Contacts of the helix formed by residues 374 - 393 (chain A) in PDB entry 5JZU
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 SER 374 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337A PHE* 5.0 5.7 - - - -
338A ASP* 3.1 20.2 - - - -
341A ILE* 4.4 3.8 - - - -
368A VAL* 5.8 0.2 - - - +
371A TYR* 2.9 29.9 + - - +
372A PRO 3.6 0.2 - - - -
373A GLN* 1.3 74.7 - - - +
375A PRO* 1.3 68.2 - - - +
377A ALA* 3.5 20.5 - - - +
378A ARG* 3.2 15.9 + - - +
411A LEU* 3.4 9.0 - - - +
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Residues in contact with PRO 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A ASN* 3.4 26.5 - - - +
338A ASP* 3.3 15.5 - - - +
373A GLN 3.1 10.5 - - - +
374A SER* 1.3 83.7 - - - +
376A ARG* 1.3 50.0 + - - +
378A ARG* 3.0 3.7 + - + +
379A TYR* 2.8 35.5 + - - +
408A VAL* 4.1 8.6 - - + +
411A LEU* 3.7 13.9 - - + -
412A PRO 4.0 12.3 - - - +
413A ASP 4.0 4.7 - - - +
414A VAL* 4.2 15.3 - - + -
415A PRO* 4.5 1.8 - - + -
418A LEU* 3.6 21.1 - - + -
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Residues in contact with ARG 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LEU* 4.3 27.8 - - - +
334A LEU* 3.5 30.0 - - + +
338A ASP* 3.0 22.7 + - - +
345A LEU* 3.9 19.7 - - + -
349A GLU* 3.2 38.5 + - - +
364A PHE* 4.1 6.2 - - - -
375A PRO* 1.3 78.5 - - - +
377A ALA* 1.3 58.2 + - - +
379A TYR* 3.4 29.2 - - - -
380A GLY* 2.9 36.9 + - - +
383A GLN* 4.3 5.1 + - - -
418A LEU* 4.0 5.6 - - - +
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Residues in contact with ALA 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A LEU* 3.6 19.3 - - + +
364A PHE* 3.5 10.6 - - - -
367A LEU* 4.0 30.3 - - + +
368A VAL* 3.6 13.4 - - + +
371A TYR* 5.3 1.3 - - + -
374A SER* 3.5 24.0 + - - +
375A PRO 3.2 0.6 - - - -
376A ARG* 1.3 78.7 - - - +
378A ARG* 1.3 58.6 + - - +
380A GLY 3.4 0.7 + - - -
381A LYS* 3.1 21.5 + - - +
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Residues in contact with ARG 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A VAL* 3.9 32.2 - - - +
372A PRO* 2.8 35.0 + - - +
374A SER 3.2 12.9 + - - +
375A PRO 3.0 8.0 + - - +
377A ALA* 1.3 75.3 - - - +
379A TYR* 1.3 60.5 + - - +
381A LYS* 3.2 6.6 + - - +
382A ALA* 2.9 23.7 + - - +
404A THR* 3.6 12.7 - - - +
407A GLU* 3.0 39.3 + - - +
408A VAL* 3.5 28.9 - - + +
411A LEU* 3.7 22.6 - - + +
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Residues in contact with TYR 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LEU* 5.0 8.1 - - + -
375A PRO 2.8 19.9 + - - +
376A ARG* 3.4 29.2 - - - +
378A ARG* 1.3 72.7 - - - +
380A GLY* 1.3 57.2 + - - +
382A ALA* 3.3 2.9 + - - +
383A GLN* 2.9 64.9 + - + +
405A TYR* 3.9 15.3 - + - -
408A VAL* 3.6 9.4 - - + +
418A LEU* 3.4 31.4 - - + -
421A LEU* 4.1 22.5 + - + +
422A SER* 3.8 38.6 - - - -
425A ARG* 5.8 2.1 - - + +
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Residues in contact with GLY 380 (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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364A PHE* 3.5 36.1 - - - -
376A ARG* 2.9 19.1 + - - +
377A ALA 3.7 0.2 - - - -
378A ARG 3.1 0.4 - - - -
379A TYR* 1.3 75.8 - - - +
381A LYS* 1.3 64.6 + - - +
383A GLN* 3.2 7.3 + - - +
384A CYS* 3.1 26.3 + - - -
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Residues in contact with LYS 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A VAL* 5.6 4.2 - - + +
364A PHE* 3.6 15.2 - - + +
365A LYS* 4.2 29.8 - - + -
368A VAL* 4.1 24.4 - - + +
377A ALA 3.1 13.8 + - - +
378A ARG* 3.2 11.6 + - - +
380A GLY* 1.3 74.7 - - - +
382A ALA* 1.3 63.5 + - - +
384A CYS* 3.3 4.3 + - - +
385A GLU* 3.0 46.4 + - + +
404A THR* 3.5 27.1 + - + +
407A GLU* 4.1 11.1 + - - -
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Residues in contact with ALA 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ARG 2.9 9.2 + - - +
379A TYR* 3.5 10.8 - - - +
380A GLY 3.2 0.2 - - - -
381A LYS* 1.3 76.8 - - - +
383A GLN* 1.3 56.1 + - - +
385A GLU* 3.4 9.1 + - - +
386A ASP* 3.0 26.9 + - - +
401A ALA* 3.8 4.9 - - - +
404A THR* 3.6 27.7 - - + +
405A TYR* 3.6 36.3 + - + +
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Residues in contact with GLN 383 (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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349A GLU* 3.9 10.0 - - - +
