Contacts of the helix formed by residues 372 - 392 (chain B) in PDB entry 2JGZ
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 372 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B TRP* 4.1 2.7 - - - +
366B GLN* 4.3 15.3 - - - +
371B TYR* 1.3 74.2 - - - +
373B GLU* 1.3 68.2 + - + +
374B GLU* 3.6 29.2 - - + +
375B SER* 2.7 31.2 + - - -
376B LEU* 2.9 16.8 + - - +
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Residues in contact with GLU 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B CYS* 4.4 12.6 - - - -
354B LYS* 3.9 24.6 + - - +
360B GLU* 2.9 26.9 - - - +
361B TRP* 3.6 36.0 + - + +
366B GLN* 5.0 0.2 - - - +
372B THR* 1.3 75.9 - - + +
374B GLU* 1.3 70.5 + - + +
376B LEU* 3.0 19.7 + - - +
377B LEU* 3.1 16.7 + - - +
380B MET* 4.9 3.3 - - - +
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Residues in contact with GLU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B THR* 3.0 20.1 - - + -
373B GLU* 1.3 80.9 - - + +
375B SER* 1.3 61.5 + - - +
377B LEU* 3.5 19.0 - - - +
378B PRO* 4.2 3.5 - - - +
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Residues in contact with SER 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B GLN* 3.1 24.5 + - - -
371B TYR* 3.9 16.7 - - - -
372B THR* 2.7 36.3 + - - -
374B GLU* 1.3 75.5 - - - +
376B LEU* 1.3 57.8 + - - +
377B LEU 3.1 6.6 + - - -
378B PRO* 3.4 10.8 - - - +
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Residues in contact with LEU 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B GLN* 4.0 19.3 - - + +
346B ALA* 3.7 22.9 - - + -
347B GLY* 4.0 9.0 - - - +
350B CYS* 3.8 20.6 - - + -
361B TRP* 3.6 39.3 - - + -
371B TYR* 3.9 17.7 - - + -
372B THR 2.9 18.2 + - - +
373B GLU* 3.0 6.7 + - - +
375B SER* 1.3 75.1 - - - +
377B LEU* 1.3 64.2 + - - +
378B PRO 3.6 0.4 - - - -
379B VAL* 3.3 7.5 + - - +
380B MET* 2.9 35.1 + - - +
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Residues in contact with LEU 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354B LYS* 6.2 2.2 - - - +
373B GLU* 3.1 10.0 + - - +
374B GLU* 3.5 15.3 - - - +
375B SER 3.1 2.4 - - - -
376B LEU* 1.3 76.0 - - - +
378B PRO* 1.4 73.2 - - + +
380B MET* 2.8 25.3 + - + +
381B GLN* 2.9 38.9 + - - +
424B GLN* 5.1 8.1 - - - +
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Residues in contact with PRO 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B PHE* 4.1 22.7 - - + -
343B GLN* 4.5 2.7 - - - +
374B GLU 4.2 3.4 - - - +
375B SER* 3.4 15.5 - - - +
377B LEU* 1.4 93.6 - - + +
379B VAL* 1.3 61.3 + - - +
381B GLN* 3.5 14.1 + - - +
382B HIS* 3.1 34.0 + - + +
426B LEU* 6.0 0.4 - - + -
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Residues in contact with VAL 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B MET* 4.1 14.3 - - + +
339B PHE* 3.8 23.1 - - + -
343B GLN* 3.4 57.4 - - + +
344B ILE* 4.1 13.9 - - + -
347B GLY* 4.2 10.1 - - - -
376B LEU* 3.5 9.0 - - - +
377B LEU 3.0 0.6 - - - -
378B PRO* 1.3 77.7 - - - +
380B MET* 1.3 58.0 + - - +
382B HIS* 3.2 3.9 + - - +
383B LEU* 2.9 33.9 + - + +
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Residues in contact with MET 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B GLY 3.6 18.8 - - - +
350B CYS* 3.5 34.5 - - - -
351B LEU* 3.7 24.4 - - + +
354B LYS* 3.5 39.7 - - + +
373B GLU* 4.9 5.2 - - - +
376B LEU* 2.9 24.3 + - - +
377B LEU* 2.8 22.8 + - + +
379B VAL* 1.3 72.0 - - - +
381B GLN* 1.3 56.4 + - - +
383B LEU* 3.4 6.4 + - - +
384B ALA* 3.0 29.6 + - - +
424B GLN* 4.2 12.8 + - - +
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Residues in contact with GLN 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B LEU* 2.9 48.2 + - + +
378B PRO* 3.9 11.8 - - - +
380B MET* 1.3 75.5 - - - +
382B HIS* 1.3 59.2 + - - +
384B ALA* 3.7 1.6 - - - +
385B LYS* 3.0 27.7 + - - +
424B GLN* 3.7 35.7 + - + +
425B ASP 4.6 8.7 + - - +
426B LEU* 3.3 36.8 - - + +
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Residues in contact with HIS 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ASP* 4.1 1.1 - - - -
335B ASP* 3.6 33.4 + - + +
336B MET* 3.6 20.9 - - + -
339B PHE* 4.5 10.0 - + + -
378B PRO* 3.1 27.6 + - + +
379B VAL* 3.8 3.6 - - - +
381B GLN* 1.3 76.4 - - - +
383B LEU* 1.3 64.9 + - - +
385B LYS* 3.3 32.0 + - - +
386B ASN* 2.8 29.6 + - - +
426B LEU* 3.6 32.7 - - + +
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326B LEU* 3.2 39.9 - - + +
327B MET 4.5 0.7 - - - +
329B LEU* 5.3 2.4 - - + +
330B THR* 3.3 21.5 - - + -
