Contacts of the helix formed by residues 346 - 363 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A VAL* 6.5 1.1 - - + -
196A GLN* 3.2 34.5 + - + +
344A GLN* 3.3 1.7 + - - +
345A VAL* 1.3 86.2 - - - +
347A GLU* 1.3 59.8 - - - +
348A THR* 3.9 12.9 + - - +
349A GLN* 2.9 30.4 + - - +
350A PHE* 3.0 26.2 + - - +
379A TYR* 3.5 18.5 - - + +
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Residues in contact with GLU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A ASP* 1.3 72.3 - - - +
348A THR* 1.3 66.6 + - - +
350A PHE* 3.1 7.8 - - + +
351A LYS* 3.0 56.2 + - + +
379A TYR* 3.6 36.4 + - + +
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Residues in contact with THR 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346A ASP* 3.4 13.4 + - - +
347A GLU* 1.3 78.9 - - - +
349A GLN* 1.3 61.3 + - - +
351A LYS* 3.6 9.2 + - - +
352A LYS* 3.0 37.8 + - + +
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Residues in contact with GLN 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A TRP* 4.1 18.1 - - + -
196A GLN* 6.2 0.2 - - - +
300A GLN* 4.9 2.0 - - - +
344A GLN* 4.7 7.9 - - + -
345A VAL* 4.0 18.8 - - + -
346A ASP* 2.9 23.7 + - - +
348A THR* 1.3 78.1 - - - +
350A PHE* 1.3 57.2 + - - +
352A LYS* 3.5 29.2 - - - +
353A ILE* 2.8 45.2 + - + +
400A ILE 3.3 23.2 - - - +
401A PHE* 4.1 13.6 - - - +
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Residues in contact with PHE 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A GLN* 4.6 3.5 - - - +
346A ASP 3.0 14.9 + - - +
347A GLU* 3.1 16.8 - - + +
349A GLN* 1.3 77.5 - - - +
351A LYS* 1.3 71.0 + - + +
353A ILE 3.5 0.3 + - - -
354A LEU* 3.2 35.3 + - + +
373A ILE* 3.8 35.4 - - + -
378A GLY 4.3 5.4 - - - -
379A TYR* 3.6 45.8 - + + -
380A PHE 3.5 21.8 - - - -
381A ILE* 3.7 23.5 - - + +
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Residues in contact with LYS 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A GLU* 3.0 48.4 + - + +
348A THR* 4.2 7.6 - - - +
350A PHE* 1.3 85.9 - - + +
352A LYS* 1.3 61.0 + - - +
354A LEU* 3.3 12.8 + - + +
355A GLY* 3.0 26.3 + - - -
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Residues in contact with LYS 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A GLU* 5.9 7.8 - - - +
348A THR* 3.0 25.6 + - + +
349A GLN* 3.2 31.7 + - - +
351A LYS* 1.3 76.3 - - - +
353A ILE* 1.3 63.2 + - + +
355A GLY* 3.5 1.8 + - - -
356A TYR* 3.1 21.8 + - - +
398A GLU* 4.0 19.6 + - - +
399A GLU 4.9 5.1 + - - -
400A ILE* 4.5 13.8 + - + +
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Residues in contact with ILE 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344A GLN* 3.4 43.7 - - + +
349A GLN* 2.8 31.3 + - + +
352A LYS* 1.3 74.3 - - - +
354A LEU* 1.3 59.1 + - - +
356A TYR* 3.1 8.0 + - - +
357A ILE* 2.9 38.4 + - + +
381A ILE* 3.5 22.2 - - + -
400A ILE* 4.1 21.8 - - + +
401A PHE 4.0 3.8 - - - +
402A GLY* 3.7 13.0 - - - -
403A PRO* 4.2 1.1 - - + -
404A VAL* 4.0 24.9 - - + -
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Residues in contact with LEU 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A PHE* 3.2 32.6 + - + +
351A LYS* 3.3 15.2 + - + +
353A ILE* 1.3 77.3 - - - +
355A GLY* 1.3 61.4 + - - +
357A ILE* 3.1 20.8 + - + +
358A ASN* 3.0 31.4 + - - +
371A GLY 4.9 1.8 - - - +
372A GLY* 4.5 14.4 - - - -
373A ILE* 4.1 33.4 - - + -
381A ILE* 4.5 11.0 - - + -
