Contacts of the helix formed by residues 378 - 393 (chain A) in PDB entry 1UDY
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 378 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A SER* 4.2 13.0 + - - +
333A LYS* 4.8 0.2 - - - -
373A GLN 3.2 10.3 - - - -
374A ILE* 3.1 33.2 - - + +
377A GLY* 1.3 74.8 - - - +
379A ALA* 1.3 66.9 + - - +
381A ILE* 3.0 30.6 + - - +
382A GLN* 3.0 11.8 + - - +
399A FAD 2.9 43.0 + - - +
349B GLN* 3.9 7.2 - - - +
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Residues in contact with ALA 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LYS* 5.0 0.8 - - - +
334A ALA* 5.6 2.9 - - - +
337A ALA* 6.4 0.9 - - + -
338A ASP* 4.5 11.4 - - - +
373A GLN* 3.1 23.6 + - + +
378A THR* 1.3 73.4 - - - +
380A GLN* 1.3 76.3 + - - +
382A GLN* 3.4 5.8 + - - +
383A ARG* 3.0 48.8 + - - +
349B GLN* 4.0 4.5 - - - +
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Residues in contact with GLN 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A THR* 3.1 0.4 + - - -
379A ALA* 1.3 89.2 - - - +
381A ILE* 1.3 59.0 + - - +
383A ARG* 3.2 7.1 + - - +
384A ILE* 3.2 24.0 + - - +
399A FAD 2.6 58.3 + - + +
293B GLY 5.8 0.9 - - - -
294B ILE* 4.3 11.0 - - + -
297B LEU* 5.0 9.6 - - + +
349B GLN* 2.9 34.8 + - - +
296D PHE* 3.6 25.2 - - + -
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Residues in contact with ILE 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A SER* 3.7 30.5 - - - +
377A GLY* 4.6 2.5 - - - -
378A THR* 3.0 29.0 + - - +
380A GLN* 1.3 73.2 - - - +
382A GLN* 1.3 60.2 + - - +
384A ILE* 2.9 23.6 + - + +
385A ILE* 2.8 36.3 + - + +
399A FAD 4.2 16.8 - - + +
400A CS8 3.8 42.8 - - + +
284B PHE* 4.3 10.5 - - + -
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Residues in contact with GLN 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ARG* 3.7 15.9 + - - +
330A SER* 3.2 47.0 + - - +
333A LYS* 3.3 19.9 - - - +
334A ALA* 3.5 22.4 - - + +
376A GLU 3.5 9.3 + - - -
377A GLY* 2.9 32.1 + - - -
378A THR 3.0 7.2 + - - +
379A ALA* 3.4 12.6 - - - +
381A ILE* 1.3 76.4 - - - +
383A ARG* 1.3 57.8 + - - +
385A ILE* 3.4 4.7 + - - +
386A ILE* 2.9 36.8 + - - +
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Residues in contact with ARG 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ALA* 3.8 15.7 + - - +
338A ASP* 2.9 27.9 + - - -
379A ALA* 3.0 45.1 + - - +
380A GLN* 3.2 10.5 + - - +
381A ILE 3.1 0.4 - - - -
382A GLN* 1.3 77.9 - - - +
384A ILE* 1.3 60.3 + - - +
386A ILE* 4.4 2.0 - - - -
387A ALA* 2.9 30.7 + - - +
296D PHE* 4.1 32.4 - - + +
299D ALA* 3.4 19.4 - - + +
300D ASP* 3.1 30.6 + - - +
303D MET* 3.8 21.7 - - + +
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Residues in contact with ILE 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A GLN 3.2 12.0 + - - +
381A ILE* 2.9 29.1 + - + +
383A ARG* 1.3 74.9 - - - +
385A ILE* 1.3 67.3 + - + +
387A ALA* 3.3 5.5 + - - +
388A ARG* 3.0 25.4 + - + +
399A FAD 3.8 19.5 - - - +
400A CS8 5.2 12.3 - - + -
284B PHE* 5.4 2.5 - - + -
292D GLN* 3.8 19.1 - - - +
295D SER* 5.6 1.6 - - - +
296D PHE* 3.8 15.5 - - + -
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Residues in contact with ILE 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ARG* 2.9 32.1 - - - +
326A THR* 3.6 26.5 - - + +
330A SER* 3.2 22.7 - - - +
381A ILE* 2.8 23.2 + - + +
382A GLN* 3.7 8.5 - - - +
384A ILE* 1.3 77.7 - - + +
386A ILE* 1.3 62.8 + - - +
388A ARG* 3.0 26.0 + - - +
389A GLU* 3.0 15.9 + - + +
400A CS8 3.6 36.1 - - + +
