Contacts of the helix formed by residues 346 - 363 (chain J) in PDB entry 1ZUM
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 346 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196J GLN* 3.4 31.9 - - + +
344J GLN* 3.3 2.1 + - - +
345J VAL* 1.3 92.0 - - + +
347J GLU* 1.3 58.0 + - - +
348J THR* 3.8 13.7 + - - -
349J GLN* 2.8 37.2 + - - +
350J PHE* 3.0 27.2 + - - +
379J TYR* 3.5 17.8 - - + +
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Residues in contact with GLU 347 (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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346J ASP* 1.3 73.2 - - - +
348J THR* 1.3 66.8 + - - +
350J PHE* 3.2 8.5 - - + +
351J LYS* 3.0 52.9 + - + +
379J TYR* 3.6 35.0 + - + +
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Residues in contact with THR 348 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346J ASP* 3.3 13.5 + - - -
347J GLU* 1.3 78.7 - - - +
349J GLN* 1.3 66.1 + - - +
351J LYS* 3.6 9.4 + - - +
352J LYS* 3.0 34.0 + - + +
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Residues in contact with GLN 349 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168J TRP* 4.0 20.4 - - + +
300J GLN* 5.0 2.0 - - - +
344J GLN* 4.7 5.6 - - + -
345J VAL* 3.8 20.4 - - + -
346J ASP* 2.8 27.5 + - - +
348J THR* 1.3 79.1 - - - +
350J PHE* 1.3 59.9 + - - +
352J LYS* 3.5 25.5 + - - +
353J ILE* 2.9 46.9 + - + +
400J ILE 3.9 17.2 - - - +
401J PHE* 4.7 9.5 - - - +
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Residues in contact with PHE 350 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344J GLN* 4.6 4.2 - - - +
346J ASP 3.0 15.1 + - - +
347J GLU* 3.2 16.8 - - + +
349J GLN* 1.3 78.5 - - - +
351J LYS* 1.3 69.5 + - + +
353J ILE 3.5 0.3 + - - -
354J LEU* 3.2 36.7 + - + +
373J ILE* 3.9 34.5 - - + -
375J ALA 5.3 0.4 - - - -
378J GLY 4.3 5.4 - - - -
379J TYR* 3.6 42.0 - + + -
380J PHE 3.5 22.9 - - - -
381J ILE* 3.5 30.0 - - + +
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Residues in contact with LYS 351 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347J GLU* 3.0 48.2 + - + +
348J THR* 4.1 7.4 - - - +
350J PHE* 1.3 81.6 - - + +
352J LYS* 1.3 59.8 + - - +
354J LEU* 3.3 11.9 + - + +
355J GLY* 2.9 26.2 + - - -
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Residues in contact with LYS 352 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348J THR* 3.0 22.7 + - + +
349J GLN* 3.2 31.8 + - - +
351J LYS* 1.3 75.3 - - - +
353J ILE* 1.3 58.3 + - + +
355J GLY* 3.3 2.4 + - - -
356J TYR* 3.0 26.5 + - - +
398J GLU* 3.7 20.3 + - - +
399J GLU 5.1 4.4 + - - -
400J ILE* 4.5 13.2 - - + +
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Residues in contact with ILE 353 (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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344J GLN* 3.7 29.6 - - + +
349J GLN* 2.9 28.9 + - + +
352J LYS* 1.3 75.7 - - + +
354J LEU* 1.3 58.5 + - - +
356J TYR* 3.2 7.3 + - - +
357J ILE* 2.9 31.3 + - + +
381J ILE* 3.7 18.4 - - + -
400J ILE* 3.8 23.6 - - + +
401J PHE 3.8 6.1 - - - +
402J GLY* 3.7 22.9 - - - -
403J PRO* 4.5 2.5 - - + -
404J VAL* 4.0 25.4 - - + -
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Residues in contact with LEU 354 (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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350J PHE* 3.2 31.4 + - + +
351J LYS* 3.3 12.1 + - + +
353J ILE* 1.3 76.3 - - - +
355J GLY* 1.3 63.4 + - - +
357J ILE* 3.3 16.0 + - + +
358J ASN* 3.1 22.0 + - - +
371J GLY 4.9 2.2 - - - +
372J GLY* 4.5 14.4 - - - -
373J ILE* 4.0 33.2 - - + -
381J ILE* 4.1 20.0 - - + -
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Residues in contact with GLY 355 (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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351J LYS 2.9 14.7 + - - -
