Contacts of the helix formed by residues 341 - 362 (chain B) in PDB entry 3JZA
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 341 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340B VAL* 1.3 76.3 - - - +
342B ARG* 1.3 59.7 + - - +
343B ILE* 3.3 11.2 + - - +
344B GLU* 2.9 43.0 + - - +
345B ASN* 2.8 34.0 + - - -
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Residues in contact with ARG 342 (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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341B THR* 1.3 74.9 - - - +
343B ILE* 1.3 59.5 + - + +
345B ASN* 3.8 9.2 - - - +
346B LEU* 2.9 47.7 + - + +
383B ASN 5.0 3.8 + - - -
384B LEU* 3.7 25.1 - - + +
385B LYS* 5.4 1.8 - - - +
388B ASP* 2.9 38.7 + - - +
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Residues in contact with ILE 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B THR* 3.2 8.8 + - - +
342B ARG* 1.3 81.8 - - + +
344B GLU* 1.3 63.9 + - + +
346B LEU* 3.4 9.2 + - + +
347B GLU* 3.1 28.7 + - + +
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Residues in contact with GLU 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B VAL* 3.1 24.0 - - + +
341B THR* 2.9 48.0 + - - +
343B ILE* 1.3 74.0 - - + +
345B ASN* 1.3 62.5 + - - +
347B GLU* 3.2 8.9 + - - +
348B ASN* 3.0 27.2 + - - +
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Residues in contact with ASN 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B VAL* 3.1 29.6 + - - +
341B THR 2.8 23.5 + - - +
342B ARG* 3.8 7.5 - - - +
344B GLU* 1.3 76.4 - - - +
346B LEU* 1.3 57.7 + - - +
348B ASN* 3.2 1.7 + - - -
349B ALA* 2.9 26.3 + - - +
378B PHE* 3.4 19.0 - - + -
382B LYS* 3.4 37.3 + - + +
384B LEU* 4.0 18.1 - - + +
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Residues in contact with LEU 346 (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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342B ARG* 2.9 48.0 + - + +
343B ILE* 3.7 7.9 - - + +
344B GLU 3.3 0.4 - - - -
345B ASN* 1.3 76.9 - - - +
347B GLU* 1.3 55.6 + - - +
349B ALA* 3.3 4.6 + - - +
350B LYS* 3.0 26.9 + - - +
384B LEU* 4.0 24.5 - - + -
388B ASP* 3.5 33.2 - - + +
389B LEU* 3.8 22.6 - - + +
392B GLU* 4.5 23.3 - - + +
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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
----------------------------------------------------------
343B ILE* 3.1 21.3 + - + +
344B GLU* 3.2 11.2 + - - +
346B LEU* 1.3 71.7 - - - +
348B ASN* 1.3 64.9 + - - +
350B LYS* 3.4 31.4 + - - +
351B LYS* 3.1 52.6 + - - +
392B GLU* 5.1 5.7 - - - +
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Residues in contact with ASN 348 (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 GLU 3.0 13.2 + - - +
345B ASN* 3.2 7.4 + - - +
347B GLU* 1.3 79.1 - - - +
349B ALA* 1.3 56.3 + - - +
351B LYS* 3.3 15.9 + - - +
352B LEU* 3.0 40.4 + - - +
378B PHE* 3.2 39.9 - - + -
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Residues in contact with ALA 349 (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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345B ASN 2.9 16.4 + - - +
346B LEU* 3.6 9.2 - - + +
348B ASN* 1.3 73.9 - - - +
350B LYS* 1.3 60.6 + - - +
352B LEU* 3.0 8.3 + - - +
353B TRP* 2.8 29.6 + - - +
375B LEU* 3.7 3.8 - - - +
378B PHE* 3.9 13.2 - - + -
379B MET* 3.9 27.4 - - + -
384B LEU* 4.3 4.5 - - + -
389B LEU* 4.0 15.5 - - + -
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Residues in contact with LYS 350 (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 LEU 3.0 13.4 + - - +
347B GLU* 3.4 34.7 + - - +
348B ASN 3.2 0.2 - - - -
349B ALA* 1.3 77.3 - - - +
351B LYS* 1.3 63.9 + - + +
353B TRP* 3.3 3.3 + - - +
354B ASP* 3.0 25.7 + - - +
389B LEU* 3.9 10.3 - - + +
392B GLU* 3.5 31.6 + - + +
393B LEU* 3.9 16.3 - - + +
396B LYS* 3.4 32.7 - - - +
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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
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347B GLU* 3.1 43.9 + - - +
348B ASN* 3.5 17.4 - - - +
350B LYS* 1.3 76.1 - - + +
352B LEU* 1.3 58.7 + - + +
354B ASP* 3.2 11.4 + - - +
355B ASN* 2.9 38.1 + - - +
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Residues in contact with LEU 352 (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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348B ASN* 3.0 30.9 + - - +
349B ALA* 3.0 6.9 + - - +
351B LYS* 1.3 74.3 - - + +
353B TRP* 1.3 64.9 + - - +
