Contacts of the helix formed by residues 325 - 342 (chain J) 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 J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23J PHE* 5.4 11.7 - - + -
176J ARG* 4.3 23.0 + - + +
323J VAL* 3.4 4.4 - - - +
324J ILE* 1.3 97.7 - - + +
326J ARG* 1.3 55.2 + - - +
327J GLN* 3.7 11.3 + - - +
328J HIS* 3.0 23.6 + - - +
329J GLN* 2.8 32.4 + - - +
362J PHE* 3.4 15.3 - - + -
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Residues in contact with ARG 326 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28J GLY* 5.5 2.6 + - - -
325J THR* 1.3 70.3 - - - +
327J GLN* 1.3 67.4 + - - +
329J GLN* 3.1 24.9 + - - +
330J GLU* 3.0 47.6 + - - +
360J ASN* 3.2 27.3 + - - +
361J GLY 3.1 26.3 + - - -
362J PHE* 3.5 37.5 - - + -
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Residues in contact with GLN 327 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G GLU* 5.0 4.2 + - - +
17G THR* 6.2 0.7 - - - +
38G SER* 4.0 11.9 + - - -
39G THR* 5.5 1.0 + - - -
40G LYS* 3.2 57.6 + - + +
176J ARG* 5.3 6.9 + - - -
325J THR* 3.3 9.0 + - - +
326J ARG* 1.3 79.7 - - - +
328J HIS* 1.3 59.5 + - - +
330J GLU* 3.6 4.4 + - - +
331J LYS* 3.3 23.6 + - - +
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Residues in contact with HIS 328 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148J PHE* 5.0 3.3 - + - -
176J ARG* 6.2 0.7 - - - +
278J GLU* 3.6 14.4 - - - -
323J VAL* 3.6 26.2 - - + -
324J ILE* 3.9 11.7 - - + -
325J THR* 3.0 21.3 + - - +
327J GLN* 1.3 75.0 - - - +
329J GLN* 1.3 65.6 + - - +
331J LYS* 3.1 31.2 + - + +
332J VAL* 2.9 33.2 + - + +
383J ILE 3.7 18.8 - - - -
384J PHE* 2.9 37.7 + + + +
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Residues in contact with GLN 329 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323J VAL* 3.4 9.5 - - + +
325J THR 2.8 17.7 + - - +
326J ARG* 3.2 40.9 + - - +
328J HIS* 1.3 73.2 - - - +
330J GLU* 1.3 60.2 + - - +
332J VAL* 3.3 3.6 + - - +
333J ILE* 2.9 41.6 + - + +
351J ARG 5.6 1.4 + - - -
353J PRO* 5.6 1.0 - - - +
361J GLY 3.8 5.5 + - - -
362J PHE* 3.8 16.7 - - + +
363J PHE 3.1 28.1 + - - +
364J VAL* 3.9 17.7 - - + -
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Residues in contact with GLU 330 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G LYS* 2.7 32.9 + - - +
326J ARG* 3.0 43.9 + - + +
327J GLN 3.9 3.4 - - - +
329J GLN* 1.3 80.7 - - + +
331J LYS* 1.3 53.4 + - - +
333J ILE* 3.4 10.0 + - + +
334J GLY* 2.7 30.7 + - - -
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Residues in contact with LYS 331 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327J GLN* 3.3 13.1 + - - +
328J HIS* 3.1 37.6 + - + +
330J GLU* 1.3 76.5 - - - +
332J VAL* 1.3 64.9 + - - +
334J GLY* 3.2 2.5 + - - -
335J TYR* 2.9 56.1 + - + +
382J GLU 5.6 1.8 + - - +
383J ILE 5.1 1.8 - - - +
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Residues in contact with VAL 332 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323J VAL* 4.4 6.5 - - + -
328J HIS* 2.9 44.6 + - + +
329J GLN* 3.6 7.2 - - - +
331J LYS* 1.3 76.5 - - - +
333J ILE* 1.3 61.7 + - - +
335J TYR* 3.2 11.0 + - - +
336J ILE* 3.1 31.4 + - + +
364J VAL* 4.1 27.6 - - + -
383J ILE* 4.2 18.1 - - + +
385J GLY* 4.2 17.7 - - - -
386J PRO* 4.4 0.7 - - + -
387J VAL* 4.3 6.5 - - + -
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Residues in contact with ILE 333 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329J GLN* 2.9 33.7 + - + +
330J GLU* 3.6 11.4 - - + +
332J VAL* 1.3 74.1 - - - +
334J GLY* 1.3 58.1 + - - +
336J ILE* 3.4 7.9 + - + +
337J ASN* 3.0 43.8 + - - +
351J ARG* 3.3 47.3 - - + +
363J PHE 5.5 0.2 - - - +
364J VAL* 4.4 18.2 - - + -
