Contacts of the helix formed by residues 375 - 393 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F CYS* 3.7 5.5 - - - -
27F ASP 3.3 6.3 + - - -
28F LEU 2.9 23.2 + - - +
29F PRO 3.5 9.9 - - - +
30F GLY* 3.7 5.5 - - - -
108F PRO* 3.3 25.9 - - - +
319F PHE 4.7 3.7 + - - +
322F PRO* 4.8 2.2 - - - +
374F GLY* 1.3 73.2 - - - -
376F PRO* 1.3 55.3 - - - +
377F TYR* 3.0 27.2 + - - +
378F LEU* 3.1 22.4 + - + +
379F ALA* 2.7 36.9 + - - +
451F TRP* 4.7 5.2 - - + -
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Residues in contact with PRO 376 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239F ALA* 4.0 16.2 - - + +
242F MET* 4.1 25.4 - - + -
243F GLN* 3.5 40.8 - - + +
246F LYS* 5.7 2.5 - - - +
275F MET* 5.1 6.7 - - + -
374F GLY 3.9 6.1 - - - +
375F ASN* 1.3 83.8 - - - +
377F TYR* 1.3 62.9 + - + +
379F ALA* 4.1 7.6 - - + -
380F PHE* 2.8 46.9 + - + -
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Residues in contact with TYR 377 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F CYS* 3.8 25.4 - - + -
32F MET* 4.3 2.8 - - - +
92F ASN* 3.8 5.4 + - - -
108F PRO* 3.3 28.0 - - + +
109F ARG* 3.6 30.3 + - + -
112F ALA* 4.1 12.1 - - + +
236F LEU* 4.0 3.8 - - + -
239F ALA* 3.3 29.6 - - + -
240F ASP* 2.4 38.7 + - - -
243F GLN* 3.5 29.5 - - + +
375F ASN* 3.0 19.3 + - - +
376F PRO* 1.3 80.6 - - + +
378F LEU* 1.3 61.6 + - - +
380F PHE* 4.3 1.1 - - - +
381F SER* 2.8 30.7 + - - -
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Residues in contact with LEU 378 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F LEU* 3.8 21.5 - - + +
108F PRO* 4.1 11.2 - - + -
111F ILE* 3.7 37.0 - - + -
319F PHE* 3.9 20.6 - - + +
375F ASN* 3.1 19.5 + - + +
377F TYR* 1.3 72.6 - - - +
379F ALA* 1.3 61.1 + - - +
381F SER* 4.4 2.2 - - - -
382F ALA* 2.8 33.1 + - - +
443F PHE* 3.7 6.8 - - + -
447F LEU* 4.5 10.8 - - + -
451F TRP* 3.5 38.1 - - + -
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Residues in contact with ALA 379 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275F MET* 4.5 10.5 - - + -
319F PHE* 3.6 27.5 + - - +
320F THR* 4.3 5.3 - - - +
371F ASP 5.9 0.4 - - - +
375F ASN 2.7 21.2 + - - +
376F PRO* 4.0 7.9 - - + +
378F LEU* 1.3 72.8 - - - +
380F PHE* 1.3 64.4 + - - +
382F ALA* 3.2 2.9 + - - +
383F MET* 3.0 44.3 + - + +
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Residues in contact with PHE 380 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F PHE* 3.4 45.2 - + + -
132F ALA* 4.3 19.7 - - + -
235F LEU* 3.8 22.7 - - + -
238F ALA* 3.7 16.8 - - + -
239F ALA* 3.6 34.3 - - + -
242F MET* 4.7 6.3 - - + -
275F MET* 3.9 13.2 - - + -
277F CYS* 3.6 22.9 - - - -
376F PRO* 2.8 33.1 + - + +
379F ALA* 1.3 73.0 - - + +
381F SER* 1.3 64.2 + - - +
383F MET* 3.3 9.6 + - + +
384F LEU* 3.1 17.8 + - - +
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Residues in contact with SER 381 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111F ILE* 4.0 7.0 - - - -
112F ALA* 3.4 26.3 + - - -
115F ALA* 3.6 14.1 - - - +
235F LEU* 3.9 11.4 - - - +
377F TYR 2.8 21.0 + - - -
378F LEU 3.7 2.7 - - - -
380F PHE* 1.3 77.6 - - - +
382F ALA* 1.3 57.1 + - - +
384F LEU* 3.1 4.7 + - - +
385F MET* 2.9 31.7 + - - +
443F PHE* 4.0 16.8 - - - -
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Residues in contact with ALA 382 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316F LEU* 3.5 23.4 - - + +
319F PHE* 3.9 20.9 - - + -
320F THR* 5.2 0.2 - - + -
378F LEU 2.8 22.1 + - - +
379F ALA 3.7 3.1 - - - +
381F SER* 1.3 72.7 - - - +
383F MET* 1.3 62.2 + - - +
385F MET* 3.3 2.8 + - - +
386F ALA* 3.0 19.4 + - - +
437F LEU* 3.8 26.2 - - + +
443F PHE* 3.8 4.9 - - + -
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Residues in contact with MET 383 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F PHE* 4.1 7.2 - - + -
275F MET* 4.4 0.4 - - + -
277F CYS* 3.6 30.7 - - - -
279F GLN* 3.5 34.8 - - - +
305F TYR* 3.6 4.6 + - - -
309F LEU* 3.6 14.5 - - + +
316F LEU* 3.7 6.5 - - + +
320F THR* 3.8 18.2 - - + -
367F PHE* 3.9 14.8 - - + -
370F PRO* 3.7 17.5 - - + -
379F ALA* 3.0 37.1 + - + +
380F PHE* 3.3 9.4 + - + +
382F ALA* 1.3 75.0 - - - +
384F LEU* 1.3 57.9 + - - +
386F ALA 3.4 0.5 + - - -
387F GLY 2.8 23.9 + - - -
