Contacts of the helix formed by residues 383 - 403 (chain A) in PDB entry 2ZXI
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 GLY 383 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A LYS* 3.7 0.7 - - - -
377A ASN* 4.3 0.5 + - - -
381A THR* 5.3 0.2 + - - -
382A THR* 1.3 76.7 + - - +
384A TYR* 1.3 64.4 + - - +
385A GLU 3.5 2.2 - - - -
386A GLU* 3.6 9.9 - - - -
387A ALA* 3.4 22.0 + - - +
618A FAD 2.9 44.0 + - - +
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Residues in contact with TYR 384 (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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17A HIS* 3.4 40.0 - + + +
46A MET* 3.4 30.4 - - + +
47A SER 3.3 9.8 + - - -
48A CYS* 2.8 28.5 + - + -
49A ASN* 2.9 32.3 + - + -
51A ALA 3.6 16.2 - - - -
52A ILE* 4.0 2.7 - - + -
57A LYS* 4.3 0.4 - - - +
71A MET* 3.9 17.7 - - + -
383A GLY* 1.3 71.7 - - - -
385A GLU* 1.3 68.4 + - - +
387A ALA* 3.2 5.6 + - - +
388A ALA* 2.9 28.8 + - - +
618A FAD 3.8 28.9 - - - -
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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
----------------------------------------------------------
51A ALA 3.9 4.3 - - - +
52A ILE* 3.4 10.8 - - + +
53A GLY 2.8 27.2 + - - +
57A LYS* 2.9 53.0 + - + +
60A VAL* 3.7 12.1 - - + +
61A VAL* 3.5 28.0 - - + -
71A MET* 4.1 13.5 - - - -
384A TYR* 1.3 80.5 + - - +
386A GLU* 1.3 63.6 + - - +
387A ALA 3.1 0.2 + - - -
388A ALA* 3.1 1.4 + - - +
389A GLY* 2.8 28.9 + - - -
435A LEU* 4.5 0.4 - - + -
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Residues in contact with GLU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LYS* 2.7 35.0 + - - +
381A THR* 4.1 14.4 - - + -
382A THR 2.9 34.3 - - - +
383A GLY* 3.6 4.5 - - - +
385A GLU* 1.3 77.2 - - - +
387A ALA* 1.3 55.7 + - - +
390A GLN* 2.8 32.1 + - - +
420A MET* 3.3 33.6 - - - +
433A TYR* 4.4 1.6 - - + +
434A ARG* 3.7 2.8 - - - +
435A LEU* 2.8 43.6 + - + +
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Residues in contact with ALA 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A HIS* 4.3 0.4 - - + -
18A ALA* 3.5 16.0 - - + +
376A GLY* 3.8 18.6 - - - -
377A ASN* 4.7 0.7 - - - +
381A THR* 4.6 0.6 + - - +
383A GLY 3.4 13.4 + - - +
384A TYR 3.2 8.9 + - - +
385A GLU 3.1 0.8 - - - -
386A GLU* 1.3 76.6 - - - +
388A ALA* 1.3 61.1 + - - +
390A GLN* 3.1 13.1 + - - +
391A GLY 2.8 25.1 + - - -
618A FAD 3.5 24.9 - - - +
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Residues in contact with ALA 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A HIS 3.5 22.1 + - - +
18A ALA* 4.3 0.7 - - - +
21A GLU* 3.6 17.4 - - + +
64A ILE* 3.5 19.1 - - + +
71A MET* 3.8 19.3 - - + -
384A TYR 2.9 16.9 + - - +
385A GLU 3.1 1.5 + - - +
387A ALA* 1.3 76.5 - - - +
389A GLY* 1.3 62.4 + - - +
392A ILE* 3.2 22.9 + - - +
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Residues in contact with GLY 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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60A VAL* 4.3 2.0 - - - -
64A ILE* 3.5 18.1 - - - +
385A GLU 2.8 16.7 + - - -
386A GLU 4.0 1.8 - - - -
388A ALA* 1.3 78.1 - - - +
390A GLN* 1.3 60.9 + - - +
392A ILE* 3.3 17.7 - - - +
393A VAL* 3.6 2.6 - - - +
417A ILE* 3.5 26.4 - - - +
420A MET* 4.3 6.3 - - - -
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Residues in contact with GLN 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LEU* 3.1 19.8 - - + +
