Contacts of the helix formed by residues 325 - 342 (chain H) in PDB entry 4ZZ7
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 THR 325 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H PHE* 5.7 9.0 - - + -
176H ARG* 4.2 26.8 + - + +
323H VAL* 3.4 7.2 - - - +
324H ILE* 1.3 94.0 - - + +
326H ARG* 1.3 58.9 + - - +
327H GLN* 3.7 12.2 + - - +
328H HIS* 2.9 29.6 + - - +
329H GLN* 2.9 25.1 + - - +
362H PHE* 3.6 14.3 - - + +
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Residues in contact with ARG 326 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H GLY* 5.5 1.6 - - - -
325H THR* 1.3 70.9 - - - +
327H GLN* 1.3 66.5 + - - +
329H GLN* 3.1 23.3 + - - +
330H GLU* 2.9 44.9 + - + +
360H ASN* 3.4 26.1 + - - +
361H GLY 3.1 28.5 + - - -
362H PHE* 3.7 36.9 - - + -
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Residues in contact with GLN 327 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176H ARG* 5.4 6.1 + - - -
325H THR* 3.7 10.6 + - - +
326H ARG* 1.3 79.8 - - - +
328H HIS* 1.3 55.5 + - - +
330H GLU* 3.6 4.8 + - - +
331H LYS* 3.1 29.3 + - + +
15K GLU* 5.5 2.1 - - - +
38K SER* 4.8 7.4 + - - -
39K THR* 5.8 0.4 + - - -
40K LYS* 3.5 57.0 + - + +
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Residues in contact with HIS 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148H PHE* 4.9 3.1 - + - -
176H ARG* 6.1 1.5 + - - +
278H GLU* 3.4 23.6 + - - -
323H VAL* 3.5 19.7 - - + -
324H ILE* 4.0 11.0 - - + -
325H THR* 2.9 23.9 + - - +
327H GLN* 1.3 73.3 - - - +
329H GLN* 1.3 60.7 + - - +
331H LYS* 3.3 29.3 + - + +
332H VAL* 2.9 39.1 + - + +
383H ILE 3.9 13.7 - - - -
384H PHE* 3.0 40.4 + + + +
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Residues in contact with GLN 329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323H VAL* 3.4 12.0 - - + +
325H THR 2.9 14.4 + - - +
326H ARG* 3.1 39.7 + - - +
328H HIS* 1.3 73.6 - - - +
330H GLU* 1.3 61.8 + - + +
332H VAL* 3.3 3.2 + - - +
333H ILE* 2.9 42.1 + - + +
351H ARG 5.8 0.4 + - - -
353H PRO* 5.5 2.0 - - - +
361H GLY 3.6 6.5 + - - -
362H PHE* 3.7 10.9 - - - +
363H PHE 2.9 31.1 + - - +
364H VAL* 3.9 17.2 - - + +
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Residues in contact with GLU 330 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326H ARG* 2.9 43.0 + - + +
327H GLN 3.7 4.0 - - - +
329H GLN* 1.3 78.0 - - + +
331H LYS* 1.3 53.0 + - - +
333H ILE* 3.2 8.6 + - - +
334H GLY* 2.7 33.4 + - - -
40K LYS* 3.0 26.4 + - - +
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Residues in contact with LYS 331 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327H GLN* 3.1 20.1 + - - +
328H HIS* 3.3 33.2 + - + +
330H GLU* 1.3 74.8 - - - +
332H VAL* 1.3 61.7 + - - +
334H GLY* 3.4 2.6 + - - +
335H TYR* 3.1 60.8 + - + +
382H GLU 5.4 1.4 + - - +
383H ILE 5.3 0.9 - - - +
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Residues in contact with VAL 332 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323H VAL* 4.3 6.1 - - + -
328H HIS* 2.9 44.0 + - + +
329H GLN 3.6 4.9 - - - +
331H LYS* 1.3 72.1 - - - +
333H ILE* 1.3 66.0 + - - +
335H TYR* 3.4 10.7 + - - +
336H ILE* 3.3 27.3 + - + +
364H VAL* 3.9 29.2 - - + -
383H ILE* 4.1 24.9 - - + +
385H GLY* 4.2 15.5 - - - -
386H PRO* 4.4 0.4 - - + -
387H VAL* 4.4 5.4 - - + -
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Residues in contact with ILE 333 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329H GLN* 2.9 36.4 + - + +
330H GLU* 3.5 9.4 - - - +
332H VAL* 1.3 75.9 - - - +
334H GLY* 1.3 57.1 + - - +
336H ILE* 3.0 9.4 + - - +
337H ASN* 2.9 43.4 + - - +
351H ARG* 3.2 51.6 - - + +
