Contacts of the helix formed by residues 342 - 355 (chain B) in PDB entry 1ZJA
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 TRP 342 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337B ASP* 3.3 28.5 - - + +
339B ARG* 3.0 35.1 + - + +
341B GLN* 1.3 114.8 - - + +
343B ARG* 1.3 61.0 + - - +
344B GLU 3.4 2.7 - - - -
345B ALA* 3.4 12.7 + - + +
346B SER* 2.8 32.2 + - - -
511B ALA* 3.8 23.8 - - + +
548B PRO* 3.5 39.3 - - + -
549B TRP* 3.9 15.9 - + + -
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Residues in contact with ARG 343 (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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332B VAL* 3.6 6.5 - - + +
337B ASP 3.2 10.5 + - - -
338B ASP* 3.8 13.5 - - - +
339B ARG 2.9 15.4 + - - +
340B PRO* 4.0 9.9 + - + +
341B GLN 3.8 0.4 - - - -
342B TRP* 1.3 76.2 - - - +
344B GLU* 1.3 92.7 + - - +
346B SER* 3.4 1.4 + - - -
347B ALA* 2.8 32.4 + - - +
369B LEU 3.5 16.2 + - - -
370B GLY* 3.1 24.2 + - - +
372B THR* 3.4 31.2 - - + -
446B GLU* 4.5 9.5 + - - +
447B ILE* 3.2 29.9 - - - +
452B GLU* 5.5 3.0 + - - -
459B VAL* 5.0 1.4 - - - +
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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 PRO 4.9 8.5 + - - +
341B GLN 5.6 0.2 - - - -
342B TRP 3.4 0.4 - - - -
343B ARG* 1.3 100.8 + - - +
345B ALA* 1.3 66.5 + - - +
347B ALA* 3.4 1.4 + - - +
348B LYS* 3.0 39.1 + - - +
451B ARG* 4.3 17.2 + - - -
452B GLU* 4.7 4.0 - - - +
455B ASP* 5.6 0.2 - - - +
457B LYS 5.4 1.7 - - - +
458B SER* 5.3 4.3 - - - -
459B VAL* 3.9 22.1 - - + +
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Residues in contact with ALA 345 (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 GLN 5.3 2.0 + - - +
342B TRP* 3.4 20.9 + - + +
344B GLU* 1.3 78.0 - - - +
346B SER* 1.3 59.9 + - - +
348B LYS* 3.3 9.3 + - - +
349B ALA* 3.0 25.1 + - - +
531B SER* 4.7 0.3 + - - -
532B SER* 3.5 25.3 + - - +
548B PRO 5.0 1.1 - - - +
549B TRP* 3.9 21.1 - - + +
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Residues in contact with SER 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B VAL* 3.2 9.1 - - - +
336B GLY* 3.9 3.4 - - - -
337B ASP 2.9 42.6 + - - -
342B TRP 2.8 18.2 + - - -
345B ALA* 1.3 69.0 - - - +
347B ALA* 1.3 67.4 + - - +
349B ALA* 3.1 2.4 + - - +
350B LEU* 2.9 27.3 + - - +
549B TRP* 3.5 33.1 - - - -
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Residues in contact with ALA 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B VAL* 3.9 20.4 - - + -
343B ARG 2.8 20.5 + - - +
344B GLU 3.8 3.1 - - - +
346B SER* 1.3 76.0 + - - +
348B LYS* 1.3 63.1 + - - +
350B LEU* 3.3 6.4 + - - +
351B ALA* 3.0 23.2 + - - +
367B ASP 5.2 2.7 - - - +
370B GLY* 4.3 11.4 - - - -
459B VAL* 4.2 23.6 - - + -
463B TYR* 4.4 5.3 + - + -
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Residues in contact with LYS 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B GLU* 3.0 30.7 + - - +
345B ALA* 3.6 7.6 - - - +
346B SER 3.2 0.2 - - - -
347B ALA* 1.3 77.2 - - - +
349B ALA* 1.3 62.6 + - - +
351B ALA* 3.1 11.2 + - - +
352B THR* 3.1 17.0 + - - -
457B LYS* 2.6 34.1 + - - +
458B SER* 3.7 16.2 - - - +
459B VAL* 4.1 12.6 - - + +
462B PHE* 3.4 36.1 - - + -
531B SER* 3.8 23.5 - - - +
532B SER* 5.3 5.1 - - - +
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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
----------------------------------------------------------
345B ALA 3.0 7.5 + - - +
346B SER 3.1 8.9 + - - +
348B LYS* 1.3 76.8 - - - +
350B LEU* 1.3 63.0 + - + +
