Contacts of the helix formed by residues 363 - 374 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250B VAL* 3.5 37.1 + - + +
359B VAL* 3.1 26.4 + - + +
360B LEU* 3.1 13.2 - - - +
362B THR* 1.3 87.7 - - + +
364B ASP* 1.3 65.1 + - - +
365B SER* 3.3 3.0 + - - +
366B TYR* 3.4 18.1 + + + +
367B GLY 3.3 14.4 + - - -
398B GLU 5.3 0.4 - - - -
399B VAL* 3.7 33.7 - - + -
402B GLN* 3.6 22.4 - - - -
403B ASP* 2.7 33.6 + - - -
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Residues in contact with ASP 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B LEU 3.8 8.9 - - - +
361B LYS 4.6 4.9 + - - +
362B THR 3.8 3.6 + - - -
363B TYR* 1.3 73.9 - - - +
365B SER* 1.3 61.3 + - - +
367B GLY* 3.6 1.9 + - - -
368B ARG* 2.7 63.6 + - - +
371B ARG* 5.9 0.2 + - - -
573B LYS* 5.4 2.2 - - - -
589B HIS* 3.5 29.8 + - - +
591B PHE* 4.1 10.9 - - + -
594B THR* 5.9 2.2 - - - +
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Residues in contact with SER 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B TYR* 3.3 1.1 - - - +
364B ASP* 1.3 76.7 - - - +
366B TYR* 1.3 62.2 + - - +
368B ARG* 3.2 12.9 + - - +
369B LEU* 2.9 28.1 + - - +
395B VAL* 3.6 19.3 - - - +
398B GLU* 2.9 26.5 + - - +
399B VAL* 5.4 1.4 - - - +
567B PRO* 3.2 28.0 - - - +
573B LYS* 4.1 8.3 - - - -
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Residues in contact with TYR 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B VAL* 3.9 26.5 - - + -
254B ILE* 3.8 32.8 - - + -
335B LEU* 3.4 23.3 + - + +
339B THR* 2.6 41.4 + - + +
340B LEU* 4.9 0.4 - - + -
359B VAL* 4.7 3.8 - - + -
360B LEU* 3.7 20.4 - - + -
363B TYR* 3.4 21.9 + - + +
364B ASP 3.4 0.2 - - - -
365B SER* 1.3 77.6 + - - +
367B GLY* 1.3 63.4 + - - +
369B LEU* 2.9 10.9 + - + +
370B LEU* 2.9 48.8 + - + +
392B LEU* 5.3 0.2 - - + -
395B VAL* 3.7 14.8 - - + +
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Residues in contact with GLY 367 (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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353B LEU* 4.7 1.7 - - - +
360B LEU* 3.6 33.5 - - - +
363B TYR 3.3 9.3 + - - -
364B ASP 3.9 3.6 - - - -
366B TYR* 1.3 79.0 - - - +
368B ARG* 1.3 62.6 + - - +
370B LEU* 3.2 3.5 + - - +
371B ARG* 3.0 31.1 + - - +
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Residues in contact with ARG 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B ASP* 2.7 56.6 + - - +
365B SER* 3.2 12.9 + - - +
367B GLY* 1.3 75.6 - - - +
369B LEU* 1.3 60.9 + - - +
371B ARG* 3.6 34.9 + - - +
372B ARG* 3.2 21.8 + - - +
560B THR* 3.5 23.6 + - - +
563B LEU* 3.6 33.8 - - - +
564B ASP* 2.9 31.5 + - - +
567B PRO* 3.7 14.3 - - + +
573B LYS* 5.9 0.2 - - - +
589B HIS* 4.3 12.9 + - - -
591B PHE* 4.1 10.7 - - - -
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Residues in contact with LEU 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B LEU* 4.1 11.0 - - + -
365B SER 2.9 13.4 + - - +
366B TYR* 2.9 11.0 + - + +
368B ARG* 1.3 75.0 - - - +
370B LEU* 1.3 69.8 + - + +
372B ARG 3.4 0.7 + - - -
373B ALA* 3.1 19.1 + - - +
382B PHE* 3.5 23.0 - - + -
388B MET* 4.0 19.7 - - + +
391B GLN* 3.9 5.2 - - + -
392B LEU* 3.6 56.8 - - + +
395B VAL* 3.7 15.7 - - + -
567B PRO* 3.7 11.9 - - + +
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Residues in contact with LEU 370 (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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332B GLY* 3.7 15.5 - - - +
335B LEU* 3.7 40.6 - - + -
336B ALA* 4.1 8.7 - - + +
340B LEU* 4.1 17.7 - - + -
353B LEU* 4.2 14.1 - - + -
360B LEU* 3.8 26.9 - - + -
366B TYR* 2.9 34.9 + - + +
367B GLY 3.6 6.1 - - - +
369B LEU* 1.3 76.1 - - + +
371B ARG* 1.3 63.4 + - - +
373B ALA* 3.0 15.6 + - - +
374B ILE* 3.1 19.5 + - + +
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Residues in contact with ARG 371 (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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353B LEU* 4.0 17.2 - - + +
367B GLY 3.0 13.0 + - - +
368B ARG* 3.6 51.6 + - - +
370B LEU* 1.3 76.2 - - - +
372B ARG* 1.3 62.8 + - - +
374B ILE* 3.5 7.7 + - - +
375B ASP* 3.2 23.4 + - - +
564B ASP* 3.6 26.9 + - - +
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Residues in contact with ARG 372 (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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368B ARG 3.2 13.8 + - - +
369B LEU* 4.8 0.2 - - - -
370B LEU 3.2 0.2 - - - -
371B ARG* 1.3 77.7 - - - +
373B ALA* 1.3 65.8 + - - +
374B ILE 3.2 1.2 + - - -
375B ASP* 3.2 19.6 + - - +
379B ARG 5.6 0.8 + - - -
380B GLN* 3.1 22.4 + - - +
381B ARG* 3.4 24.8 + - - -
382B PHE* 3.2 44.2 - - + +
383B THR* 4.6 3.6 + - - +
387B GLU* 3.2 24.0 + - - -
564B ASP 3.6 22.0 - - - +
565B THR* 2.7 48.0 + - - +
566B PHE* 4.8 3.0 - - - -
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Residues in contact with ALA 373 (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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328B ILE* 3.7 8.0 - - - +
329B TYR* 3.4 13.0 + - - -
332B GLY* 3.7 23.3 - - - -
369B LEU* 3.1 13.4 + - + +
370B LEU* 3.0 9.6 + - - +
372B ARG* 1.3 77.2 - - - +
374B ILE* 1.3 57.9 + - - +
375B ASP 3.4 0.2 - - - -
381B ARG* 3.3 22.4 - - - -
382B PHE* 3.7 11.1 - - + -
388B MET* 3.8 20.4 - - + -
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Residues in contact with ILE 374 (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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329B TYR* 3.3 32.9 - - + +
332B GLY* 3.6 37.0 - - - +
333B ARG* 3.6 26.0 - - - +
352B GLY* 4.4 10.8 - - - +
353B LEU* 3.7 38.4 - - + -
370B LEU* 3.1 17.2 + - + +
371B ARG* 4.0 6.3 - - - +
373B ALA* 1.3 74.8 - - - +
375B ASP* 1.3 67.0 + - - +
376B PRO* 3.2 6.9 - - - +
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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