Contacts of the helix formed by residues 363 - 374 (chain A) in PDB entry 2PZI
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 TYR 363 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A VAL* 3.7 32.4 + - + -
359A VAL* 3.0 19.1 + - + +
360A LEU* 3.4 10.4 - - - +
362A THR* 1.3 101.3 - - - +
364A ASP* 1.3 64.5 + - - +
365A SER 3.5 2.2 - - - -
366A TYR* 3.4 20.2 + - + +
367A GLY 3.3 14.2 + - - -
399A VAL* 3.7 42.2 - - + -
402A GLN* 3.8 18.7 + - - -
403A ASP* 2.9 26.8 + - - +
756A GOL 4.2 6.1 - - - +
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Residues in contact with ASP 364 (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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360A LEU 3.9 9.6 + - - +
361A LYS 4.3 4.5 + - - +
362A THR 3.8 3.0 + - - -
363A TYR* 1.3 72.5 - - - +
365A SER* 1.3 62.9 + - - +
367A GLY* 3.1 12.8 + - - -
368A ARG* 2.8 50.5 + - - +
371A ARG* 5.7 0.2 + - - -
589A HIS* 3.7 24.8 + - + +
591A PHE* 3.9 4.7 - - - -
756A GOL 2.6 34.4 + - - +
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Residues in contact with SER 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ASP* 1.3 77.9 + - - +
366A TYR* 1.3 61.7 + - - +
368A ARG* 3.3 8.8 + - - +
369A LEU* 2.9 30.0 + - - +
395A VAL* 3.5 17.0 - - - +
398A GLU* 2.7 13.0 + - - +
399A VAL* 5.7 0.7 - - - +
567A PRO* 3.0 32.5 - - - +
573A LYS* 3.9 6.1 - - - -
756A GOL 2.6 25.2 + - - -
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Residues in contact with TYR 366 (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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250A VAL* 4.0 30.1 - - + -
254A ILE* 3.8 31.2 - - + -
335A LEU* 3.2 27.2 + - + +
339A THR* 2.7 33.6 + - + +
340A LEU* 4.8 0.4 - - + -
359A VAL* 4.5 4.5 - - + -
360A LEU* 4.1 15.0 - - + -
363A TYR* 3.4 21.8 + - + +
364A ASP 3.2 0.8 - - - -
365A SER* 1.3 80.9 + - - +
367A GLY* 1.3 60.6 + - - +
369A LEU* 3.4 7.6 + - + +
370A LEU* 3.1 56.4 + - + +
392A LEU* 5.0 0.7 - - + -
395A VAL* 3.7 15.7 - - + -
399A VAL* 4.7 3.3 - - + +
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Residues in contact with GLY 367 (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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353A LEU* 4.3 0.7 - - - +
360A LEU* 3.7 31.1 - - - +
363A TYR 3.3 5.2 + - - -
364A ASP 3.1 8.2 + - - -
366A TYR* 1.3 80.9 - - - +
368A ARG* 1.3 55.7 + - - +
370A LEU* 3.3 5.0 + - - +
371A ARG* 3.1 42.2 + - - +
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Residues in contact with ARG 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ASP* 2.8 44.6 + - - +
365A SER* 3.3 11.1 + - - +
367A GLY* 1.3 72.7 - - - +
369A LEU* 1.3 64.9 + - - +
371A ARG* 3.5 27.8 + - - +
372A ARG* 3.2 23.6 + - - +
560A THR* 3.8 14.6 - - - +
563A LEU* 3.7 29.8 - - - +
564A ASP* 2.6 50.8 + - - +
567A PRO* 3.7 14.6 - - + +
589A HIS* 3.8 17.8 + - - -
591A PHE* 3.7 18.4 - - - -
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Residues in contact with LEU 369 (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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335A LEU* 4.4 9.4 - - + -
365A SER 2.9 16.5 + - - +
366A TYR* 3.5 7.6 - - + +
368A ARG* 1.3 75.2 - - - +
370A LEU* 1.3 74.2 + - + +
372A ARG 3.5 0.2 + - - -
373A ALA* 3.1 19.3 + - + +
382A PHE* 3.6 24.6 - - + -
388A MET* 3.8 25.6 - - + +
391A GLN* 3.9 11.2 - - + +
392A LEU* 3.9 49.8 - - + +
395A VAL* 4.3 8.5 - - + -
567A PRO* 3.6 13.2 - - + +
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Residues in contact with LEU 370 (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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332A GLY* 3.9 12.1 - - - +
335A LEU* 3.7 35.2 - - + -
336A ALA* 4.3 3.1 - - + +
340A LEU* 3.9 28.5 - - + -
353A LEU* 4.0 18.2 - - + -
360A LEU* 4.0 11.4 - - + -
366A TYR* 3.1 46.0 + - + +
367A GLY 3.6 6.7 - - - +
368A ARG 3.3 0.2 - - - -
369A LEU* 1.3 80.3 - - + +
371A ARG* 1.3 61.7 + - - +
373A ALA* 3.3 4.6 + - - +
374A ILE* 3.1 31.0 + - + +
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Residues in contact with ARG 371 (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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353A LEU* 3.6 20.5 - - + +
360A LEU* 5.2 5.3 - - - +
364A ASP 5.7 0.2 + - - -
367A GLY* 3.1 30.4 + - - +
368A ARG* 3.7 33.4 - - - +
369A LEU 3.3 0.2 - - - -
370A LEU* 1.3 73.3 - - - +
372A ARG* 1.3 64.7 + - - +
374A ILE* 3.6 9.1 + - + +
375A ASP* 3.1 27.4 + - - +
564A ASP* 4.6 9.1 + - - -
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Residues in contact with ARG 372 (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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368A ARG 3.2 15.0 + - - +
369A LEU 3.8 4.3 - - - +
371A ARG* 1.3 77.8 - - - +
373A ALA* 1.3 65.1 + - - +
375A ASP* 3.2 10.5 + - - +
379A ARG 5.2 1.4 + - - -
380A GLN* 3.2 22.4 + - - +
381A ARG* 3.2 45.0 + - - +
382A PHE* 3.7 32.4 - - + +
383A THR* 5.0 1.8 + - - +
387A GLU* 2.9 26.6 + - - -
564A ASP 3.6 17.9 - - - +
565A THR* 2.9 49.6 + - - +
566A PHE* 4.4 3.4 - - - -
567A PRO* 5.6 0.2 - - + -
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Residues in contact with ALA 373 (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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328A ILE* 3.7 15.2 - - + +
329A TYR* 3.4 12.9 + - - -
332A GLY* 3.8 16.2 - - - -
369A LEU* 3.1 15.5 + - + +
370A LEU* 3.3 5.6 + - - +
372A ARG* 1.3 78.7 - - - +
374A ILE* 1.3 58.5 + - - +
381A ARG* 3.1 22.7 - - - +
382A PHE* 3.7 5.6 - - + -
388A MET* 3.7 28.0 - - + -
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Residues in contact with ILE 374 (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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329A TYR* 3.2 34.3 - - + +
332A GLY* 3.8 7.0 - - - +
333A ARG* 3.7 47.3 - - + +
336A ALA* 6.3 0.4 - - + -
352A GLY* 4.2 19.7 - - - +
353A LEU* 4.0 33.4 - - + -
370A LEU* 3.1 20.8 + - + +
371A ARG* 3.9 7.9 - - + +
372A ARG 3.2 0.2 - - - -
373A ALA* 1.3 75.2 - - - +
375A ASP* 1.3 68.6 + - - +
376A PRO* 3.3 5.4 - - - +
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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