Contacts of the helix formed by residues 375 - 393 (chain A) in PDB entry 3ZXR
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 ASN 375 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A CYS* 3.5 5.6 - - - -
27A ASP 3.3 7.3 + - - -
28A LEU 2.8 23.8 + - - +
29A PRO 3.4 11.0 + - - +
30A GLY* 3.6 5.2 - - - -
108A PRO* 3.2 24.9 - - - +
319A PHE 4.6 3.5 + - - +
322A PRO* 4.8 2.6 - - - +
374A GLY* 1.3 72.8 - - - -
376A PRO* 1.3 54.0 - - - +
377A TYR* 3.0 31.2 + - - +
378A LEU* 3.2 19.3 + - + +
379A ALA* 2.7 37.6 + - - +
451A TRP* 4.7 4.3 - - + -
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Residues in contact with PRO 376 (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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239A ALA* 4.0 15.9 - - + +
242A MET* 4.0 26.2 - - + -
243A GLN* 3.5 41.1 - - + +
246A LYS* 5.7 2.2 - - + +
275A MET* 5.0 6.7 - - + -
374A GLY 3.7 8.1 - - - +
375A ASN* 1.3 83.1 - - - +
377A TYR* 1.3 62.4 + - + +
379A ALA* 4.1 7.4 - - + -
380A PHE* 2.8 46.6 + - + -
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Residues in contact with TYR 377 (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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26A CYS* 3.9 25.4 - - + -
32A MET* 4.2 2.9 - - - +
92A ASN* 3.9 5.2 + - - -
108A PRO* 3.3 27.1 - - + +
109A ARG* 3.6 30.5 + - + -
112A ALA* 4.1 13.6 - - + +
235A LEU* 4.6 0.2 - - - +
236A LEU* 4.1 3.8 - - + -
239A ALA* 3.3 25.1 - - + -
240A ASP* 2.5 36.0 + - - -
243A GLN* 3.5 32.8 - - + +
375A ASN* 3.0 18.3 + - - +
376A PRO* 1.3 81.2 - - + +
378A LEU* 1.3 60.5 + - - +
380A PHE* 4.4 1.3 - - - +
381A SER* 2.8 28.4 + - - -
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Residues in contact with LEU 378 (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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28A LEU* 3.9 17.9 - - + +
108A PRO* 3.9 14.8 - - + -
111A ILE* 3.7 33.9 - - + -
319A PHE* 4.0 24.2 - - + +
375A ASN* 3.2 18.0 + - + +
377A TYR* 1.3 74.1 - - - +
379A ALA* 1.3 55.4 + - - +
381A SER* 3.4 4.6 + - - -
382A ALA* 2.8 37.9 + - - +
443A PHE* 3.7 5.3 - - + -
447A LEU* 4.5 10.8 - - + -
451A TRP* 3.5 37.9 - - + -
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Residues in contact with ALA 379 (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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275A MET* 4.5 10.8 - - + -
319A PHE* 3.5 28.0 + - - +
320A THR* 4.3 4.6 - - - +
371A ASP 5.9 0.2 - - - +
375A ASN 2.7 22.1 + - - +
376A PRO* 4.0 7.9 - - + +
378A LEU* 1.3 71.4 - - - +
380A PHE* 1.3 67.3 + - - +
382A ALA* 3.3 2.3 + - - +
383A MET* 3.0 43.2 + - + +
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Residues in contact with PHE 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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130A PHE* 3.5 43.0 - + + -
132A ALA* 4.2 19.7 - - + -
235A LEU* 3.9 23.6 - - + -
238A ALA* 3.7 16.6 - - + -
239A ALA* 3.6 36.1 - - + -
242A MET* 4.8 3.4 - - + -
275A MET* 4.0 15.3 - - + -
277A CYS* 3.7 22.2 - - - -
376A PRO* 2.8 32.5 + - + +
379A ALA* 1.3 70.7 - - + +
381A SER* 1.3 63.6 + - - +
383A MET* 3.3 11.1 + - + +
384A LEU* 3.0 19.1 + - - +
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Residues in contact with SER 381 (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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111A ILE* 4.0 6.7 - - - -
112A ALA* 3.4 25.6 + - - -
115A ALA* 3.5 15.3 - - - +
235A LEU* 3.9 11.2 - - - +
377A TYR 2.8 21.2 + - - -
378A LEU 3.7 3.1 - - - -
379A ALA 3.2 0.4 - - - -
380A PHE* 1.3 78.7 - - - +
382A ALA* 1.3 63.6 + - - +
384A LEU* 3.0 6.1 + - - +
385A MET* 2.9 23.6 + - - +
442A VAL* 4.8 0.2 - - - -
443A PHE* 3.9 17.9 - - - -
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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
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316A LEU* 3.4 23.6 - - + +
319A PHE* 3.9 20.9 - - + -
378A LEU 2.8 21.9 + - - +
379A ALA* 3.7 3.1 - - - +
381A SER* 1.3 73.5 - - - +
383A MET* 1.3 56.3 + - - +
385A MET* 3.3 2.6 + - - +
386A ALA* 3.0 24.1 + - - +
437A LEU* 3.8 26.0 - - + +
443A PHE* 3.8 5.3 - - + -
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Residues in contact with MET 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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130A PHE* 4.2 5.6 - - + -
275A MET* 4.5 0.4 - - + -
277A CYS* 3.7 29.4 - - - -
279A GLN* 3.6 34.8 - - - +
305A TYR* 3.5 6.8 + - - -
309A LEU* 3.6 11.3 - - + +
316A LEU* 3.9 6.5 - - + -
320A THR* 3.8 17.9 - - + -
367A PHE* 3.8 16.6 - - + -
370A PRO* 3.7 16.6 - - + -
379A ALA* 3.0 37.3 + - + +
380A PHE* 3.6 10.5 - - + +
381A SER 3.2 0.2 - - - -
382A ALA* 1.3 73.2 - - - +
384A LEU* 1.3 60.6 + - - +
386A ALA 3.4 0.7 + - - -
