Contacts of the helix formed by residues 375 - 393 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C CYS* 3.6 2.7 - - - -
27C ASP 3.3 6.5 + - - -
28C LEU 2.8 24.6 + - - +
29C PRO 3.5 9.4 - - - +
30C GLY* 3.6 7.8 - - - -
108C PRO* 3.3 24.4 - - - +
319C PHE 4.7 4.1 + - - +
322C PRO* 4.8 2.0 - - - +
374C GLY* 1.3 72.1 - - - -
376C PRO* 1.3 56.9 - - - +
377C TYR* 3.0 31.5 + - - +
378C LEU* 3.1 20.1 + - + +
379C ALA* 2.7 36.7 + - - +
451C TRP* 4.7 4.6 - - + -
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Residues in contact with PRO 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C ALA* 4.1 14.4 - - + +
242C MET* 4.1 25.4 - - + -
243C GLN* 3.5 41.7 - - + +
246C LYS* 5.7 2.5 - - - +
275C MET* 5.1 6.7 - - + -
374C GLY 3.8 7.4 - - - +
375C ASN* 1.3 82.4 - - - +
377C TYR* 1.3 62.0 + - + +
379C ALA* 4.1 8.1 - - + -
380C PHE* 2.8 47.1 + - + -
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Residues in contact with TYR 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C CYS* 3.9 14.8 - - + -
32C MET* 4.2 2.6 - - - +
92C ASN* 3.8 6.1 + - - -
108C PRO* 3.2 33.2 - - + +
109C ARG* 3.6 30.8 + - + -
112C ALA* 4.1 12.5 - - + +
236C LEU* 4.1 4.3 - - + -
239C ALA* 3.4 26.0 - - + -
240C ASP* 2.5 34.5 + - - -
243C GLN* 3.5 39.0 - - + +
375C ASN* 3.0 19.5 + - - +
376C PRO* 1.3 81.3 - - + +
378C LEU* 1.3 60.8 + - - +
380C PHE* 4.3 1.7 - - - +
381C SER* 2.8 28.2 + - - -
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Residues in contact with LEU 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C LEU* 3.9 18.8 - - + +
108C PRO* 4.0 11.2 - - + -
111C ILE* 3.7 36.8 - - + -
319C PHE* 4.0 22.7 - - + +
375C ASN* 3.1 18.9 + - + +
377C TYR* 1.3 73.2 - - - +
379C ALA* 1.3 61.5 + - - +
381C SER* 4.4 2.9 - - - -
382C ALA* 2.8 33.9 + - - +
443C PHE* 3.7 6.9 - - + -
447C LEU* 4.4 10.8 - - + -
451C TRP* 3.6 37.0 - - + -
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Residues in contact with ALA 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C MET* 4.5 9.9 - - + -
319C PHE* 3.5 27.1 + - - +
320C THR* 4.3 5.2 - - - +
371C ASP 5.9 0.4 - - - +
375C ASN 2.7 22.3 + - - +
376C PRO* 4.0 8.1 - - + +
378C LEU* 1.3 75.2 - - - +
380C PHE* 1.3 64.1 + - + +
382C ALA* 3.7 1.6 - - - +
383C MET* 3.0 44.1 + - + +
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Residues in contact with PHE 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C PHE* 3.4 44.9 - + + -
132C ALA* 4.2 20.9 - - + -
235C LEU* 3.9 22.4 - - + -
238C ALA* 3.7 16.2 - - + -
239C ALA* 3.7 34.8 - - + -
242C MET* 4.7 6.3 - - + -
275C MET* 4.0 12.6 - - + -
277C CYS* 3.6 22.4 - - - -
376C PRO* 2.8 33.0 + - + +
379C ALA* 1.3 74.0 - - + +
381C SER* 1.3 61.7 + - - +
383C MET* 3.3 10.9 + - + +
384C LEU* 3.1 18.0 + - - +
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Residues in contact with SER 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C ILE* 3.8 17.7 - - - -
112C ALA* 3.4 25.5 + - - -
115C ALA* 3.6 14.1 - - - +
235C LEU* 3.9 11.2 - - - +
377C TYR 2.8 21.9 + - - -
378C LEU 3.7 3.1 - - - -
379C ALA 3.2 0.2 - - - -
380C PHE* 1.3 78.1 - - - +
382C ALA* 1.3 57.7 + - - +
384C LEU* 3.1 4.5 + - - +
385C MET* 2.9 31.4 + - - +
443C PHE* 4.0 7.6 - - - -
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Residues in contact with ALA 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316C LEU* 3.5 23.3 - - + +
319C PHE* 3.9 20.2 - - + -
378C LEU 2.8 21.7 + - - +
379C ALA* 3.7 3.1 - - - +
381C SER* 1.3 73.5 - - - +
383C MET* 1.3 62.9 + - - +
385C MET* 3.3 3.1 + - - +
386C ALA* 3.0 19.8 + - - +
437C LEU* 3.8 26.0 - - + +
443C PHE* 3.8 5.3 - - + -
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Residues in contact with MET 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C PHE* 4.2 6.3 - - + -
275C MET* 4.5 0.4 - - + -
277C CYS* 3.6 32.1 - - - -
279C GLN* 3.6 34.5 - - - +
305C TYR* 3.7 2.7 + - - -
309C LEU* 3.6 13.9 - - + +
316C LEU* 3.9 6.7 - - + -
320C THR* 3.8 17.7 - - + -
367C PHE* 3.9 16.6 - - + -
370C PRO* 3.7 17.0 - - + -
379C ALA* 3.0 37.2 + - + +
380C PHE* 3.5 10.1 - - + +
381C SER 3.3 0.2 - - - -
382C ALA* 1.3 74.8 - - - +
384C LEU* 1.3 58.2 + - - +
386C ALA 3.3 0.9 + - - -