352J LYS 3.3 4.0 + - - -
353J ILE 3.3 0.2 - - - -
354J LEU* 1.3 75.0 - - - +
356J TYR* 1.3 57.5 + - - +
358J ASN* 3.3 9.1 + - - +
359J THR* 3.0 30.6 + - - -
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Residues in contact with TYR 356 (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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272J LYS* 3.4 3.5 + - - -
352J LYS 3.0 14.4 + - - +
353J ILE* 3.4 9.9 - - - +
354J LEU 3.2 0.2 - - - -
355J GLY* 1.3 74.5 - - - +
357J ILE* 1.3 69.6 + - - +
359J THR* 3.1 9.6 + - - -
360J GLY 3.0 18.0 + - - -
386J PHE* 5.0 0.2 - + - -
394J THR* 4.5 2.7 - - + -
395J ILE* 3.0 45.6 + - + +
398J GLU* 3.6 25.4 - - - +
400J ILE* 3.2 50.2 - - + +
404J VAL* 3.5 28.0 - - + -
406J GLN* 2.9 30.8 + - - -
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Residues in contact with ILE 357 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353J ILE* 2.9 21.1 + - + +
354J LEU* 3.3 13.4 + - + +
356J TYR* 1.3 78.6 - - + +
358J ASN* 1.3 63.5 + - - +
360J GLY 3.1 9.5 + - - -
361J LYS* 3.1 21.8 + - + +
367J LEU* 4.9 0.2 - - + -
371J GLY* 3.6 38.1 - - - +
381J ILE* 4.2 15.9 - - + -
384J THR* 3.7 23.8 - - + +
386J PHE* 3.4 22.3 - - + -
404J VAL* 3.9 24.9 - - + -
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Residues in contact with ASN 358 (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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354J LEU 3.1 12.7 + - - +
355J GLY* 3.5 11.5 - - - +
357J ILE* 1.3 77.1 - - - +
359J THR* 1.3 62.9 + - - +
361J LYS* 3.1 24.0 + - - +
362J GLN* 3.0 55.5 + - - +
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Residues in contact with THR 359 (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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355J GLY 3.0 15.4 + - - -
356J TYR* 3.1 13.0 + - - -
358J ASN* 1.3 76.5 + - - +
360J GLY* 1.3 63.9 + - - +
362J GLN* 3.3 6.8 + - - +
363J GLU* 3.0 47.2 + - + +
394J THR* 3.7 25.1 - - + -
395J ILE* 5.0 2.5 - - + -
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Residues in contact with GLY 360 (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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356J TYR 3.0 10.9 + - - -
357J ILE 3.1 5.1 + - - -
359J THR* 1.3 79.4 - - - +
361J LYS* 1.3 60.0 + - - +
363J GLU* 3.6 7.1 + - - +
364J GLY 3.7 0.2 + - - -
365J ALA* 3.1 30.5 + - - +
386J PHE* 4.0 5.4 - - - -
395J ILE* 3.7 31.6 - - - +
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Residues in contact with LYS 361 (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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357J ILE* 3.1 25.5 + - + +
358J ASN* 3.1 22.8 + - - +
360J GLY* 1.3 74.4 - - - +
362J GLN* 1.3 66.6 + - + +
364J GLY* 3.2 14.2 + - - -
365J ALA 4.3 9.1 + - - +
367J LEU* 4.1 29.7 - - + +
371J GLY 5.1 7.7 + - - +
386J PHE* 4.0 12.5 - - + -
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Residues in contact with GLN 362 (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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358J ASN* 3.0 47.2 + - - +
359J THR* 3.3 7.4 + - - +
361J LYS* 1.3 78.2 - - - +
363J GLU* 1.3 62.9 + - + +
364J GLY 3.3 1.3 + - - -
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Residues in contact with GLU 363 (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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359J THR* 3.0 29.9 + - + +
360J GLY* 3.6 5.4 + - - +
361J LYS 3.2 0.8 - - - -
362J GLN* 1.3 80.5 - - + +
364J GLY* 1.3 59.5 + - - +
365J ALA 3.6 1.1 - - - -
393J MET* 3.4 29.3 - - + +
394J THR* 2.7 48.7 + - - -
395J ILE* 4.4 1.4 + - - +
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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