336B MET* 4.3 3.5 - - + +
344B ILE 4.8 0.9 - - - +
347B GLY 3.7 8.1 - - - +
348B ALA* 3.5 36.6 - - + +
351B LEU* 3.5 20.4 - - + -
379B VAL* 2.9 23.4 + - + +
380B MET* 3.6 5.8 - - - +
381B GLN 3.4 0.2 - - - -
382B HIS* 1.3 73.9 - - - +
384B ALA* 1.3 55.5 + - - +
386B ASN* 2.6 30.7 + - - +
387B VAL* 2.9 15.9 + - - +
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Residues in contact with ALA 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B LEU* 4.0 5.3 - - + +
380B MET 3.0 14.8 + - - +
381B GLN 3.7 4.0 - - - +
383B LEU* 1.3 77.3 - - - +
385B LYS* 1.3 65.5 + - - +
387B VAL* 3.0 5.5 + - - +
388B VAL* 2.9 27.9 + - + +
422B LEU* 3.7 26.2 - - + -
424B GLN* 3.9 30.7 - - + +
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Residues in contact with LYS 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ASP* 2.5 37.4 + - - -
335B ASP* 3.7 15.7 + - - -
381B GLN 3.0 20.4 + - - +
382B HIS* 3.3 28.0 - - + +
383B LEU 3.2 0.2 - - - -
384B ALA* 1.3 75.2 - - - +
386B ASN* 1.3 62.3 + - - +
388B VAL* 3.6 7.6 + - - +
389B MET* 3.1 52.4 + - + +
424B GLN 4.7 9.1 + - - +
426B LEU* 4.1 22.4 - - + +
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Residues in contact with ASN 386 (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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329B LEU* 4.3 33.2 + - + +
330B THR* 5.0 0.6 - - - +
332B LEU* 5.6 2.8 - - - +
333B ASP* 2.7 40.5 + - - +
336B MET* 3.7 8.3 - - - +
382B HIS 2.8 17.4 + - - +
383B LEU* 2.6 19.9 + - + +
385B LYS* 1.3 72.1 - - - +
387B VAL* 1.3 62.7 + - - +
389B MET* 3.5 19.4 + - - +
390B VAL* 3.1 28.7 + - - +
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Residues in contact with VAL 387 (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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325B TYR* 5.3 4.5 - - + +
326B LEU* 3.7 29.2 - - + -
329B LEU* 4.4 12.8 - - + -
351B LEU* 5.5 0.7 - - + -
355B ILE* 5.8 1.8 - - + -
383B LEU 2.9 16.4 + - - +
384B ALA* 3.4 6.5 - - - +
386B ASN* 1.3 72.9 - - - +
388B VAL* 1.3 68.7 + - - +
390B VAL* 3.1 4.7 + - - +
391B ASN* 2.8 31.3 + - + +
417B GLN* 3.8 33.9 - - + +
418B LEU* 5.0 1.1 - - + -
422B LEU* 3.7 22.4 - - + -
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Residues in contact with VAL 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B ALA 2.9 19.6 + - - +
385B LYS* 3.7 9.6 - - - +
387B VAL* 1.3 77.1 - - + +
389B MET* 1.3 67.4 + - + +
391B ASN* 3.5 3.9 - - - +
392B GLN* 2.8 48.4 + - - +
394B LEU* 4.4 11.9 - - + -
418B LEU* 5.2 6.7 - - + -
422B LEU* 4.4 26.5 - - + +
424B GLN 6.1 1.3 - - - +
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Residues in contact with MET 389 (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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385B LYS* 3.1 47.4 + - + +
386B ASN* 3.6 18.8 - - - +
387B VAL 3.3 0.2 - - - -
388B VAL* 1.3 80.5 - - + +
390B VAL* 1.3 63.4 + - + +
392B GLN 3.5 0.2 + - - -
393B GLY 3.3 2.1 + - - -
394B LEU* 2.9 54.9 + - + +
395B THR* 3.4 35.2 + - + +
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Residues in contact with VAL 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B TYR* 3.8 8.7 - - - +
329B LEU* 4.2 19.1 - - + -
386B ASN* 3.1 17.9 + - + +
387B VAL* 3.8 2.9 - - - +
389B MET* 1.3 80.9 - - + +
391B ASN* 1.3 65.4 + - - +
392B GLN 3.4 0.5 + - - -
393B GLY* 3.7 5.7 + - - -
395B THR* 4.6 8.1 - - - +
397B HIS 4.2 18.2 - - - +
398B MET* 3.4 27.8 - - + +
401B LYS* 3.3 45.7 + - + +
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Residues in contact with ASN 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B TYR* 4.7 1.4 + - - -
387B VAL* 2.8 19.8 + - - +
388B VAL 3.9 1.1 - - - +
390B VAL* 1.3 78.2 - - - +
392B GLN* 1.3 62.6 + - - +
393B GLY 3.7 0.9 - - - -
401B LYS* 3.3 30.4 + - - +
413B SER 4.1 5.7 + - - +
414B THR 5.6 1.2 + - - -
415B LEU 4.8 2.4 + - - -
417B GLN* 3.9 25.5 + - - +
418B LEU* 3.4 46.2 - - + +
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Residues in contact with GLN 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B VAL* 2.8 37.0 + - - +
389B MET 3.7 0.4 - - - -
391B ASN* 1.3 77.7 - - - +
393B GLY* 1.3 64.3 + - - +
394B LEU* 3.0 22.5 + - + +
418B LEU* 4.1 21.6 - - + +
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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
------------------------------------------------------------
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