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Residues in contact with GLY 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351A LYS 3.0 15.6 + - - -
352A LYS* 3.9 2.2 - - - -
353A ILE 3.3 0.2 - - - -
354A LEU* 1.3 75.8 - - - +
356A TYR* 1.3 56.3 + - - +
358A ASN* 3.3 14.1 + - - +
359A THR* 3.0 31.6 + - - -
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Residues in contact with TYR 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A LYS* 3.1 10.0 + - - -
352A LYS 3.1 15.1 + - - +
353A ILE* 3.1 10.9 + - - +
355A GLY* 1.3 75.1 - - - +
357A ILE* 1.3 66.8 + - - +
359A THR* 3.2 8.0 + - - -
360A GLY 3.0 17.3 + - - -
386A PHE* 5.3 0.2 - + - -
394A THR* 4.4 7.4 - - + -
395A ILE* 2.8 52.8 + - + +
398A GLU* 3.5 26.5 - - + +
400A ILE* 3.2 47.4 - - + +
404A VAL* 3.6 19.3 - - + -
406A GLN* 2.9 23.1 + - - -
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Residues in contact with ILE 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353A ILE* 2.9 32.2 + - + +
354A LEU* 3.1 15.2 + - + +
356A TYR* 1.3 75.3 - - - +
358A ASN* 1.3 64.7 + - - +
360A GLY 3.1 8.8 + - - -
361A LYS* 3.1 24.1 + - + +
367A LEU* 4.8 0.4 - - + -
371A GLY* 3.7 37.7 - - - +
381A ILE* 4.2 11.4 - - + -
384A THR* 3.9 18.4 - - + +
386A PHE* 3.4 25.1 - - + -
404A VAL* 3.9 19.5 - - + -
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Residues in contact with ASN 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354A LEU* 3.0 18.8 + - - +
355A GLY* 3.4 14.7 - - - +
357A ILE* 1.3 79.5 - - - +
359A THR* 1.3 56.2 + - - +
361A LYS* 3.1 26.8 + - - +
362A GLN* 2.9 38.3 + - + +
371A GLY 5.6 2.2 + - - -
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Residues in contact with THR 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A GLY 3.0 15.9 + - - -
356A TYR* 3.2 11.9 + - - -
358A ASN* 1.3 76.3 - - - +
360A GLY* 1.3 63.4 + - - +
362A GLN* 3.3 8.9 + - + +
363A GLU* 3.0 53.6 + - + +
394A THR* 3.9 21.8 - - + +
395A ILE* 5.0 0.9 - - + -
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Residues in contact with GLY 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356A TYR 3.0 10.5 + - - -
357A ILE 3.1 5.3 + - - -
359A THR* 1.3 78.7 - - - +
361A LYS* 1.3 60.5 + - - +
363A GLU* 3.5 7.1 + - - +
365A ALA* 3.1 25.8 + - - +
386A PHE* 4.0 10.5 - - - -
395A ILE* 3.6 31.6 - - - +
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Residues in contact with LYS 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357A ILE* 3.3 25.8 - - + +
358A ASN* 3.1 26.3 + - - +
360A GLY* 1.3 76.1 - - - +
362A GLN* 1.3 62.7 + - + +
364A GLY* 3.2 13.7 + - - -
365A ALA 4.4 8.9 + - - +
367A LEU* 4.5 22.4 - - + +
371A GLY 5.1 6.1 + - - -
386A PHE* 4.1 12.6 - - + -
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Residues in contact with GLN 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358A ASN* 2.9 28.3 + - + +
359A THR* 3.3 9.8 + - + +
361A LYS* 1.3 77.1 - - + +
363A GLU* 1.3 61.8 + - + +
364A GLY 3.5 1.0 + - - -
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Residues in contact with GLU 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359A THR* 3.0 31.9 + - + +
360A GLY* 4.0 5.4 - - - +
361A LYS 3.2 0.6 - - - -
362A GLN* 1.3 79.3 - - + +
364A GLY* 1.3 58.9 + - - +
365A ALA 3.6 0.2 - - - -
392A GLY 5.1 0.5 - - - +
393A MET* 3.7 27.8 - - + +
394A THR* 2.8 53.6 + - - -
395A ILE* 3.7 8.0 + - - +
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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