Contacts of the helix formed by residues 368 - 384 (chain A) in PDB entry 4U0Z
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 GLY 368 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A HIS* 4.1 5.7 - - - -
297A VAL* 4.5 6.6 - - - +
298A LEU* 4.9 1.8 - - - -
367A ASP* 1.3 74.5 - - - +
369A ASN* 1.3 56.7 + - - +
370A GLY 3.5 1.8 - - - -
371A ARG* 3.7 18.7 - - - +
372A THR* 2.7 36.7 + - - -
501A APC 2.9 25.4 + - - -
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Residues in contact with ASN 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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359A LEU* 5.0 2.5 - - + +
360A VAL* 4.5 8.3 - - + -
363A HIS* 3.1 45.9 + - + +
364A PRO* 3.4 6.6 - - + +
365A PHE* 2.9 55.5 + - - +
366A ILE 4.2 0.8 + - - -
367A ASP* 4.1 4.8 - - - +
368A GLY* 1.3 69.7 - - - +
370A GLY* 1.3 56.3 + - - +
372A THR* 3.4 2.4 + - - -
373A SER* 2.8 38.7 + - - +
501A APC 2.8 28.4 + - - +
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Residues in contact with GLY 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A VAL* 4.3 4.0 - - - +
369A ASN* 1.3 79.8 - - - +
371A ARG* 1.4 54.0 + - - +
373A SER* 3.5 1.9 + - - -
374A ARG* 2.9 49.6 + - - +
399A TYR* 4.5 0.6 + - - -
501A APC 3.5 39.6 + - - -
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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
----------------------------------------------------------
230A THR* 3.7 19.9 + - - +
231A VAL* 4.6 8.7 - - - +
263A GLU* 3.6 45.2 + - - +
267A MET* 4.0 20.6 - - - +
297A VAL* 3.8 28.1 + - + +
298A LEU* 4.4 12.1 - - - +
367A ASP* 3.6 18.4 + - - -
368A GLY* 3.7 13.8 - - - +
369A ASN 3.3 0.2 - - - -
370A GLY* 1.4 72.5 - - - +
372A THR* 1.4 62.4 + - - +
374A ARG* 3.5 21.8 + - - +
375A LEU* 3.1 29.8 + - - +
501A APC 2.9 40.2 + - - +
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Residues in contact with THR 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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290A VAL* 4.1 25.4 - - + +
293A ILE* 4.3 14.6 - - + +
294A HIS* 3.7 15.8 - - - +
297A VAL* 4.0 10.9 - - - +
359A LEU* 4.0 16.6 - - + -
365A PHE* 4.2 11.2 - - + -
368A GLY 2.7 24.8 + - - -
369A ASN 3.4 3.3 + - - -
371A ARG* 1.4 71.1 - - - +
373A SER* 1.4 55.5 + - - +
375A LEU* 3.4 11.2 + - - +
376A LEU* 2.8 32.2 + - + +
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Residues in contact with SER 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A HIS* 3.7 23.7 - - - +
359A LEU* 3.5 27.0 - - - +
360A VAL* 3.2 27.2 + - - +
369A ASN* 2.8 21.1 + - - +
370A GLY 3.7 2.2 - - - -
372A THR* 1.4 72.3 - - - +
374A ARG* 1.4 54.6 + - - +
376A LEU* 2.9 6.5 + - - +
377A MET* 2.7 36.1 + - - +
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Residues in contact with ARG 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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226A HIS* 4.9 9.5 + - + +
230A THR* 2.9 50.5 + - - +
233A ILE* 3.4 14.6 - - - +
356A HIS* 3.8 8.0 + - + -
370A GLY 2.9 28.5 + - - +
371A ARG* 3.5 15.2 - - - +
372A THR 3.5 0.2 - - - -
373A SER* 1.4 72.8 - - - +
375A LEU* 1.4 58.0 + - + +
377A MET* 3.5 16.4 - - + +
378A ASN* 3.2 30.7 + - - +
391A ILE* 4.2 25.8 - - + +
399A TYR* 3.3 36.1 + - - +
501A APC 3.2 37.0 + - - -
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Residues in contact with LEU 375 (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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226A HIS* 4.1 15.9 - - + -
267A MET* 3.7 24.7 - - + -
270A ALA* 3.6 21.5 - - + -
271A MET* 4.3 14.8 - - + -
274A ILE* 3.8 25.5 - - + +
293A ILE* 3.6 25.8 - - + -
297A VAL* 3.8 11.0 - - + -
371A ARG 3.1 20.5 + - - +
372A THR 3.7 4.0 - - - +
373A SER 3.2 0.2 - - - -
374A ARG* 1.4 73.3 - - + +
376A LEU* 1.3 61.8 + - - +
377A MET 3.2 0.4 - - - -
378A ASN* 3.4 9.1 + - + +
379A LEU* 3.1 24.1 + - - +
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Residues in contact with LEU 376 (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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285A VAL* 4.8 15.9 - - + -
290A VAL* 5.0 9.0 - - + -
293A ILE* 5.2 11.8 - - + +
334A PHE* 3.6 34.3 - - + -
338A LEU* 4.8 4.7 - - + -
355A ALA* 4.7 11.0 - - + +
