Contacts of the helix formed by residues 323 - 340 (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 THR 323 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B VAL* 3.4 12.2 - - - +
300B ILE* 4.3 8.7 - - + -
301B ASN* 3.8 18.4 - - - +
316B GLU* 4.8 0.9 + - - -
320B THR* 4.2 14.0 + - - +
321B GLY 3.5 10.3 + - - +
322B PRO* 1.3 80.4 - - - +
324B VAL* 1.3 65.5 + - - +
325B ALA* 3.3 14.0 + - - +
326B THR* 2.7 46.6 + - - +
327B ASP 3.0 6.1 + - - -
378B PRO* 5.3 0.3 - - - +
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Residues in contact with VAL 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B HIS* 3.7 42.2 - - + +
273B VAL* 4.4 0.4 - - - +
300B ILE* 4.1 17.9 - - + +
323B THR* 1.3 71.8 - - - +
325B ALA* 1.3 57.7 + - - +
327B ASP* 3.0 10.5 + - - +
328B ILE* 2.8 40.0 + - + +
383B THR 3.6 24.2 - - - +
384B THR* 4.3 7.2 - - + -
385B ALA 4.6 0.2 - - - +
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Residues in contact with ALA 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B THR* 3.3 11.3 + - - +
324B VAL* 1.3 79.2 - - - +
326B THR* 1.3 61.8 + - - +
328B ILE* 3.2 10.8 + - - +
329B TYR 3.1 15.1 + - - -
378B PRO* 3.6 39.0 - - + +
381B ARG* 2.9 19.4 + - + +
382B PHE 5.2 2.0 - - - +
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Residues in contact with THR 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B VAL* 4.4 2.4 - - - +
275B ASN* 4.5 1.9 + - - -
314B ALA* 3.8 17.9 - - + +
316B GLU* 3.5 20.6 - - - +
317B ILE* 4.3 19.8 - - + +
320B THR* 4.4 2.0 - - - +
321B GLY 4.0 11.4 - - - +
322B PRO* 3.6 7.1 - - - +
323B THR* 2.7 48.9 + - - +
325B ALA* 1.3 75.1 - - - +
327B ASP* 1.3 61.5 + - - +
329B TYR* 3.2 17.0 + - - +
330B THR* 3.3 14.7 + - - +
381B ARG* 3.8 4.5 - - - +
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Residues in contact with ASP 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU* 4.4 7.7 - - + +
268B HIS* 2.6 34.2 + - + +
273B VAL* 3.0 16.4 - - + +
274B TYR* 3.0 24.7 + - - +
275B ASN* 2.9 28.1 + - - +
277B LEU* 5.8 0.9 + - - +
323B THR 3.0 5.3 + - - -
324B VAL 3.3 7.6 - - - +
326B THR* 1.3 78.7 + - - +
328B ILE* 1.3 60.4 + - - +
330B THR* 2.7 28.5 + - - +
331B VAL* 3.3 12.1 + - - +
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Residues in contact with ILE 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B HIS* 5.7 0.7 - - + -
324B VAL* 2.8 42.3 + - + +
325B ALA* 3.2 8.3 + - - +
327B ASP* 1.3 69.8 - - + +
329B TYR* 1.3 66.3 + - - +
331B VAL* 3.1 19.6 + - + +
332B GLY 3.2 10.4 + - - -
373B ALA* 3.7 23.9 - - - +
381B ARG* 3.9 15.7 - - + -
382B PHE* 2.9 35.2 - - + +
384B THR 4.0 16.6 - - - +
385B ALA* 4.7 7.2 - - + +
388B MET* 4.2 19.7 - - - -
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Residues in contact with TYR 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B PHE 3.1 24.5 - - - -
313B GLN 3.2 25.0 + - - -
314B ALA* 3.5 13.0 - - + -
315B PRO* 3.7 19.0 - - + +
325B ALA 3.1 12.2 + - - +
326B THR 3.2 10.5 + - - +
328B ILE* 1.3 77.6 - - - +
330B THR* 1.3 56.5 + - - +
332B GLY* 3.3 2.6 + - - -
333B ARG* 3.0 57.9 + - + +
351B ASP* 4.2 19.8 + - - +
352B GLY 5.0 1.7 + - - -
373B ALA 3.4 10.5 + - - -
374B ILE* 3.3 40.8 - - + +
381B ARG* 3.7 23.3 - - - +
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Residues in contact with THR 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B LEU* 5.7 0.3 - - - +
275B ASN* 4.1 21.8 - - - +
277B LEU* 3.4 35.0 - - - +
312B PHE* 3.6 24.9 - - + +
313B GLN* 4.9 4.0 - - - -
326B THR 3.3 14.3 + - - +
327B ASP* 2.7 24.4 + - - +
329B TYR* 1.3 73.0 - - + +
331B VAL* 1.3 54.3 + - - +
333B ARG* 3.9 2.5 - - - +
334B THR* 2.6 41.3 + - - -
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Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B LEU* 3.7 21.5 - - + +
261B LEU* 4.1 15.3 - - + -
264B LEU* 3.7 26.7 - - + -
277B LEU* 3.7 12.8 - - + -
327B ASP 3.5 13.7 - - - +
328B ILE* 3.1 13.3 + - + +
330B THR* 1.3 76.2 + - - +
332B GLY* 1.3 62.8 + - - +
334B THR* 3.2 3.5 + - - -
335B LEU* 3.0 29.3 + - + +
388B MET* 3.5 27.8 - - + -
392B LEU* 5.0 0.9 - - + -
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Residues in contact with GLY 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ILE 3.2 8.7 + - - -
