Contacts of the helix formed by residues 346 - 363 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196B GLN* 3.2 31.5 - - + +
344B GLN* 3.3 2.1 + - - +
345B VAL* 1.3 91.6 - - + +
347B GLU* 1.3 60.6 + - - +
348B THR* 3.2 13.6 + - - -
349B GLN* 2.8 39.9 + - - +
350B PHE* 3.0 26.3 + - - +
379B TYR* 3.5 17.7 - - + +
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Residues in contact with GLU 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B ASP* 1.3 72.5 - - - +
348B THR* 1.3 65.9 + - - +
350B PHE* 3.2 6.5 + - + +
351B LYS* 3.0 46.6 + - + +
379B TYR* 3.5 34.7 + - + +
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Residues in contact with THR 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ASP* 3.2 13.8 + - - -
347B GLU* 1.3 77.8 - - - +
349B GLN* 1.3 65.9 + - - +
351B LYS* 3.5 4.9 + - - +
352B LYS* 3.0 36.6 + - + +
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Residues in contact with GLN 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B TRP* 4.1 17.8 - - + -
300B GLN* 4.9 1.6 - - - +
344B GLN* 4.6 7.9 - - + -
345B VAL* 3.7 22.4 - - + -
346B ASP* 2.8 26.4 + - - +
348B THR* 1.3 75.9 - - - +
350B PHE* 1.3 66.8 + - - +
352B LYS* 3.5 27.8 - - - +
353B ILE* 2.9 36.2 + - + +
400B ILE 3.7 18.7 - - - +
401B PHE* 4.4 14.8 - - - +
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Residues in contact with PHE 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B GLN* 4.6 4.0 - - - +
346B ASP 3.0 13.8 + - - +
347B GLU* 3.3 15.5 - - + +
349B GLN* 1.3 77.1 - - - +
351B LYS* 1.3 79.5 + - + +
353B ILE* 3.4 2.4 + - - +
354B LEU* 3.1 38.7 + - + +
373B ILE* 3.6 37.2 - - + -
375B ALA 5.3 0.2 - - - -
378B GLY 4.5 5.2 - - - -
379B TYR* 3.6 45.8 - + + -
380B PHE 3.5 21.8 - - - -
381B ILE* 3.6 23.2 - - + +
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Residues in contact with LYS 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B GLU* 3.0 36.4 + - + +
348B THR* 3.8 5.2 - - - +
350B PHE* 1.3 94.0 - - + +
352B LYS* 1.3 62.3 + - - +
354B LEU* 3.2 15.2 + - + +
355B GLY* 2.9 26.9 + - - -
373B ILE* 5.5 3.6 - - - +
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Residues in contact with LYS 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B THR* 3.0 24.0 + - + +
349B GLN* 3.5 32.1 - - - +
351B LYS* 1.3 76.5 - - - +
353B ILE* 1.3 62.9 + - + +
355B GLY* 3.3 2.2 + - - -
356B TYR* 3.0 22.9 + - - +
398B GLU* 3.7 20.7 + - - +
399B GLU 5.2 4.2 + - - -
400B ILE* 4.3 13.5 - - + +
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Residues in contact with ILE 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B GLN* 3.4 40.4 - - + +
349B GLN* 2.9 27.0 + - + +
352B LYS* 1.3 73.2 - - + +
354B LEU* 1.3 61.5 + - - +
356B TYR* 3.2 8.0 + - - +
357B ILE* 2.9 32.0 + - + +
381B ILE* 3.4 22.0 - - + -
400B ILE* 3.8 22.0 - - + +
401B PHE 3.7 4.9 - - - +
402B GLY* 3.5 15.3 - - - -
403B PRO* 4.5 1.8 - - + -
404B VAL* 3.9 26.0 - - + -
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Residues in contact with LEU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B PHE* 3.1 36.7 + - + +
351B LYS* 3.6 19.1 - - + +
353B ILE* 1.3 77.0 - - - +
355B GLY* 1.3 62.3 + - - +
357B ILE* 3.2 15.4 + - + +
358B ASN* 3.1 22.0 + - - +
371B GLY 4.9 1.8 - - - +
372B GLY* 4.5 15.5 - - - -
373B ILE* 3.9 34.5 - - + -
381B ILE* 4.5 16.2 - - + -