363H PHE 5.4 0.4 - - - +
364H VAL* 4.4 18.2 - - + -
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Residues in contact with GLY 334 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330H GLU 2.7 20.4 + - - -
331H LYS* 3.7 3.6 - - - -
333H ILE* 1.3 72.6 - - - +
335H TYR* 1.3 56.6 + - - +
337H ASN* 3.4 11.8 + - - +
338H SER* 2.9 29.2 + - - -
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Residues in contact with TYR 335 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331H LYS* 3.1 56.4 + - + +
332H VAL 3.7 6.1 - - - +
333H ILE 3.3 0.2 - - - -
334H GLY* 1.3 74.2 - - - +
336H ILE* 1.3 53.1 + - - +
338H SER* 3.1 8.7 + - - -
339H ALA* 2.8 35.0 + - - +
369H ILE* 5.7 0.2 - - - -
377H THR* 4.5 7.6 - - + -
378H SER* 3.7 23.7 - - - -
381H GLU* 2.7 42.1 + - + +
382H GLU 3.7 24.5 + - - -
383H ILE* 3.9 39.0 - - + -
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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
----------------------------------------------------------
332H VAL* 3.4 24.7 - - + +
333H ILE* 3.0 7.5 + - - +
335H TYR* 1.3 71.7 - - + +
337H ASN* 1.3 65.2 + - - +
339H ALA* 3.5 8.1 - - - +
340H GLU* 3.2 22.2 + - - +
346H ILE* 3.9 18.1 - - + +
349H ASP* 4.9 1.1 - - - +
351H ARG* 3.5 42.1 + - + +
364H VAL* 4.4 6.7 - - + -
367H THR* 3.8 31.4 - - + +
369H ILE* 4.4 8.5 - - + -
383H ILE* 6.0 0.4 - - + -
387H VAL* 4.1 20.0 - - + -
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Residues in contact with ASN 337 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333H ILE* 2.9 29.9 + - - +
334H GLY* 3.5 11.8 - - - +
336H ILE* 1.3 73.8 - - - +
338H SER* 1.3 66.3 + - - +
340H GLU* 3.2 5.6 + - - +
341H GLN* 3.0 25.8 + - - +
351H ARG* 2.8 41.3 + - - +
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Residues in contact with SER 338 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334H GLY 2.9 14.9 + - - -
335H TYR* 3.4 13.7 - - - -
337H ASN* 1.3 75.8 - - - +
339H ALA* 1.3 64.1 + - - +
341H GLN* 3.4 13.4 + - - +
342H GLN* 2.9 48.4 + - - +
377H THR* 4.1 12.0 - - - -
378H SER* 4.3 4.6 + - - -
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Residues in contact with ALA 339 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335H TYR 2.8 16.2 + - - +
336H ILE 3.5 10.3 - - - +
338H SER* 1.3 71.1 - - - +
340H GLU* 1.3 64.1 + - - +
342H GLN* 3.0 16.1 + - - +
343H GLY 3.3 0.9 + - - -
344H ALA* 3.1 30.2 + - + +
346H ILE* 4.4 0.4 - - + -
369H ILE* 3.8 26.9 - - + -
376H MET* 4.4 2.8 - - - +
378H SER* 3.6 21.0 + - - +
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Residues in contact with GLU 340 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336H ILE 3.2 8.1 + - - +
337H ASN* 3.2 8.4 + - - +
339H ALA* 1.3 76.2 - - - +
341H GLN* 1.3 59.1 - - - +
343H GLY* 3.0 21.0 + - - -
344H ALA 3.6 16.5 + - - +
346H ILE* 3.7 19.6 - - + +
351H ARG* 2.7 43.2 + - - -
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Residues in contact with GLN 341 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337H ASN 3.0 16.6 + - - +
338H SER* 3.6 13.2 + - - +
340H GLU* 1.3 76.6 - - - +
342H GLN* 1.3 64.9 + - - +
343H GLY* 3.3 1.4 + - - -
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Residues in contact with GLN 342 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338H SER* 2.9 36.4 + - - +
339H ALA* 3.0 6.4 + - - +
341H GLN* 1.3 82.2 - - - +
343H GLY* 1.3 56.6 + - - +
344H ALA 3.7 0.4 - - - -
375H GLU 4.7 3.0 + - - -
376H MET* 3.6 32.9 - - + +
377H THR* 3.1 39.9 + - - +
378H SER 4.2 1.2 + - - -
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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