Contacts of the helix formed by residues 375 - 393 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B CYS* 3.5 3.1 - - - -
27B ASP 3.2 16.2 + - - -
28B LEU 2.9 23.2 + - - +
29B PRO 3.4 9.2 - - - +
30B GLY* 3.5 8.3 - - - -
108B PRO* 3.3 15.3 - - - +
319B PHE 4.6 4.2 + - - +
322B PRO* 4.8 2.6 - - - +
374B GLY* 1.3 74.3 - - - -
376B PRO* 1.3 54.2 - - - +
377B TYR* 3.0 30.8 + - - +
378B LEU* 3.2 19.7 + - + +
379B ALA* 2.7 37.4 + - - +
451B TRP* 4.7 3.9 - - + -
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Residues in contact with PRO 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ALA* 3.9 16.2 - - + +
242B MET* 4.1 24.7 - - + -
243B GLN* 3.5 41.7 - - + +
246B LYS* 5.8 2.0 - - - +
275B MET* 5.1 7.4 - - + -
374B GLY 3.8 7.4 - - - +
375B ASN* 1.3 85.0 - - - +
377B TYR* 1.3 60.5 + - + +
379B ALA* 4.1 7.2 - - + -
380B PHE* 2.8 49.7 + - + -
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Residues in contact with TYR 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B CYS* 3.7 26.2 - - + -
32B MET* 4.3 2.4 - - - +
92B ASN* 3.8 6.1 + - - -
108B PRO* 3.3 26.2 - - + +
109B ARG* 3.6 29.5 + - + -
112B ALA* 4.2 12.6 - - + +
236B LEU* 4.0 3.6 - - + -
239B ALA* 3.4 25.8 - - + -
240B ASP* 2.4 40.9 + - - -
243B GLN* 3.5 28.9 - - + +
375B ASN* 3.0 18.3 + - - +
376B PRO* 1.3 79.0 - - + +
378B LEU* 1.3 58.2 + - - +
380B PHE* 4.3 1.4 - - - +
381B SER* 2.8 33.3 + - - -
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Residues in contact with LEU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 3.8 21.1 - - + +
108B PRO* 4.0 12.3 - - + -
111B ILE* 3.7 35.9 - - + -
319B PHE* 3.9 23.1 - - + +
375B ASN* 3.2 18.0 + - + +
377B TYR* 1.3 73.3 - - - +
379B ALA* 1.3 56.8 + - - +
381B SER* 4.4 3.1 - - - -
382B ALA* 2.7 37.6 + - - +
443B PHE* 3.6 5.8 - - + -
447B LEU* 4.5 10.5 - - + -
451B TRP* 3.6 37.2 - - + -
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Residues in contact with ALA 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B MET* 4.5 10.1 - - + -
319B PHE* 3.5 27.6 + - - +
320B THR* 4.2 4.7 - - - +
371B ASP 5.9 0.2 - - - +
375B ASN 2.7 22.2 + - - +
376B PRO* 3.9 7.4 - - + +
378B LEU* 1.3 70.2 - - - +
380B PHE* 1.3 66.9 + - + +
382B ALA* 3.3 2.6 + - - +
383B MET* 2.9 45.1 + - + +
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Residues in contact with PHE 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B PHE* 3.5 43.1 - + + -
132B ALA* 4.2 20.2 - - + -
235B LEU* 3.8 34.3 - - + -
238B ALA* 3.7 17.0 - - + -
239B ALA* 3.6 27.4 - - + -
242B MET* 4.7 6.1 - - + -
275B MET* 4.0 13.0 - - + -
277B CYS* 3.5 23.1 - - - -
376B PRO* 2.8 32.8 + - + +
379B ALA* 1.3 73.3 - - + +
381B SER* 1.3 61.8 + - - +
383B MET* 3.3 10.3 + - + +
384B LEU* 3.0 18.9 + - - +
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Residues in contact with SER 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ILE* 4.0 7.0 - - - -
112B ALA* 3.4 25.1 + - - -
115B ALA* 3.6 15.1 - - - +
235B LEU* 3.8 11.1 - - - +
377B TYR 2.8 22.4 + - - -
378B LEU 3.7 3.1 - - - -
379B ALA 3.2 0.2 - - - -
380B PHE* 1.3 77.5 - - - +
382B ALA* 1.3 63.1 + - - +
384B LEU* 3.1 4.2 + - - +
385B MET* 2.9 26.2 + - - +
443B PHE* 3.9 17.7 - - - -
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Residues in contact with ALA 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B LEU* 3.5 25.1 - - + +
319B PHE* 3.9 20.0 - - + -
378B LEU 2.7 22.2 + - - +
379B ALA 3.8 2.5 - - - +
381B SER* 1.3 73.5 - - - +
383B MET* 1.3 61.0 + - - +
385B MET* 3.3 2.1 + - - +
386B ALA* 3.0 19.9 + - - +
437B LEU* 3.8 26.7 - - + +
443B PHE* 3.8 4.9 - - + -
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Residues in contact with MET 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B PHE* 4.2 5.8 - - + -
275B MET* 4.5 0.4 - - + -
277B CYS* 3.6 31.0 - - - -
279B GLN* 3.6 35.2 - - - +
305B TYR* 3.6 6.3 + - - -
309B LEU* 3.6 11.8 - - + +
316B LEU* 3.7 6.5 - - + +
320B THR* 3.7 18.8 - - + -
367B PHE* 3.9 15.5 - - + -
370B PRO* 3.7 17.5 - - + -
379B ALA* 2.9 37.6 + - + +
380B PHE* 3.5 9.0 - - + +
382B ALA* 1.3 74.6 - - - +
384B LEU* 1.3 58.9 + - - +
386B ALA 3.4 0.7 + - - -
387B GLY* 2.8 25.1 + - - -
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Residues in contact with LEU 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ALA* 3.9 25.8 - - + +
116B GLU* 4.9 1.1 - - - +
119B LEU* 4.2 14.6 - - + -