352B THR* 3.3 5.7 + - - -
353B VAL* 3.2 24.0 + - - +
507B VAL* 3.7 19.4 - - + +
531B SER* 4.3 0.6 + - - -
549B TRP* 3.6 42.6 - - + +
551B SER* 3.9 12.1 - - - -
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Residues in contact with LEU 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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302B PHE* 5.3 2.0 - - + -
323B LEU* 3.6 19.0 - - + +
331B ALA* 3.4 39.0 - - + +
332B VAL* 3.8 8.7 - - + +
335B PHE* 3.8 20.9 - - + +
336B GLY* 3.6 17.9 - - - +
346B SER 2.9 18.5 + - - +
347B ALA* 3.8 5.6 - - - +
349B ALA* 1.3 73.9 - - - +
351B ALA* 1.3 60.7 + - - +
353B VAL* 3.4 4.2 + - + -
354B THR* 2.8 33.2 + - - -
463B TYR* 4.8 4.0 - - - +
509B PHE* 4.1 27.4 - - + -
549B TRP* 4.9 2.9 - - + -
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Residues in contact with ALA 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 ALA 3.0 8.9 + - - +
348B LYS* 3.1 11.6 + - - +
350B LEU* 1.3 76.0 - - - +
352B THR* 1.3 65.6 + - - +
354B THR* 3.3 2.8 + - - -
355B LEU* 3.0 23.0 + - - +
462B PHE* 4.4 1.6 - - + -
463B TYR* 3.4 47.5 + - + -
466B LEU* 3.5 21.3 - - + +
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Residues in contact with THR 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 LYS 3.1 3.7 + - - -
349B ALA 3.6 7.0 - - - -
351B ALA* 1.3 76.1 - - - +
353B VAL* 1.3 55.2 + - - +
355B LEU 3.6 0.3 + - - -
356B THR* 2.7 35.3 + - - +
462B PHE* 3.2 19.8 - - - -
466B LEU* 3.5 9.9 - - - +
505B VAL* 4.1 16.4 - - + -
507B VAL* 4.4 1.8 - - + -
529B ILE* 5.8 0.4 - - + +
551B SER* 2.8 33.4 + - - +
552B GLY* 4.3 4.7 - - - +
553B ILE* 3.8 29.6 - - + -
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Residues in contact with VAL 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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302B PHE* 4.5 12.1 - - + -
321B PHE* 4.2 17.0 - - + -
323B LEU* 4.7 3.6 - - + -
349B ALA 3.2 14.0 + - - +
350B LEU* 3.7 10.1 - - - +
351B ALA 3.2 0.2 - - - -
352B THR* 1.3 76.1 - - - +
354B THR* 1.3 64.0 + - - +
356B THR* 3.1 12.3 + - - -
357B GLN* 3.1 36.5 + - - +
492B TYR* 4.1 22.7 - - + -
494B TYR* 3.5 6.9 + - - +
507B VAL* 4.0 19.7 - - + -
509B PHE* 4.2 14.8 - - + -
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Residues in contact with THR 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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321B PHE* 3.7 24.0 - - + +
322B PHE* 5.1 2.9 - - - -
323B LEU* 3.2 21.2 - - - +
350B LEU 2.8 23.1 + - - -
351B ALA* 3.7 7.3 - - - -
353B VAL* 1.3 78.0 - - - +
355B LEU* 1.3 67.1 + - + +
356B THR 3.5 0.5 + - - -
357B GLN* 3.9 7.1 + - - +
361B PRO* 3.4 29.2 - - + +
362B PHE 4.8 12.3 - - - +
363B ILE* 4.9 9.6 - - + -
463B TYR* 4.8 7.6 + - + +
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Residues in contact with LEU 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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11B VAL* 4.2 18.4 - - + -
351B ALA 3.0 16.9 + - - +
352B THR 4.5 1.1 - - - +
353B VAL 3.2 0.2 - - - -
354B THR* 1.3 81.0 - - + +
356B THR* 1.3 67.3 + - + +
357B GLN 3.6 0.4 - - - -
361B PRO* 3.9 24.0 - - + -
363B ILE* 4.5 6.1 - - + -
463B TYR* 4.1 18.2 - - + +
466B LEU* 3.5 38.1 - - + +
467B ILE* 3.8 19.7 - - + +
470B ARG* 3.1 43.1 + - - +
476B LEU* 4.1 0.5 - - - +
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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
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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