Contacts of the helix formed by residues 378 - 391 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A GLN* 4.3 1.6 - - - +
352A GLY* 5.6 1.1 - - - -
142B SER* 4.1 11.6 + - - +
333B LYS* 4.8 0.4 - - - -
373B GLN 3.5 11.2 - - - +
374B ILE* 3.1 28.2 + - + +
377B GLY* 1.3 81.0 - - - +
379B ALA* 1.3 60.1 + - - +
380B GLN* 4.0 2.5 - - - -
381B ILE* 3.2 25.1 + - - +
382B GLN* 2.9 23.4 + - - +
1399B FAD 3.0 48.3 + - - +
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Residues in contact with ALA 379 (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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349A GLN* 4.2 4.5 + - - +
333B LYS* 5.8 0.7 - - - +
334B ALA* 5.5 4.0 - - - +
337B ALA* 6.0 2.2 - - + -
338B ASP* 4.6 10.8 - - - +
373B GLN* 3.2 23.3 + - + +
378B THR* 1.3 75.1 - - - +
380B GLN* 1.3 73.4 - - - +
382B GLN* 3.4 7.1 + - - +
383B ARG* 3.0 50.5 + - - +
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Residues in contact with GLN 380 (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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293A GLY 5.8 1.6 - - - +
294A ILE* 4.6 13.0 - - + -
297A LEU* 5.2 8.8 - - + +
349A GLN* 3.0 35.2 + - - +
378B THR* 3.2 1.1 + - - -
379B ALA* 1.3 85.2 - - - +
381B ILE* 1.3 61.8 + - - +
383B ARG* 3.1 14.7 + - - +
384B ILE* 3.2 17.5 + - - +
1399B FAD 2.6 59.0 + - + +
296C PHE* 3.6 20.9 - - + -
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Residues in contact with ILE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A PHE* 4.7 6.1 - - + -
142B SER* 3.5 24.2 - - - +
256B ARG* 5.1 0.2 - - - +
377B GLY* 4.1 13.5 - - - -
378B THR* 3.2 28.8 + - - +
380B GLN* 1.3 76.6 - - - +
382B GLN* 1.3 66.6 + - - +
384B ILE* 3.2 11.0 + - + +
385B ILE* 3.1 29.8 + - + +
1399B FAD 4.0 31.4 - - + +
1400B CS8 3.5 48.7 - - + +
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Residues in contact with GLN 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ARG* 3.3 27.7 + - - +
330B SER* 3.0 38.2 + - - +
333B LYS* 3.8 20.5 - - + +
334B ALA* 3.8 22.7 - - + +
376B GLU 3.4 10.3 + - - -
377B GLY* 3.3 22.7 + - - +
378B THR 2.9 23.2 + - - +
379B ALA* 3.6 7.2 - - - +
380B GLN 3.2 0.2 - - - -
381B ILE* 1.3 77.1 - - - +
383B ARG* 1.3 57.9 + - - +
385B ILE* 3.5 4.8 + - - +
386B ILE* 2.9 35.2 + - - +
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Residues in contact with ARG 383 (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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334B ALA* 3.9 19.8 + - - +
338B ASP* 3.1 26.7 + - - -
379B ALA* 3.0 47.0 + - - +
380B GLN* 3.1 11.8 + - - +
381B ILE 3.1 0.4 - - - -
382B GLN* 1.3 74.9 - - - +
384B ILE* 1.3 66.1 + - - +
385B ILE 3.0 1.3 - - - -
386B ILE* 3.0 6.5 + - - -
387B ALA* 2.9 26.2 + - - +
296C PHE* 3.9 31.9 - - + -
299C ALA* 3.7 19.4 - - + +
300C ASP* 3.1 34.2 + - - +
303C MET* 4.2 11.8 - - - +
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Residues in contact with ILE 384 (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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380B GLN 3.4 14.1 - - - +
381B ILE* 3.4 14.4 - - + +
383B ARG* 1.3 76.9 - - - +
385B ILE* 1.3 60.4 + - + +
387B ALA* 3.7 5.8 + - - +
388B ARG* 3.2 31.8 + - + +
1399B FAD 4.5 10.8 - - + +
1400B CS8 5.3 8.5 - - + -
292C GLN* 3.1 33.4 - - + +
295C SER* 5.6 3.6 - - - -
296C PHE* 3.2 16.8 - - + -