329B TYR 3.3 0.2 + - - -
331B VAL* 1.3 78.7 - - - +
333B ARG* 1.3 56.0 + - - +
335B LEU* 3.4 3.8 + - - -
336B ALA* 3.0 28.2 + - - +
370B LEU* 3.7 16.7 - - - +
373B ALA* 3.7 15.1 - - - +
374B ILE* 3.6 21.1 - - - +
388B MET* 4.7 0.2 - - - -
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Residues in contact with ARG 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B GLY 3.2 22.4 + - - -
312B PHE* 3.7 26.0 - - + +
329B TYR* 3.0 57.0 + - + +
330B THR 3.9 2.0 - - - +
332B GLY* 1.3 72.6 - - - +
334B THR* 1.3 60.5 + - - +
336B ALA* 3.6 5.6 + - - +
337B ALA* 2.9 30.5 + - - +
342B LEU* 4.6 13.6 - - - +
349B TYR* 3.7 14.5 + - - +
350B VAL 2.7 26.4 + - - -
351B ASP* 4.0 6.7 + - - +
352B GLY* 3.1 37.4 + - - +
353B LEU* 5.0 3.4 - - - +
374B ILE* 3.9 15.9 - - + +
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Residues in contact with THR 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B LEU* 3.8 26.0 - - + -
277B LEU* 3.4 21.5 + - - +
278B LYS* 3.6 3.6 - - - -
279B PRO* 4.1 14.8 - - + -
282B ILE* 4.0 18.6 - - + -
312B PHE* 3.8 8.4 - - - -
330B THR 2.6 28.8 + - - -
331B VAL 3.6 4.5 - - - -
333B ARG* 1.3 74.2 - - - +
335B LEU* 1.3 61.3 + - - +
337B ALA* 3.3 2.3 + - - +
338B LEU* 3.0 32.0 + - + +
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Residues in contact with LEU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ALA* 4.0 2.9 - - + -
254B ILE* 3.8 34.5 - - + +
257B LEU* 3.6 26.5 - - + -
331B VAL* 3.0 25.0 + - + +
332B GLY* 4.7 0.2 - - - -
334B THR* 1.3 74.5 - - - +
336B ALA* 1.3 58.8 + - - +
338B LEU* 3.2 6.4 + - - +
339B THR* 2.6 35.0 + - - +
366B TYR* 3.4 13.6 + - + +
369B LEU* 4.1 9.0 - - + -
370B LEU* 3.7 20.4 - - + -
388B MET* 4.5 2.0 - - + -
392B LEU* 4.1 27.8 - - + -
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Residues in contact with ALA 336 (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 3.0 18.7 + - - +
333B ARG* 3.8 10.3 - - - +
335B LEU* 1.3 75.9 - - - +
337B ALA* 1.3 56.6 + - - +
339B THR* 3.7 5.2 - - - -
340B LEU* 2.7 45.3 + - + +
342B LEU* 3.6 14.3 - - + +
353B LEU* 4.1 25.6 - - + -
370B LEU* 4.1 7.0 - - + +
374B ILE* 6.0 0.2 - - + -
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Residues in contact with ALA 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LYS* 2.8 30.5 + - - +
279B PRO* 4.7 6.3 - - + -
312B PHE* 3.9 13.2 - - + -
333B ARG 2.9 18.7 + - - +
334B THR 3.7 4.5 - - - +
336B ALA* 1.3 75.4 - - - +
338B LEU* 1.3 59.8 + - - +
339B THR 3.4 0.5 + - - -
340B LEU 3.8 0.5 - - - +
342B LEU* 3.5 13.0 - - + +
349B TYR* 3.7 31.7 + - + +
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Residues in contact with LEU 338 (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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240B LEU* 3.6 47.6 - - + +
246B GLN 4.7 2.0 - - - +
247B LYS* 3.6 6.8 - - - -
248B LEU* 2.8 45.5 + - + +
253B ALA* 4.1 22.4 - - + -
257B LEU* 3.6 28.0 - - + -
279B PRO* 3.8 15.9 - - + -
334B THR* 3.0 27.0 + - + +
335B LEU* 3.7 4.3 - - - +
337B ALA* 1.3 77.5 - - - +
339B THR* 1.3 53.2 + - - +
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Residues in contact with THR 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LYS* 4.3 10.9 - - - +
248B LEU 3.9 11.8 - - - +
250B VAL* 3.9 24.6 - - - +
253B ALA* 3.5 28.7 - - + -
335B LEU 2.6 18.2 + - - +
336B ALA* 3.5 4.2 + - - -
338B LEU* 1.3 78.2 - - - +
340B LEU* 1.3 70.1 + - - +
359B VAL* 4.2 13.9 - - - +
366B TYR* 2.6 34.7 + - + +
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Residues in contact with LEU 340 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LYS* 3.3 24.9 + - - -
336B ALA* 2.7 27.0 + - + +
337B ALA 3.8 0.7 - - - +
339B THR* 1.3 89.4 - - - +
341B ASP* 1.3 60.8 + - - +
342B LEU* 3.0 29.9 + - + +
353B LEU* 4.2 6.7 - - + -
354B PRO* 4.2 7.6 - - + -
357B ASP* 3.4 28.7 - - - +
359B VAL* 3.8 18.8 - - + -
360B LEU* 4.1 28.3 - - + -
366B TYR* 4.9 0.4 - - + -
370B LEU* 4.1 14.4 - - + -
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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
------------------------------------------------------------
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