375A ALA* 3.8 11.2 - - + -
376A GLY 3.2 17.9 + - - +
379A ASN* 2.9 30.9 + - - +
381A THR* 2.8 34.6 + - - +
386A GLU 2.8 22.6 + - - +
387A ALA 3.1 4.8 + - - +
389A GLY* 1.3 74.2 - - - +
391A GLY* 1.3 65.2 + - - +
393A VAL 3.1 2.6 + - - -
394A ALA* 2.9 19.6 + - - +
420A MET* 3.9 12.7 - - + -
421A ILE* 4.5 15.3 - - + -
424A LEU* 3.8 9.5 - - + +
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Residues in contact with GLY 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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18A ALA* 3.5 19.7 - - - -
22A ALA* 3.1 18.7 - - - +
375A ALA* 3.9 13.7 - - - +
387A ALA 2.8 14.1 + - - -
388A ALA 3.4 3.0 + - - -
390A GLN* 1.3 77.5 - - - +
392A ILE* 1.3 56.0 + - - +
394A ALA* 3.3 0.4 + - - -
395A GLY 2.8 26.0 + - - -
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Residues in contact with ILE 392 (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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21A GLU* 3.7 18.0 - - + +
25A ALA* 4.1 12.6 - - + +
64A ILE* 4.0 9.2 - - + +
67A LEU* 3.7 42.8 - - + -
69A GLY* 3.8 27.8 - - - +
388A ALA 3.2 13.1 + - - +
389A GLY* 3.3 18.2 - - - +
391A GLY* 1.3 75.7 - - - +
393A VAL* 1.3 63.9 + - + +
395A GLY* 3.9 0.4 - - - +
396A ILE* 2.8 44.9 + - + +
417A ILE* 4.6 4.3 - - + -
464A LEU* 4.4 8.5 - - + -
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Residues in contact with VAL 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 5.3 1.3 - - + -
362A PRO 4.6 4.3 - - - +
363A THR 4.3 2.9 - - - +
364A LEU* 3.9 18.2 - - + -
389A GLY 3.6 14.4 - - - +
390A GLN 3.1 7.5 + - - +
392A ILE* 1.3 83.1 - - + +
394A ALA* 1.3 58.1 + - - +
396A ILE* 3.3 11.1 + - + +
397A ASN* 3.0 44.6 + - - +
408A ILE* 4.8 5.8 - - + +
409A TYR* 5.2 4.5 - - - -
410A LEU* 3.7 32.8 - - + +
421A ILE* 3.8 15.7 - - + -
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Residues in contact with ALA 394 (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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153A VAL* 3.8 25.4 - - + +
364A LEU* 3.9 12.7 - - + +
373A PHE* 4.0 23.7 - - + -
374A HIS 4.3 0.4 - - - +
375A ALA* 4.2 8.3 - - + -
390A GLN 2.9 16.3 + - - +
391A GLY 3.7 3.8 - - - +
393A VAL* 1.3 77.1 - - - +
395A GLY* 1.3 58.2 + - - +
397A ASN* 3.4 1.4 + - - +
398A ALA* 2.9 31.9 + - - +
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Residues in contact with GLY 395 (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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10A VAL* 5.8 0.7 - - - -
22A ALA* 3.5 31.5 - - - +
25A ALA* 4.4 0.9 - - - -
26A ALA* 3.8 6.5 - - - +
29A MET* 4.3 3.4 - - - -
153A VAL* 4.5 1.8 - - - -
391A GLY 2.8 15.6 + - - -
392A ILE 3.9 0.7 - - - -
394A ALA* 1.3 75.8 - - - +
396A ILE* 1.3 63.6 + - - +
398A ALA* 3.3 6.3 + - - +
399A ALA* 3.2 23.7 + - - +
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Residues in contact with ILE 396 (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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25A ALA* 4.2 2.0 - - + +
29A MET* 3.1 25.8 - - + +
67A LEU* 4.8 11.7 - - + -
392A ILE* 2.8 42.7 + - + +
393A VAL* 3.5 9.9 - - + +
395A GLY* 1.3 78.5 - - - +
397A ASN* 1.3 62.3 + - - +
399A ALA* 3.4 3.5 + - - +
400A LEU* 3.1 28.4 + - + +
408A ILE* 3.8 19.5 - - + -
458A LEU* 6.0 0.2 - - + -
462A LEU* 3.5 41.5 - - + -
464A LEU* 4.0 10.1 - - + -