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Residues in contact with ILE 385 (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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256B ARG* 3.4 22.0 - - - +
326B THR* 3.8 24.9 - - + +
330B SER* 3.6 19.5 - - - +
381B ILE* 3.1 20.3 + - + +
382B GLN* 3.8 8.1 - - - +
383B ARG 3.0 0.4 - - - -
384B ILE* 1.3 78.1 - - + +
386B ILE* 1.3 59.5 + - - +
387B ALA 3.2 0.2 - - - -
388B ARG* 3.3 21.3 + - - +
389B GLU* 2.9 33.6 + - + +
1400B CS8 3.4 40.6 - - + -
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Residues in contact with ILE 386 (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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327B TYR* 4.4 9.5 - - + +
330B SER* 3.7 33.0 - - - +
331B ILE* 3.7 33.4 - - + -
334B ALA* 4.2 11.2 - - + -
382B GLN 2.9 24.1 + - - +
383B ARG* 3.0 9.5 + - - +
385B ILE* 1.3 77.6 - - - +
387B ALA* 1.3 57.7 + - - +
389B GLU* 4.2 4.2 - - - +
390B HIS* 3.0 28.4 + - - +
299C ALA* 3.8 28.0 - - + +
302C ALA* 4.6 5.2 - - + -
303C MET* 4.5 9.6 - - + -
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Residues in contact with ALA 387 (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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383B ARG 2.9 16.7 + - - +
384B ILE* 3.9 5.8 - - - +
386B ILE* 1.3 76.4 - - - +
388B ARG* 1.3 60.0 + - - +
390B HIS* 4.5 3.8 - - - -
391B ILE* 2.9 47.7 + - + +
295C SER* 3.7 36.3 - - - +
298C LEU* 5.5 0.7 - - + -
299C ALA* 4.0 6.0 - - + +
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Residues in contact with ARG 388 (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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324B ARG* 5.0 0.2 - - - +
326B THR* 4.7 4.6 - - - +
384B ILE* 3.2 21.9 + - + +
385B ILE* 3.3 34.8 + - - +
387B ALA* 1.3 80.3 - - - +
389B GLU* 1.3 76.8 + - - +
391B ILE* 3.9 3.9 - - - +
392B GLY* 3.4 17.2 + - - -
1400B CS8 2.7 72.9 + - - +
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Residues in contact with GLU 389 (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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324B ARG* 2.9 42.6 + - - -
326B THR* 4.5 1.6 - - - -
327B TYR* 3.7 41.3 - - + +
385B ILE* 2.9 27.1 + - + +
388B ARG* 1.3 98.9 + - - +
390B HIS* 1.3 67.4 + - - +
392B GLY* 3.1 9.5 + - - -
393B ARG* 3.1 25.7 + - - +
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Residues in contact with HIS 390 (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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327B TYR* 4.3 12.8 + - + -
386B ILE 3.0 20.6 + - - +
387B ALA* 4.0 2.5 - - - +
389B GLU* 1.3 73.3 - - - +
391B ILE* 1.3 70.0 + - + +
392B GLY 2.6 15.9 + - - -
393B ARG* 2.8 29.4 + - - +
271C LEU* 3.8 29.0 - - + +
272C ASP* 5.3 5.6 - - - -
275C THR* 2.9 33.0 + - + +
298C LEU* 4.6 19.5 - - + -
299C ALA* 5.8 0.4 - - - -
302C ALA* 4.1 15.6 - - + +
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Residues in contact with ILE 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B ALA* 2.9 38.5 + - + +
388B ARG* 3.9 5.2 - - - +
390B HIS* 1.3 84.1 - - + +
392B GLY* 1.3 55.9 + - - +
393B ARG 3.7 1.6 - - - -
275C THR* 4.7 6.1 - - + -
279C LEU* 3.9 34.1 - - + -
289C ALA* 4.0 27.4 - - + +
295C SER* 5.1 2.5 - - - +
298C LEU* 4.1 15.3 - - + -
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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