387A GLY 2.8 24.1 + - - -
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Residues in contact with LEU 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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115A ALA* 4.0 25.6 - - + +
116A GLU* 5.0 0.9 - - - +
119A LEU* 4.2 14.4 - - + -
128A ALA* 3.9 22.9 - - + -
130A PHE* 4.5 2.0 - - + -
235A LEU* 3.7 24.0 - - + -
281A LEU* 3.9 14.4 - - + -
305A TYR* 3.5 16.8 + - + +
380A PHE 3.0 11.7 + - - +
381A SER 3.0 9.2 + - - +
383A MET* 1.3 76.3 - - - +
385A MET* 1.3 61.1 + - + +
387A GLY* 3.3 0.3 + - - -
388A LEU* 2.7 58.4 + - + +
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Residues in contact with MET 385 (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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115A ALA* 5.1 5.6 - - - -
118A TYR* 3.7 29.2 - - + -
381A SER 2.9 18.9 + - - +
382A ALA 3.7 6.7 - - - +
384A LEU* 1.3 80.3 - - - +
386A ALA* 1.3 56.7 + - - +
388A LEU* 3.5 5.5 + - - +
389A ASP* 3.0 29.1 + - - +
436A TYR* 3.4 34.7 - - + +
437A LEU* 4.0 13.7 - - + +
439A GLU* 3.3 28.9 - - + +
442A VAL* 3.7 35.7 - - + -
443A PHE* 4.4 7.6 - - + -
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Residues in contact with ALA 386 (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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308A GLY* 3.3 19.5 - - - +
309A LEU* 4.3 1.6 - - + -
312A HIS* 3.9 18.8 - - + -
316A LEU* 4.0 17.0 - - + -
382A ALA 3.0 16.5 + - - +
383A MET 3.7 3.6 - - - +
385A MET* 1.3 76.8 - - - +
387A GLY* 1.3 62.7 + - - +
389A ASP* 3.4 3.6 + - - +
390A GLY 3.1 17.2 + - - -
436A TYR* 3.7 22.3 - - + -
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Residues in contact with GLY 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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305A TYR* 3.5 51.2 - - - -
309A LEU* 4.4 1.2 - - - +
383A MET 2.8 15.1 + - - -
384A LEU 3.6 0.4 - - - -
386A ALA* 1.3 74.6 - - - +
388A LEU* 1.3 61.4 + - - +
390A GLY 3.3 1.9 + - - -
391A ILE* 3.2 24.8 + - - +
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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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118A TYR* 4.0 34.5 - - + -
119A LEU* 3.8 35.2 - - + -
122A THR* 4.7 3.4 - - + -
124A ILE* 4.0 23.7 - - + +
281A LEU* 4.1 10.3 - - + -
384A LEU* 2.7 44.4 + - + +
385A MET* 4.0 5.4 - - - +
387A GLY* 1.3 69.6 - - - +
389A ASP* 1.3 61.3 + - - +
391A ILE* 3.3 17.1 + - + +
392A LYS* 2.9 32.5 + - - +
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Residues in contact with ASP 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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312A HIS* 2.7 31.0 + - - +
385A MET 3.0 18.8 + - - +
386A ALA 3.7 4.5 - - - +
388A LEU* 1.3 75.2 - - - +
390A GLY* 1.3 58.2 + - - +
392A LYS* 3.5 5.8 + - - +
393A ASN* 2.9 56.2 + - - +
395A ILE* 4.1 6.1 - - - +
436A TYR* 3.8 18.3 - - + +
439A GLU* 4.9 10.6 - - + +
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Residues in contact with GLY 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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304A HIS* 3.3 21.7 - - - +
308A GLY* 3.8 6.9 - - - -
386A ALA 3.1 10.3 + - - -
387A GLY 3.3 2.4 + - - -
388A LEU 3.2 0.2 - - - -
389A ASP* 1.3 75.7 - - - +
391A ILE* 1.3 57.4 + - - +
394A LYS* 2.9 9.9 + - - -
395A ILE* 2.9 42.8 + - - +
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Residues in contact with ILE 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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124A ILE* 3.8 31.2 - - + -
281A LEU* 3.6 31.6 - - + -
301A THR* 3.6 39.9 - - + +
304A HIS* 3.8 9.8 + - + +
305A TYR* 3.8 11.4 - - + +
387A GLY 3.2 15.7 + - - +
388A LEU* 3.7 10.3 - - + +
390A GLY* 1.3 73.7 - - - +
392A LYS* 1.3 64.1 + - - +
394A LYS* 3.1 20.3 + - - +
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Residues in contact with LYS 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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118A TYR* 3.3 18.4 + - - +
122A THR* 3.2 33.1 - - - +
124A ILE* 4.1 19.5 - - - -
388A LEU* 2.9 17.0 + - - +
389A ASP* 3.8 8.3 - - - +
391A ILE* 1.3 79.3 - - - +
393A ASN* 1.3 66.3 + - - +
394A LYS* 3.4 6.3 + - - +
439A GLU* 5.8 4.0 - - - +
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Residues in contact with ASN 393 (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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389A ASP* 2.9 51.6 + - - +
392A LYS* 1.3 82.1 - - - +
394A LYS* 1.3 71.0 + - - +
395A ILE* 3.1 17.6 + - + +
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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
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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