Contacts of the helix formed by residues 323 - 340 (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 THR 323 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A VAL* 3.3 16.2 - - - +
300A ILE* 4.6 12.1 - - + -
301A ASN* 5.2 1.1 - - + +
316A GLU* 4.7 0.3 + - - -
320A THR* 4.1 18.7 + - + +
321A GLY 3.6 9.6 - - - +
322A PRO* 1.3 81.2 - - - +
324A VAL* 1.3 66.8 + - - +
325A ALA* 3.2 14.6 - - + +
326A THR* 2.8 42.7 + - - +
327A ASP 3.3 4.2 + - - -
378A PRO* 5.4 0.3 - - - +
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Residues in contact with VAL 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A HIS* 3.9 46.9 - - + +
300A ILE* 4.4 17.1 - - + +
323A THR* 1.3 72.2 - - - +
325A ALA* 1.3 58.6 + - - +
327A ASP* 2.9 21.5 + - - +
328A ILE* 2.9 22.6 + - + +
383A THR 3.5 25.4 - - - +
384A THR* 4.2 9.6 - - + -
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Residues in contact with ALA 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A THR* 3.2 12.1 - - - +
324A VAL* 1.3 79.3 - - - +
326A THR* 1.3 61.7 + - - +
328A ILE* 3.3 12.4 + - - +
329A TYR 3.2 14.2 + - - -
378A PRO* 3.7 39.7 - - + +
381A ARG* 3.2 16.4 + - - +
382A PHE 5.1 4.0 - - - +
383A THR 6.0 0.2 - - - -
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Residues in contact with THR 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A VAL* 4.0 5.4 - - - +
275A ASN* 4.4 1.3 + - - -
314A ALA* 3.7 22.6 + - + +
316A GLU* 3.5 21.3 - - - +
317A ILE* 4.2 19.6 - - + +
320A THR* 4.2 2.2 - - - +
321A GLY 3.9 15.7 - - - +
322A PRO* 3.6 5.5 - - - +
323A THR* 2.8 46.6 + - - +
325A ALA* 1.3 69.2 - - - +
327A ASP* 1.3 62.2 + - - +
329A TYR* 3.4 9.5 - - - +
330A THR* 3.4 19.1 - - - +
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Residues in contact with ASP 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 4.6 9.6 - - + +
268A HIS* 2.9 30.5 + - + +
273A VAL* 3.2 17.1 - - + +
274A TYR* 2.8 29.4 + - - +
275A ASN* 2.9 27.5 + - - +
277A LEU* 5.8 0.6 + - - -
323A THR 3.3 4.2 + - - -
324A VAL 2.9 9.6 + - - +
326A THR* 1.3 75.4 + - - +
328A ILE* 1.3 67.1 + - - +
330A THR* 2.7 28.1 + - - +
331A VAL* 3.3 11.3 + - - +
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Residues in contact with ILE 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 5.5 0.2 - - + -
268A HIS* 5.4 1.8 - - + -
324A VAL* 2.9 26.2 + - + +
325A ALA* 3.4 8.5 - - - +
327A ASP* 1.3 77.1 - - - +
329A TYR* 1.3 61.3 + - - +
331A VAL* 3.2 19.3 + - + +
332A GLY 3.2 9.4 + - - -
373A ALA* 3.7 27.8 - - - +
381A ARG* 4.0 13.0 - - + -
382A PHE* 3.6 27.8 - - + +
384A THR 3.7 23.8 - - - +
385A ALA* 3.8 21.1 - - + +
388A MET* 4.1 14.6 - - - -
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Residues in contact with TYR 329 (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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311A GLY 5.5 0.4 - - - -
312A PHE 3.0 26.0 - - - -
313A GLN 3.2 19.8 + - - -
314A ALA* 3.3 17.9 - - + -
315A PRO* 3.7 20.6 - - + +
325A ALA 3.2 9.5 + - - +
326A THR 3.4 11.0 - - - +
327A ASP 3.2 0.2 - - - -
328A ILE* 1.3 78.7 - - - +
330A THR* 1.3 56.6 + - - +
332A GLY* 3.3 3.3 + - - -
333A ARG* 2.9 56.0 + - + +
351A ASP* 4.3 19.6 + - - +
373A ALA 3.4 10.7 + - - -
374A ILE* 3.2 42.2 - - + +
376A PRO* 5.6 0.2 - - + -
381A ARG* 3.7 18.6 - - - +
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Residues in contact with THR 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 5.7 0.3 - - - +
275A ASN* 4.3 20.0 - - - +
276A ASP* 5.6 0.2 - - - -
277A LEU* 3.4 35.3 - - - +
312A PHE* 3.4 26.2 - - + +
313A GLN* 4.3 6.3 - - + -
326A THR 3.4 14.6 - - - +
327A ASP* 2.7 26.3 + - - +
329A TYR* 1.3 72.3 - - - +
331A VAL* 1.3 53.1 + - - +
333A ARG* 3.8 1.4 - - - +
334A THR* 2.7 42.0 + - - -
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Residues in contact with VAL 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 3.9 19.9 - - + +
261A LEU* 4.1 17.3 - - + -
264A LEU* 3.8 26.2 - - + -
277A LEU* 3.8 11.9 - - + -
327A ASP 3.5 14.6 - - - +
328A ILE* 3.2 13.8 + - + +
330A THR* 1.3 72.9 + - - +
332A GLY* 1.3 62.0 + - - +
334A THR* 3.2 2.0 + - - -
335A LEU* 2.8 37.0 + - + +
388A MET* 3.4 27.6 - - + -
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Residues in contact with GLY 332 (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 3.2 8.1 + - - -