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Residues in contact with LEU 384 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115F ALA* 3.9 25.8 - - + +
116F GLU* 5.2 1.1 - - + -
119F LEU* 4.2 14.8 - - + -
128F ALA* 3.9 22.2 - - + -
130F PHE* 4.5 2.9 - - + -
235F LEU* 3.7 24.2 - - + -
281F LEU* 3.9 13.2 - - + -
305F TYR* 3.5 18.1 + - + +
380F PHE 3.1 12.6 + - - +
381F SER 3.4 8.7 - - - +
383F MET* 1.3 75.8 - - - +
385F MET* 1.3 55.8 + - + +
387F GLY* 3.1 1.4 + - - -
388F LEU* 2.8 60.8 + - + +
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Residues in contact with MET 385 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F ALA* 5.2 5.8 - - - -
118F TYR* 3.7 35.9 - - + -
381F SER 2.9 20.2 + - - +
382F ALA 3.3 4.5 + - - +
384F LEU* 1.3 79.7 - - - +
386F ALA* 1.3 61.3 + - - +
388F LEU* 3.4 5.4 + - - +
389F ASP* 3.0 25.5 + - - +
436F TYR* 3.4 34.2 - - + +
437F LEU* 4.0 13.9 - - + +
439F GLU* 3.3 29.4 - - + +
442F VAL* 3.8 27.1 - - + -
443F PHE* 4.4 7.6 - - + -
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Residues in contact with ALA 386 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308F GLY* 3.3 18.7 - - - +
309F LEU* 4.3 1.3 - - + -
312F HIS* 4.0 18.7 - - + -
316F LEU* 4.0 16.4 - - + -
382F ALA 3.0 17.1 + - - +
383F MET 3.7 4.0 - - - +
385F MET* 1.3 75.9 - - - +
387F GLY* 1.3 63.8 + - - +
389F ASP* 3.4 2.4 + - - +
390F GLY 3.1 17.3 + - - -
436F TYR* 3.7 23.4 - - + -
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Residues in contact with GLY 387 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305F TYR* 3.6 45.5 - - - -
309F LEU* 4.5 1.5 - - - +
383F MET 2.8 15.3 + - - -
384F LEU 3.5 3.1 - - - -
386F ALA* 1.3 75.8 - - - +
388F LEU* 1.3 60.6 + - - +
390F GLY 3.3 1.9 + - - -
391F ILE* 3.2 24.4 + - - +
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Residues in contact with LEU 388 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F TYR* 4.0 33.9 - - + -
119F LEU* 3.8 35.0 - - + -
122F THR* 4.6 3.8 - - + -
124F ILE* 4.0 19.9 - - + +
281F LEU* 4.2 9.0 - - + -
305F TYR* 5.0 0.2 - - + -
384F LEU* 2.8 44.2 + - + +
385F MET* 3.9 5.6 - - - +
387F GLY* 1.3 71.5 - - - +
389F ASP* 1.3 59.6 + - - +
391F ILE* 3.2 22.1 + - + +
392F LYS* 2.9 32.8 + - - +
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Residues in contact with ASP 389 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312F HIS* 2.8 31.3 + - - +
385F MET 3.0 17.5 + - - +
386F ALA 3.7 5.2 - - - +
388F LEU* 1.3 75.2 - - - +
390F GLY* 1.3 57.8 + - - +
392F LYS* 4.3 6.8 - - - +
393F ASN* 3.0 57.9 + - - +
395F ILE* 4.1 5.7 - - - +
436F TYR* 3.9 18.1 - - + +
439F GLU* 4.9 10.9 - - + +
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Residues in contact with GLY 390 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304F HIS* 3.4 22.9 - - - +
308F GLY* 3.8 13.6 - - - -
386F ALA 3.1 10.5 + - - -
387F GLY 3.6 2.2 - - - -
388F LEU 3.2 0.4 - - - -
389F ASP* 1.3 73.6 - - - +
391F ILE* 1.3 58.1 + - - +
394F LYS* 2.9 24.8 + - - -
395F ILE* 2.9 22.0 + - - +
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Residues in contact with ILE 391 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F ILE* 3.8 30.3 - - + -
281F LEU* 3.6 31.4 - - + -
301F THR* 3.5 38.8 - - + +
304F HIS* 3.8 10.3 + - + +
305F TYR* 3.8 11.4 - - + +
387F GLY 3.2 15.3 + - - +
388F LEU* 3.2 12.1 + - + +
390F GLY* 1.3 70.9 - - - +
392F LYS* 1.3 67.9 + - - +
394F LYS* 3.1 20.6 + - - +
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Residues in contact with LYS 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F TYR* 3.3 26.5 + - - +
122F THR* 3.3 25.8 - - - +
124F ILE* 4.1 19.3 - - - +
388F LEU* 2.9 17.7 + - - +
389F ASP* 3.8 9.4 - - - +
391F ILE* 1.3 79.8 - - - +
393F ASN* 1.3 64.4 + - - +
394F LYS* 3.3 6.3 + - - +
439F GLU* 5.9 3.6 - - - +
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Residues in contact with ASN 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389F ASP* 3.0 51.8 + - - +
392F LYS* 1.3 82.4 - - - +
394F LYS* 1.3 70.9 + - - +
395F ILE* 3.1 17.8 + - + +
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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
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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