5 3.3 + - - -
351H ILE* 3.2 24.7 - - + +
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Residues in contact with SER 345 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341H CYS 2.9 15.5 + - - -
342H LYS 4.9 1.8 + - - -
344H PHE* 1.3 75.0 - - - +
346H THR* 1.3 49.2 + - - +
347H THR* 3.0 10.7 + - - -
349H ASN* 2.9 29.3 - - - +
351H ILE* 4.3 7.2 - - - +
352H GLN* 3.9 35.7 + - - -
303I GLU* 5.2 6.9 + - - +
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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