329A TYR 3.3 3.3 + - - -
331A VAL* 1.3 78.9 - - - +
333A ARG* 1.3 59.8 + - - +
335A LEU* 3.3 8.6 + - - +
336A ALA* 3.0 23.7 + - - +
370A LEU* 3.9 12.0 - - - +
373A ALA* 3.8 15.8 - - - +
374A ILE* 3.8 18.1 - - - +
388A MET* 4.9 0.2 - - - -
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Residues in contact with ARG 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A GLY 2.8 25.6 + - - -
312A PHE* 3.4 35.5 - - + +
329A TYR* 2.9 41.5 + - + +
330A THR 3.8 4.3 - - - +
332A GLY* 1.3 75.7 - - - +
334A THR* 1.3 57.1 + - - +
336A ALA* 3.3 9.7 + - - +
337A ALA* 2.8 31.7 + - - +
342A LEU* 4.7 12.4 - - - +
349A TYR* 3.7 15.0 + - - +
350A VAL 2.9 26.6 + - - -
351A ASP* 4.0 6.7 + - - +
352A GLY* 3.2 33.7 + - - +
374A ILE* 3.7 21.6 - - - +
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Residues in contact with THR 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LEU* 3.7 30.1 - - + -
277A LEU* 3.4 8.9 + - - +
278A LYS* 3.4 19.2 - - - -
279A PRO* 4.1 10.8 - - + -
282A ILE* 3.9 17.5 - - + -
312A PHE* 4.1 9.3 - - - -
330A THR 2.7 23.7 + - - -
331A VAL 3.2 5.4 + - - -
333A ARG* 1.3 73.9 - - - +
335A LEU* 1.3 63.8 + - - +
337A ALA* 3.3 2.5 + - - +
338A LEU* 3.0 30.1 + - + +
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Residues in contact with LEU 335 (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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253A ALA* 3.7 25.8 - - + +
254A ILE* 4.1 7.2 - - + +
257A LEU* 3.5 28.9 - - + -
331A VAL* 2.8 29.1 + - + +
332A GLY* 3.6 4.5 - - - +
334A THR* 1.3 77.0 - - - +
336A ALA* 1.3 55.0 + - - +
338A LEU* 3.3 4.3 + - - +
339A THR* 2.6 35.7 + - - +
366A TYR* 3.2 16.2 + - + +
369A LEU* 4.4 8.1 - - + -
370A LEU* 3.7 14.8 - - + -
388A MET* 4.6 0.9 - - + -
392A LEU* 3.9 31.9 - - + -
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Residues in contact with ALA 336 (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 3.0 16.6 + - - +
333A ARG* 3.6 11.2 - - - +
335A LEU* 1.3 72.9 - - - +
337A ALA* 1.3 62.1 + - - +
339A THR* 3.8 4.5 - - - -
340A LEU* 2.9 52.5 + - + +
342A LEU* 3.7 18.9 - - + +
353A LEU* 4.1 13.9 - - + -
370A LEU* 4.3 4.9 - - + +
374A ILE* 6.3 0.4 - - + -
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Residues in contact with ALA 337 (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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247A LYS* 3.4 26.2 + - - -
279A PRO* 4.4 8.1 - - + -
312A PHE* 3.6 24.0 - - + -
333A ARG 2.8 17.2 + - - +
334A THR 3.6 4.9 - - - +
336A ALA* 1.3 77.9 - - - +
338A LEU* 1.3 61.8 + - - +
339A THR 3.4 0.5 + - - -
342A LEU* 3.5 13.0 - - + +
349A TYR* 3.7 21.9 + - + +
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Residues in contact with LEU 338 (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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240A LEU* 3.3 45.1 - - + +
241A LYS 5.3 0.9 - - - -
246A GLN 6.0 0.2 - - - -
247A LYS* 3.6 7.5 - - - -
248A LEU* 2.9 41.2 + - + +
253A ALA* 4.2 20.4 - - + -
257A LEU* 3.7 29.6 - - + -
279A PRO* 3.8 21.3 - - + -
334A THR* 3.0 23.5 + - + +
335A LEU* 3.8 5.4 - - - +
336A ALA 3.2 0.2 - - - -
337A ALA* 1.3 77.0 - - - +
339A THR* 1.3 56.1 + - - +
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Residues in contact with THR 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A LYS* 4.0 11.6 - - - +
248A LEU 3.7 17.7 - - - +
250A VAL* 3.9 19.5 - - - +
253A ALA* 3.5 30.1 - - + -
335A LEU 2.6 19.1 + - - +
336A ALA 3.2 1.8 + - - -
338A LEU* 1.3 78.5 - - - +
340A LEU* 1.3 71.4 + - - +
359A VAL* 4.0 13.3 - - - +
366A TYR* 2.7 30.5 + - - +
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Residues in contact with LEU 340 (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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247A LYS* 3.0 22.6 - - - -
336A ALA* 2.9 23.5 + - + +
339A THR* 1.3 85.7 - - - +
341A ASP* 1.3 59.8 + - - +
342A LEU* 2.9 22.3 + - + +
353A LEU* 3.9 18.8 - - + -
354A PRO* 4.7 5.6 - - + -
357A ASP* 3.6 15.9 - - - +
359A VAL* 3.5 38.4 - - + -
360A LEU* 4.0 17.9 - - + -
366A TYR* 4.8 0.9 - - + -
370A LEU* 3.9 23.6 - - + -
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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