128B ALA* 3.9 11.9 - - + -
130B PHE* 4.5 2.2 - - + -
235B LEU* 3.7 24.5 - - + -
281B LEU* 3.9 26.7 - - + -
305B TYR* 3.5 15.2 + - + +
380B PHE 3.0 13.3 + - - +
381B SER 3.1 8.3 + - - +
383B MET* 1.3 77.0 - - - +
385B MET* 1.3 54.7 + - + +
387B GLY* 3.1 1.4 + - - -
388B LEU* 2.7 61.6 + - + +
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Residues in contact with MET 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ALA* 5.1 5.4 - - - -
118B TYR* 3.6 35.0 - - + -
381B SER 2.9 22.0 + - - +
382B ALA 3.7 3.8 - - - +
384B LEU* 1.3 77.5 - - - +
386B ALA* 1.3 57.3 + - - +
388B LEU* 3.9 6.4 - - - +
389B ASP* 2.9 31.2 + - - +
436B TYR* 3.4 29.8 - - + +
437B LEU* 4.0 12.3 - - + +
439B GLU* 3.3 29.2 - - + +
442B VAL* 3.7 29.2 - - + -
443B PHE* 4.3 7.6 - - + -
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Residues in contact with ALA 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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308B GLY* 3.3 19.8 - - - +
309B LEU* 4.3 1.1 - - + -
312B HIS* 3.9 20.0 - - + -
316B LEU* 4.0 17.9 - - + -
382B ALA 3.0 16.3 + - - +
383B MET 3.7 4.0 - - - +
385B MET* 1.3 76.1 - - - +
387B GLY* 1.3 63.6 + - - +
389B ASP* 3.4 2.8 + - - +
390B GLY 3.1 17.5 + - - -
436B TYR* 3.8 22.1 - - + -
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Residues in contact with GLY 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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305B TYR* 3.5 47.4 - - - -
309B LEU* 4.5 1.3 - - - +
383B MET 2.8 13.1 + - - -
384B LEU 3.1 3.1 + - - -
386B ALA* 1.3 75.3 - - - +
388B LEU* 1.3 60.7 + - - +
390B GLY* 3.2 4.5 + - - -
391B ILE* 3.2 24.3 + - - +
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Residues in contact with LEU 388 (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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118B TYR* 4.0 33.9 - - + -
119B LEU* 3.7 35.9 - - + -
122B THR* 4.7 4.0 - - + -
124B ILE* 4.0 24.4 - - + +
281B LEU* 4.2 8.1 - - + -
305B TYR* 5.0 0.2 - - + -
384B LEU* 2.7 42.2 + - + +
385B MET* 3.9 6.1 - - - +
387B GLY* 1.3 70.1 - - - +
389B ASP* 1.3 59.9 + - - +
391B ILE* 3.1 17.5 + - + +
392B LYS* 2.9 32.2 + - - +
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Residues in contact with ASP 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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312B HIS* 2.7 30.5 + - - +
385B MET 2.9 19.6 + - - +
386B ALA 3.7 4.9 - - - +
388B LEU* 1.3 75.4 - - - +
390B GLY* 1.3 57.1 + - - +
392B LYS* 4.4 6.0 - - - +
393B ASN* 3.0 59.2 + - - +
395B ILE* 4.0 5.6 - - - +
436B TYR* 3.8 19.3 - - + +
439B GLU* 5.0 9.3 - - + +
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Residues in contact with GLY 390 (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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304B HIS* 3.4 22.2 - - - +
308B GLY* 3.7 6.7 - - - -
386B ALA 3.1 10.5 + - - -
387B GLY 3.2 2.2 + - - -
388B LEU 3.2 0.4 - - - -
389B ASP* 1.3 77.9 - - - +
391B ILE* 1.3 55.9 + - - +
394B LYS* 2.9 9.5 + - - -
395B ILE* 2.8 43.4 + - - +
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Residues in contact with ILE 391 (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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124B ILE* 3.8 30.5 - - + -
281B LEU* 3.6 31.4 - - + -
301B THR* 3.6 40.6 - - + +
304B HIS* 3.8 10.1 + - + +
305B TYR* 3.8 12.3 - - + +
387B GLY 3.2 13.9 + - - +
388B LEU* 3.1 11.8 + - + +
390B GLY* 1.3 73.4 - - - +
392B LYS* 1.3 67.8 + - - +
394B LYS* 3.1 20.6 + - - +
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Residues in contact with LYS 392 (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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118B TYR* 3.3 18.2 + - - +
122B THR* 3.3 33.5 - - - +
124B ILE* 4.1 19.2 - - - +
388B LEU* 2.9 16.2 + - - +
389B ASP* 3.9 9.0 - - - +
391B ILE* 1.3 79.6 - - - +
393B ASN* 1.3 63.8 + - - +
394B LYS* 3.3 6.1 + - - +
439B GLU* 5.9 3.8 - - - +
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Residues in contact with ASN 393 (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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389B ASP* 3.0 51.0 + - - +
392B LYS* 1.3 81.7 - - - +
394B LYS* 1.3 71.3 + - - +
395B ILE* 3.2 17.3 + - + +
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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