387C GLY* 2.8 26.0 + - - -
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Residues in contact with LEU 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ALA* 3.8 26.9 - - + +
116C GLU* 5.2 0.7 - - - -
119C LEU* 4.2 14.4 - - + -
128C ALA* 3.9 23.8 - - + -
130C PHE* 4.4 2.7 - - + -
235C LEU* 3.7 24.2 - - + -
281C LEU* 3.9 13.5 - - + -
305C TYR* 3.5 18.6 + - + +
380C PHE 3.1 12.9 + - - +
381C SER 3.1 8.3 + - - +
383C MET* 1.3 75.1 - - - +
385C MET* 1.3 55.7 + - - +
387C GLY* 3.2 1.7 + - - -
388C LEU* 2.8 60.0 + - + +
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Residues in contact with MET 385 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C ALA* 5.1 5.6 - - - -
118C TYR* 3.7 29.2 - - + -
381C SER 2.9 19.6 + - - +
382C ALA 3.3 6.0 + - - +
384C LEU* 1.3 79.5 - - - +
386C ALA* 1.3 60.6 + - - +
388C LEU* 3.9 6.2 - - - +
389C ASP* 3.0 25.3 + - - +
436C TYR* 3.5 30.1 - - + +
437C LEU* 4.0 13.0 - - + +
439C GLU* 3.3 28.9 - - + +
442C VAL* 3.6 35.7 - - + -
443C PHE* 4.3 7.6 - - + -
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Residues in contact with ALA 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C GLY* 3.3 19.3 - - - +
309C LEU* 4.3 1.8 - - + -
312C HIS* 3.9 18.7 - - + -
316C LEU* 4.1 16.4 - - + -
382C ALA 3.0 13.7 + - - +
383C MET 3.7 6.1 - - - +
385C MET* 1.3 76.9 - - - +
387C GLY* 1.3 62.9 + - - +
389C ASP* 3.5 2.9 + - - +
390C GLY 3.2 16.8 + - - -
436C TYR* 3.7 23.9 - - + -
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Residues in contact with GLY 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C TYR* 3.6 46.8 - - - -
309C LEU* 4.4 1.5 - - - +
383C MET 2.8 14.6 + - - -
384C LEU 3.6 2.9 - - - -
386C ALA* 1.3 78.4 - - - +
388C LEU* 1.3 58.9 + - - +
390C GLY 3.3 1.7 + - - -
391C ILE* 3.2 25.1 + - - +
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Residues in contact with LEU 388 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C TYR* 3.9 34.3 - - + -
119C LEU* 3.8 36.1 - - + -
122C THR* 4.6 3.4 - - + -
124C ILE* 4.1 20.8 - - + +
281C LEU* 4.2 3.8 - - + -
305C TYR* 5.0 0.2 - - + -
384C LEU* 2.8 46.8 + - + +
385C MET* 4.0 6.1 - - - +
387C GLY* 1.3 69.9 - - - +
389C ASP* 1.3 58.6 + - - +
390C GLY 3.2 0.4 - - - -
391C ILE* 3.2 21.3 + - + +
392C LYS* 2.9 33.5 + - - +
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Residues in contact with ASP 389 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C HIS* 2.7 30.5 + - - +
385C MET 3.0 19.0 + - - +
386C ALA 3.7 4.7 - - - +
388C LEU* 1.3 74.4 - - - +
390C GLY* 1.3 57.6 + - - +
392C LYS* 4.3 5.6 - - - +
393C ASN* 2.9 59.3 + - - +
395C ILE* 4.0 6.4 - - - +
436C TYR* 3.9 18.4 - - + +
439C GLU* 4.9 10.0 - - + +
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Residues in contact with GLY 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C HIS* 3.4 22.2 - - - +
308C GLY* 3.8 7.6 - - - -
386C ALA 3.2 10.5 + - - -
387C GLY 3.7 2.0 - - - -
388C LEU 3.2 0.4 - - - -
389C ASP* 1.3 77.6 + - - +
391C ILE* 1.3 55.3 + - - +
394C LYS* 2.8 24.9 + - - -
395C ILE* 2.9 27.9 + - - -
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Residues in contact with ILE 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ILE* 3.8 30.1 - - + -
281C LEU* 3.6 31.0 - - + -
301C THR* 3.5 39.5 - - + +
304C HIS* 3.8 8.9 + - + +
305C TYR* 3.8 11.2 - - + +
387C GLY 3.2 15.6 + - - +
388C LEU* 3.2 12.1 + - + +
390C GLY* 1.3 71.3 - - - +
392C LYS* 1.3 67.8 + - - +
394C LYS* 3.1 21.3 + - - +
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Residues in contact with LYS 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C TYR* 3.3 26.6 + - - +
122C THR* 3.3 25.7 - - - +
124C ILE* 4.1 19.9 - - - +
388C LEU* 2.9 17.1 + - - +
389C ASP* 3.8 8.7 - - - +
391C ILE* 1.3 81.1 - - - +
393C ASN* 1.3 64.2 + - - +
394C LYS* 3.6 5.5 + - - +
439C GLU* 5.8 4.0 - - - +
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Residues in contact with ASN 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389C ASP* 2.9 52.0 + - - +
392C LYS* 1.3 82.1 - - - +
394C LYS* 1.3 70.8 + - - +
395C ILE* 3.1 16.9 + - + +
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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