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Residues in contact with ILE 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A TYR* 4.5 14.4 - - + +
330A SER* 3.6 20.2 - - - +
331A ILE* 3.8 38.4 - - + +
334A ALA* 4.5 1.6 - - + -
382A GLN 2.9 28.5 + - - +
383A ARG* 3.9 4.9 - - - +
385A ILE* 1.3 75.8 - - - +
387A ALA* 1.3 58.0 + - - +
389A GLU* 3.4 5.4 + - - +
390A HIS* 3.0 29.1 + - - +
299D ALA* 3.6 26.9 - - + +
302D ALA* 4.5 10.1 - - + -
303D MET* 3.9 22.7 - - + +
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Residues in contact with ALA 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A ARG 2.9 20.6 + - - +
384A ILE* 3.6 5.6 - - - +
386A ILE* 1.3 77.3 - - - +
388A ARG* 1.3 61.5 + - - +
390A HIS* 4.6 4.5 - - - -
391A ILE* 3.2 35.6 + - + +
295D SER* 3.6 39.5 - - - +
298D LEU* 5.7 1.3 - - + -
299D ALA* 4.0 5.6 - - + +
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Residues in contact with ARG 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ARG* 3.8 8.4 - - - +
326A THR* 3.7 10.1 - - - +
384A ILE* 3.0 16.6 + - + +
385A ILE* 3.3 34.4 + - - +
387A ALA* 1.3 74.7 - - - +
389A GLU* 1.3 87.5 + - - +
391A ILE* 4.1 1.8 - - - +
392A GLY* 3.2 20.4 + - - -
400A CS8 3.1 62.4 + - - +
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Residues in contact with GLU 389 (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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324A ARG* 3.1 34.1 + - - -
326A THR* 4.2 13.4 - - + -
327A TYR* 3.8 43.9 + - + +
385A ILE* 3.0 18.0 + - + +
386A ILE 3.9 0.9 - - - +
388A ARG* 1.3 96.1 + - - +
390A HIS* 1.3 61.7 + - - +
392A GLY* 3.4 7.8 + - - -
393A ARG* 3.6 21.7 + - - +
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Residues in contact with HIS 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A TYR* 4.3 18.9 + - + -
386A ILE 3.0 19.3 + - - +
387A ALA* 4.2 3.8 - - - +
389A GLU* 1.3 77.5 - - - +
391A ILE* 1.3 71.1 + - + +
393A ARG* 3.3 16.1 + - - +
394A TYR* 3.1 55.7 - + - -
268D GLN* 5.6 0.7 - - - -
271D LEU* 3.6 33.0 - - + +
275D THR* 2.9 23.7 + - + -
298D LEU* 4.7 13.0 - - + +
299D ALA* 6.0 0.4 - - - -
302D ALA* 4.0 16.0 - - + +
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Residues in contact with ILE 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A ALA* 3.2 24.6 + - + +
388A ARG* 4.4 2.9 - - - +
390A HIS* 1.3 87.6 - - + +
392A GLY* 1.3 65.0 + - - +
393A ARG 3.1 2.2 - - - -
394A TYR* 3.2 19.0 + - - +
395A LYS* 3.2 25.2 + - - +
275D THR* 4.4 7.6 - - + -
279D LEU* 4.2 13.7 - - + -
289D ALA* 3.5 34.1 - - + +
295D SER* 5.3 3.6 - - - -
298D LEU* 4.0 19.5 - - + -
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Residues in contact with GLY 392 (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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388A ARG 3.2 16.6 + - - -
389A GLU 3.4 3.3 + - - -
390A HIS 3.3 0.6 - - - -
391A ILE* 1.3 78.8 - - - +
393A ARG* 1.3 56.7 + - - +
394A TYR 3.1 4.8 + - - -
395A LYS* 3.3 24.1 + - - -
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Residues in contact with ARG 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A TYR* 2.9 63.7 + - - +
328A TYR* 4.9 7.7 + - - -
389A GLU* 3.6 20.2 + - - +
390A HIS* 3.3 13.6 + - - +
391A ILE 3.1 1.0 - - - -
392A GLY* 1.3 77.3 - - - +
394A TYR* 1.3 68.0 + - + +
395A LYS 3.4 1.8 - - - -
306D GLU* 4.4 4.2 + - - -
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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
------------------------------------------------------------
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