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Residues in contact with GLY 334 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330J GLU 2.7 20.4 + - - -
331J LYS* 3.2 2.9 + - - -
333J ILE* 1.3 71.5 - - - +
335J TYR* 1.3 59.4 + - - +
337J ASN* 3.5 11.0 + - - +
338J SER* 2.8 30.2 + - - -
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Residues in contact with TYR 335 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331J LYS* 2.9 53.4 + - + +
332J VAL* 3.2 6.9 + - - +
334J GLY* 1.3 73.4 - - - +
336J ILE* 1.3 55.2 + - - +
338J SER* 2.9 10.9 + - - -
339J ALA* 2.8 33.4 + - - +
377J THR* 4.3 8.3 - - + -
378J SER* 3.8 25.4 - - - -
381J GLU* 2.5 48.0 + - + +
382J GLU 4.2 15.3 + - - -
383J ILE* 4.0 34.3 - - + -
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Residues in contact with ILE 336 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332J VAL* 3.1 23.6 + - + +
333J ILE* 3.7 6.3 - - - +
335J TYR* 1.3 75.9 - - + +
337J ASN* 1.3 61.4 + - - +
339J ALA* 3.2 10.1 + - - +
340J GLU* 3.1 21.8 + - - +
346J ILE* 3.9 21.2 - - + +
349J ASP* 5.4 0.2 - - - +
351J ARG* 3.5 37.5 - - + +
364J VAL* 4.5 6.3 - - + -
367J THR* 3.7 36.6 - - + +
369J ILE* 4.6 7.6 - - + -
383J ILE* 5.6 0.9 - - + +
387J VAL* 3.9 20.9 - - + -
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Residues in contact with ASN 337 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333J ILE* 3.0 30.6 + - - +
334J GLY* 3.6 12.3 - - - +
336J ILE* 1.3 75.6 - - - +
338J SER* 1.3 57.0 + - - +
340J GLU* 3.2 4.9 + - - +
341J GLN* 3.0 32.1 + - - +
351J ARG* 2.8 42.9 + - - +
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Residues in contact with SER 338 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334J GLY 2.8 18.5 + - - -
335J TYR* 2.9 16.4 + - - -
337J ASN* 1.3 71.7 - - - +
339J ALA* 1.3 59.0 - - - +
341J GLN* 4.1 12.3 + - - +
342J GLN* 2.9 48.4 + - - +
377J THR* 4.2 10.7 - - - +
378J SER* 4.6 5.6 - - - -
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Residues in contact with ALA 339 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335J TYR 2.8 11.9 + - - +
336J ILE 3.2 9.9 - - - +
338J SER* 1.3 71.4 - - - +
340J GLU* 1.3 66.9 + - - +
342J GLN* 3.2 13.6 + - - +
343J GLY 3.2 0.7 + - - -
344J ALA* 3.1 33.2 + - + +
346J ILE* 4.4 0.9 - - + -
369J ILE* 4.0 25.4 - - + -
376J MET* 4.7 3.3 - - - +
378J SER* 3.5 21.9 + - - +
389J GLN* 5.2 0.4 - - - +
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Residues in contact with GLU 340 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336J ILE 3.1 9.0 + - - +
337J ASN* 3.6 7.0 - - - +
339J ALA* 1.3 77.9 - - - +
341J GLN* 1.3 62.8 + - - +
343J GLY* 3.3 13.9 + - - -
344J ALA 3.7 14.6 + - - +
346J ILE* 3.9 18.3 - - + +
351J ARG* 2.7 43.2 + - - +
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Residues in contact with GLN 341 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337J ASN 3.0 16.5 + - - +
338J SER* 4.1 13.0 + - - +
340J GLU* 1.3 78.5 - - - +
342J GLN* 1.3 63.8 + - - +
343J GLY 3.4 0.4 + - - -
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Residues in contact with GLN 342 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338J SER* 2.9 32.2 + - - +
339J ALA* 3.2 7.0 + - - +
341J GLN* 1.3 82.7 - - + +
343J GLY* 1.3 56.6 + - - +
344J ALA 3.9 0.2 - - - -
375J GLU 4.7 3.0 + - - -
376J MET* 3.6 31.9 - - + +
377J THR* 3.3 42.1 + - - +
378J SER 4.4 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
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Atomic class I II III IV V VI VII VIII
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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