355B ASN* 3.1 28.7 + - + +
356B ALA* 3.2 12.5 + - - +
371B ALA 4.5 5.4 - - - +
374B GLU* 4.1 22.7 - - + +
375B LEU* 4.1 17.7 - - + +
378B PHE* 3.4 43.5 - - + -
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Residues in contact with TRP 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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349B ALA 2.8 14.9 + - - +
350B LYS* 3.5 9.2 - - - +
352B LEU* 1.3 72.3 - - - +
354B ASP* 1.3 73.1 + - - +
356B ALA* 3.1 6.4 + - - +
357B ASN* 2.9 56.2 + - + -
375B LEU* 3.7 23.2 - - + +
389B LEU* 4.2 6.7 - - + -
393B LEU* 3.7 22.8 - - + +
396B LYS* 3.7 26.5 - - + -
397B THR 4.6 2.0 - - - -
398B ILE* 3.8 14.6 - - + -
443B PHE* 2.9 51.9 + + - -
446B CYS* 3.7 12.5 - - + +
447B LYS* 3.5 24.9 - - + +
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Residues in contact with ASP 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LYS* 3.0 19.9 + - - +
351B LYS* 3.4 12.8 - - - +
352B LEU 3.2 0.2 - - - -
353B TRP* 1.3 89.1 - - - +
355B ASN* 1.3 60.4 + - - +
357B ASN* 3.3 5.1 + - - +
358B SER* 2.8 29.6 + - - -
396B LYS* 2.7 47.0 + - - +
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Residues in contact with ASN 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 23.0 + - - +
352B LEU* 3.1 25.6 + - + +
354B ASP* 1.3 76.4 - - - +
356B ALA* 1.3 61.4 + - - +
358B SER* 2.3 27.3 + - - +
359B MET* 3.1 13.3 + - + +
371B ALA* 4.2 10.3 - - + -
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Residues in contact with ALA 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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352B LEU 3.2 7.9 + - - +
353B TRP* 3.1 10.0 + - - +
355B ASN* 1.3 77.0 - - - +
357B ASN* 1.3 64.9 + - - +
359B MET* 3.2 5.9 + - - +
360B LEU* 3.0 19.1 + - - +
368B TYR* 3.6 17.5 - - + -
371B ALA* 3.6 22.4 - - + +
372B ALA* 4.1 12.1 - - - +
375B LEU* 5.5 1.1 - - + -
443B PHE* 3.5 21.1 - - + -
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Residues in contact with ASN 357 (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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353B TRP* 2.9 42.1 + - + +
354B ASP* 3.7 6.6 + - - +
356B ALA* 1.3 76.9 - - - +
358B SER* 1.3 55.2 + - - +
360B LEU* 3.3 20.9 - - - +
361B GLU* 3.1 31.3 + - - +
396B LYS* 5.6 0.2 - - - +
397B THR 3.0 25.1 + - - +
398B ILE* 4.0 15.9 - - - +
399B SER 4.9 0.9 + - - -
402B GLY* 5.7 0.3 - - - -
443B PHE* 3.8 9.0 - - + -
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Residues in contact with SER 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 ASP 2.8 16.2 + - - -
355B ASN* 2.3 33.4 + - - -
357B ASN* 1.3 69.8 - - - +
359B MET* 1.3 67.0 + - - +
361B GLU* 3.4 9.2 + - - +
362B LYS* 3.4 36.3 + - - +
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Residues in contact with MET 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 ASN* 3.1 15.3 + - + +
356B ALA 3.2 7.4 + - - +
358B SER* 1.3 81.8 + - - +
360B LEU* 1.3 63.9 - - - +
362B LYS* 3.2 19.2 + - + +
364B ASN* 2.8 64.0 + - - +
367B GLY* 3.6 21.3 - - - +
368B TYR* 3.4 19.7 - - - +
371B ALA* 4.6 2.9 - - + -
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Residues in contact with LEU 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 ALA 3.0 9.2 + - - +
357B ASN* 3.3 20.9 - - - +
359B MET* 1.3 76.6 - - - +
361B GLU* 1.3 55.7 + - - +
363B GLY 3.0 6.8 + - - -
364B ASN 5.1 0.4 - - - +
368B TYR* 3.7 27.8 - - + +
398B ILE* 4.3 1.3 - - + -
402B GLY* 3.9 19.7 - - - +
405B ILE* 2.8 59.5 - - + +
406B LEU* 3.7 26.9 - - + -
443B PHE* 3.6 32.5 - - + -
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Residues in contact with GLU 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 ASN* 3.1 17.3 + - - +
358B SER* 3.6 12.1 - - - +
359B MET 3.3 0.4 - - - -
360B LEU* 1.3 76.5 - - - +
362B LYS* 1.3 56.0 + - + +
363B GLY 3.2 1.8 - - - -
399B SER* 2.5 39.2 + - - -
401B LYS* 2.9 36.0 + - - +
402B GLY* 4.3 2.8 + - - -
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Residues in contact with LYS 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 SER* 3.4 26.0 + - - +
359B MET* 3.5 26.0 - - + +
360B LEU 3.1 1.0 - - - -
361B GLU* 1.3 78.0 - - + +
363B GLY* 1.3 61.0 + - - +
364B ASN* 3.3 10.3 + - + +
401B LYS* 4.1 6.5 + - - +
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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
------------------------------------------------------------
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