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Residues in contact with GLY 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B LYS 2.9 13.7 + - - -
352B LYS* 3.3 3.5 + - - -
353B ILE 3.2 0.2 - - - -
354B LEU* 1.3 76.4 - - - +
356B TYR* 1.3 56.6 + - - +
358B ASN* 3.2 9.0 + - - +
359B THR* 3.0 31.1 + - - -
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Residues in contact with TYR 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LYS* 3.2 8.0 + - - -
352B LYS 3.0 7.3 + - - +
353B ILE 3.2 8.5 + - - +
355B GLY* 1.3 75.7 - - - +
357B ILE* 1.3 68.7 + - - +
359B THR* 3.2 9.0 + - - -
360B GLY 2.9 17.8 + - - -
394B THR* 4.4 3.8 - - + -
395B ILE* 2.9 47.2 + - + +
398B GLU* 3.4 32.8 - - - +
400B ILE* 3.2 55.0 - - + +
404B VAL* 3.7 16.8 - - + -
406B GLN* 2.9 29.7 + - - -
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Residues in contact with ILE 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B ILE* 2.9 20.0 + - + +
354B LEU* 3.2 15.2 + - + +
356B TYR* 1.3 77.9 - - - +
358B ASN* 1.3 62.9 + - - +
360B GLY 3.1 1.9 + - - -
361B LYS* 3.1 33.2 + - + +
367B LEU* 5.2 0.2 - - + -
371B GLY* 3.5 37.0 - - - +
381B ILE* 4.2 16.6 - - + -
384B THR* 3.9 20.2 - - + +
386B PHE* 3.4 19.1 - - + -
404B VAL* 3.8 30.5 - - + -
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Residues in contact with ASN 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B LEU 3.1 12.8 + - - +
355B GLY* 3.4 12.3 - - - +
356B TYR 3.2 0.2 - - - -
357B ILE* 1.3 78.4 - - - +
359B THR* 1.3 58.5 + - - +
361B LYS* 3.2 20.4 + - - +
362B GLN* 2.9 64.4 + - - +
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Residues in contact with THR 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B GLY 3.0 15.6 + - - -
356B TYR* 3.2 11.0 + - - -
358B ASN* 1.3 76.6 + - - +
360B GLY* 1.3 58.6 + - - +
362B GLN* 3.8 7.3 - - + +
363B GLU* 2.9 56.5 + - + +
394B THR* 3.8 21.9 - - + +
395B ILE* 5.1 0.9 - - + -
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Residues in contact with GLY 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356B TYR 2.9 10.5 + - - -
357B ILE 3.1 5.3 + - - -
359B THR* 1.3 79.7 - - - +
361B LYS* 1.3 57.4 + - - +
363B GLU* 3.6 3.7 + - - +
364B GLY 3.6 2.8 + - - -
365B ALA* 3.1 29.3 + - - +
386B PHE* 3.8 14.1 - - - -
393B MET* 6.4 0.2 - - - -
395B ILE* 3.7 27.8 - - - +
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Residues in contact with LYS 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B ILE* 3.1 27.6 + - + +
358B ASN* 3.2 18.9 + - - +
360B GLY* 1.3 75.0 - - - +
362B GLN* 1.3 67.0 + - + +
364B GLY* 3.2 13.9 + - - -
365B ALA 4.4 5.8 - - - +
367B LEU* 4.5 25.0 - - + +
371B GLY 5.1 6.8 + - - +
386B PHE* 4.1 15.7 - - + -
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Residues in contact with GLN 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B ASN* 2.9 51.6 + - - +
359B THR* 3.8 8.1 - - + +
361B LYS* 1.3 78.1 - - - +
363B GLU* 1.3 64.4 + - + +
364B GLY 3.2 1.4 + - - -
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Residues in contact with GLU 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B THR* 2.9 31.7 + - + +
360B GLY* 4.3 3.8 - - - +
361B LYS 3.3 0.4 - - - -
362B GLN* 1.3 78.3 - - + +
364B GLY* 1.3 58.8 + - - +
365B ALA 3.6 1.1 - - - -
393B MET* 3.3 31.3 - - + +
394B THR* 2.7 48.6 + - - -
395B ILE* 4.5 1.0 + - - +
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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