359A LEU* 3.8 18.2 - - + -
372A THR* 2.8 16.1 + - + +
373A SER* 2.9 8.9 + - - +
375A LEU* 1.3 71.7 - - - +
377A MET* 1.3 64.8 + - - +
379A LEU* 3.2 25.8 + - + +
380A ILE* 3.1 44.2 + - + +
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Residues in contact with MET 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ALA* 3.6 32.0 - - + +
356A HIS* 3.4 30.7 - - + +
373A SER 2.7 16.3 + - - +
374A ARG* 3.5 21.1 - - + +
375A LEU 3.2 0.2 - - - -
376A LEU* 1.3 71.4 - - - +
378A ASN* 1.3 66.2 + - - +
380A ILE* 3.2 10.7 + - - +
381A LEU* 3.1 26.8 + - + +
389A ILE* 3.7 30.7 - - + +
391A ILE* 4.3 13.9 - - + -
418A ILE* 3.9 27.4 - - + -
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Residues in contact with ASN 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A HIS* 3.3 30.7 + - - -
271A MET* 5.8 2.0 - - - +
274A ILE* 6.1 0.2 - - - -
374A ARG 3.2 10.7 + - - +
375A LEU* 3.7 11.8 - - + +
376A LEU 3.3 0.4 - - - -
377A MET* 1.3 78.7 - - - +
379A LEU* 1.4 58.4 + - - +
381A LEU* 3.8 7.6 - - - +
382A MET* 2.9 41.1 + - - +
388A PRO* 3.5 22.1 - - + +
389A ILE* 2.8 37.7 + - - +
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Residues in contact with LEU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A ILE* 3.7 21.5 - - + +
278A LEU* 3.8 33.4 - - + +
279A VAL* 4.3 17.0 - - + +
285A VAL* 5.3 13.5 - - + -
289A ASP* 6.1 0.9 - - + -
293A ILE* 4.7 6.7 - - + -
375A LEU 3.1 12.0 + - - +
376A LEU* 3.2 29.1 + - + +
378A ASN* 1.4 74.7 - - - +
380A ILE* 1.4 56.4 + - + +
382A MET* 3.9 3.1 - - - +
383A GLN* 3.0 63.8 + - + +
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Residues in contact with ILE 380 (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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285A VAL* 5.8 5.8 - - + -
338A LEU* 4.0 21.5 - - + -
348A PRO* 4.2 6.7 - - + +
351A PHE* 3.3 44.2 - - + -
352A ALA* 3.7 21.5 - - + +
355A ALA* 4.3 13.2 - - + -
376A LEU* 3.1 26.0 + - + +
377A MET 3.2 6.5 + - - +
379A LEU* 1.4 77.3 - - + +
381A LEU* 1.4 63.2 + - - +
383A GLN* 3.5 16.4 + - - +
384A ALA* 3.4 18.7 + - - +
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Residues in contact with LEU 381 (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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348A PRO* 4.2 10.8 - - - +
349A VAL* 4.3 20.6 - - + -
352A ALA* 3.8 19.1 - - + -
377A MET* 3.1 23.1 + - + +
378A ASN* 3.8 15.0 - - - +
379A LEU 3.4 0.2 - - - -
380A ILE* 1.4 73.9 - - - +
382A MET* 1.4 58.8 + - + +
384A ALA* 2.9 22.3 + - - +
385A GLY 3.3 0.3 + - - -
386A TYR* 3.1 39.6 + - + +
387A PRO 4.2 5.4 - - - +
389A ILE* 3.8 40.4 - - + -
418A ILE* 5.8 1.1 - - + -
422A THR* 4.2 8.3 - - + -
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Residues in contact with MET 382 (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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274A ILE* 6.3 0.9 - - - -
275A ASN* 3.7 27.1 - - - +
279A VAL* 4.7 24.7 - - + +
378A ASN* 2.9 29.0 + - - +
379A LEU* 4.1 3.4 - - - +
381A LEU* 1.4 72.4 - - - +
383A GLN* 1.3 59.7 + - - +
385A GLY* 3.1 13.5 + - - -
386A TYR 3.3 19.5 - - - +
388A PRO* 3.6 44.6 - - + -
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Residues in contact with GLN 383 (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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278A LEU 4.0 4.9 - - - +
279A VAL* 3.3 30.0 - - - +
281A ARG 3.9 12.5 - - - +
283A GLY 5.6 1.7 - - - +
285A VAL* 4.5 17.4 - - - +
379A LEU* 3.0 44.1 + - + +
380A ILE* 3.7 15.1 - - - +
381A LEU 3.3 0.4 - - - -
382A MET* 1.3 75.7 - - - +
384A ALA* 1.4 57.0 + - - +
385A GLY 3.3 0.9 + - - -
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Residues in contact with ALA 384 (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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348A PRO* 3.8 32.7 - - + +
380A ILE* 3.4 7.7 + - + +
381A LEU 2.9 10.8 + - - +
383A GLN* 1.4 76.0 - - - +
385A GLY* 1.3 61.3 + - - +
386A TYR* 3.6 9.2 - - + -
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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
------------------------------------------------------------
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