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Residues in contact with ASN 397 (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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363A THR* 2.9 28.9 + - - +
373A PHE* 3.3 22.4 - - + -
393A VAL* 3.0 22.0 + - - +
396A ILE* 1.3 74.3 - - - +
398A ALA* 1.3 60.1 + - - +
400A LEU* 3.6 7.9 - - - +
401A ARG* 2.9 32.2 + - - +
407A PRO* 3.5 12.5 - - + +
408A ILE* 2.8 51.4 + - - +
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Residues in contact with ALA 398 (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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10A VAL* 3.8 19.5 - - + -
151A ALA* 3.7 14.9 - - + +
153A VAL* 3.7 21.5 - - + -
373A PHE* 3.9 13.9 - - + -
394A ALA 2.9 19.0 + - - +
395A GLY 3.7 4.0 - - - +
397A ASN* 1.3 72.3 - - - +
399A ALA* 1.3 65.9 + - - +
401A ARG* 3.3 4.0 + - - +
402A ALA* 2.9 23.2 + - - +
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Residues in contact with ALA 399 (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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10A VAL* 3.8 11.1 - - - +
26A ALA* 4.0 21.1 - - - +
29A MET* 4.3 10.1 - - - -
31A ALA* 4.1 6.7 - - + -
395A GLY 3.2 10.7 + - - +
396A ILE 3.6 8.3 - - - +
398A ALA* 1.3 76.4 - - - +
400A LEU* 1.3 67.3 + - - +
402A ALA* 3.0 6.1 + - - +
403A PHE* 2.9 42.3 + - + -
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Residues in contact with LEU 400 (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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29A MET* 5.2 6.1 - - - -
396A ILE* 3.1 23.9 + - + +
397A ASN* 3.6 28.3 - - - +
398A ALA 3.3 0.2 - - - -
399A ALA* 1.3 75.4 - - - +
401A ARG* 1.3 64.1 + - - +
403A PHE* 2.9 19.6 + - + -
405A LYS* 2.9 47.3 + - + +
406A GLU 3.4 28.9 - - - +
407A PRO* 3.9 1.6 - - + -
408A ILE* 4.1 11.4 - - + -
462A LEU* 4.6 12.8 - - + -
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Residues in contact with ARG 401 (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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150A LYS* 5.5 3.2 - - - +
151A ALA* 4.5 8.3 - - + -
365A GLU* 2.8 42.5 + - - +
370A ARG* 3.3 56.6 + - - +
371A GLY* 4.5 4.5 - - - +
373A PHE* 3.7 10.3 - - + -
397A ASN 2.9 16.6 + - - +
398A ALA* 3.4 10.8 - - - +
400A LEU* 1.3 74.3 - - - +
402A ALA* 1.3 59.5 + - - +
404A GLY* 2.9 19.4 + - - -
405A LYS 3.5 13.1 + - - -
406A GLU* 4.1 12.3 + - - -
407A PRO* 3.3 31.9 - - + +
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Residues in contact with ALA 402 (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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9A ASP* 3.8 41.1 - - + +
150A LYS* 3.5 32.8 - - + +
151A ALA* 5.0 0.6 - - - +
398A ALA 2.9 13.3 + - - +
399A ALA* 3.0 12.8 + - - +
401A ARG* 1.3 76.5 - - - +
403A PHE* 1.3 65.7 + - + +
404A GLY 3.2 0.7 + - - -
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Residues in contact with PHE 403 (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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9A ASP* 4.4 9.4 - - - -
29A MET* 3.4 22.4 - - + -
30A GLY* 3.7 4.9 - - - -
31A ALA* 3.5 41.5 - - + -
399A ALA* 2.9 27.5 + - + -
400A LEU* 2.9 17.4 + - + +
402A ALA* 1.3 84.5 - - + +
404A GLY* 1.3 63.4 + - - +
405A LYS* 3.3 27.5 + - + +
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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