352A ARG* 3.5 41.4 + - - +
376A ARG* 4.3 3.8 + - - -
379A TYR* 2.9 60.3 + - + +
380A GLY* 3.2 4.6 + - - +
382A ALA* 1.3 76.2 - - - +
384A CYS* 1.3 62.4 + - - +
386A ASP* 3.1 5.0 + - - +
387A ASP* 3.1 25.5 + - - +
405A TYR* 3.6 17.2 + - - +
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Residues in contact with CYS 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ARG* 3.5 29.2 - - - +
357A ILE* 4.7 5.1 - - + +
360A ALA* 3.7 20.9 - - - -
361A VAL* 3.4 25.3 - - + +
364A PHE* 3.7 19.1 - - - -
380A GLY 3.1 19.9 + - - +
381A LYS 3.8 3.8 - - - +
383A GLN* 1.3 72.9 - - - +
385A GLU* 1.3 62.1 + - - +
387A ASP* 3.2 6.4 + - - +
388A LEU* 2.8 30.7 + - - +
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Residues in contact with GLU 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A VAL* 4.6 10.3 - - + +
381A LYS* 3.0 37.6 + - + +
382A ALA* 3.5 6.2 - - - +
384A CYS* 1.3 74.5 - - - +
386A ASP* 1.3 57.5 + - - +
388A LEU* 3.6 12.7 - - + +
389A ALA* 3.0 27.9 + - - +
397A VAL* 4.3 12.6 - - + +
400A GLY* 4.4 6.1 - - - +
401A ALA* 3.6 19.9 - - + -
404A THR* 2.5 39.9 + - - +
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Residues in contact with ASP 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ALA 3.0 13.2 + - - +
383A GLN* 3.2 11.2 - - - +
384A CYS 3.1 0.2 - - - -
385A GLU* 1.3 75.1 - - - +
387A ASP* 1.3 67.4 + - - +
389A ALA* 3.0 17.1 + - - +
390A GLU* 3.2 16.8 + - - +
398A LEU* 4.2 11.0 - - - +
401A ALA* 3.9 5.8 - - + +
405A TYR* 3.3 20.6 + - + +
425A ARG* 2.7 45.9 + - - -
429A ARG* 4.0 8.5 + - - +
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Residues in contact with ASP 387 (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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352A ARG* 2.9 43.3 + - - +
357A ILE* 4.4 16.3 - - + +
383A GLN 3.1 9.9 + - - +
384A CYS 3.2 6.0 + - - +
386A ASP* 1.3 80.5 - - - +
388A LEU* 1.3 57.7 + - - +
390A GLU* 2.8 26.9 + - - +
391A LYS* 2.9 15.8 + - - +
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Residues in contact with LEU 388 (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* 4.6 23.2 - - + +
358A GLU* 5.3 4.5 - - + -
361A VAL* 4.9 13.0 - - + -
384A CYS 2.8 16.6 + - - +
385A GLU* 3.6 12.1 - - + +
387A ASP* 1.3 77.7 - - - +
389A ALA* 1.3 56.7 + - - +
391A LYS* 4.4 8.1 - - + +
392A ARG* 2.8 75.9 + - + +
397A VAL* 4.4 9.4 - - + -
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Residues in contact with ALA 389 (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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385A GLU 3.0 14.3 + - - +
386A ASP 3.0 11.6 + - - +
388A LEU* 1.3 76.5 - - - +
390A GLU* 1.3 53.9 + - + +
393A ARG* 2.7 32.1 + - - -
394A SER 3.3 3.8 + - - +
397A VAL* 3.4 24.4 - - + +
398A LEU* 3.6 32.3 - - + -
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Residues in contact with GLU 390 (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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386A ASP* 3.2 17.9 + - - +
387A ASP* 2.8 15.0 + - - +
389A ALA* 1.3 76.8 - - + +
391A LYS* 1.3 68.1 + - - +
393A ARG* 3.4 11.3 + - - +
425A ARG* 4.5 2.1 + - - +
429A ARG* 3.4 26.3 + - - -
432A PHE* 5.8 5.2 - - - -
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Residues in contact with LYS 391 (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* 6.3 2.9 - - + -
387A ASP 2.9 13.6 + - - +
388A LEU* 3.9 11.9 - - + +
390A GLU* 1.3 79.4 - - - +
392A ARG* 1.3 63.8 + - + +
393A ARG* 4.6 1.7 - - - +
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Residues in contact with ARG 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LEU* 2.8 52.0 + - + +
391A LYS* 1.3 75.9 - - + +
393A ARG* 1.3 71.1 + - - +
394A SER* 4.2 17.1 - - - +
397A VAL* 3.6 28.1 - - + +
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Residues in contact with ARG 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ALA 2.7 22.5 + - - -
390A GLU* 3.4 7.5 + - - +
391A LYS 3.3 2.9 - - - +
392A ARG* 1.3 79.6 - - - +
394A SER* 1.3 56.2 + - - +
395A ASN 4.2 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
------------------------------------------------------------
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