Contacts of the helix formed by residues 372 - 382 (chain B) in PDB entry 1UN0
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 ASN 372 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331B ASP* 3.9 24.5 + - - +
335B GLN* 5.2 1.0 + - - -
371B GLY* 1.3 77.9 - - - +
373B THR* 1.3 60.0 + - - +
374B GLU* 3.1 23.1 + - - +
375B GLN* 2.9 50.0 + - - +
376B ILE* 3.0 27.1 + - - +
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Residues in contact with THR 373 (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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372B ASN* 1.3 72.4 - - - +
374B GLU* 1.3 69.1 + - - +
375B GLN 3.1 1.8 - - - -
376B ILE* 3.3 9.4 + - - +
377B GLN* 2.9 23.0 + - - +
413B GLY* 4.6 6.1 - - - +
416B GLN* 3.4 31.9 + - + +
417B ARG* 3.6 45.8 - - + +
420B ILE* 4.4 7.5 - - + +
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Residues in contact with GLU 374 (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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335B GLN* 5.3 4.5 - - - +
372B ASN* 3.1 23.2 + - - +
373B THR* 1.3 82.5 + - - +
375B GLN* 1.3 61.2 + - + +
377B GLN* 3.5 7.4 + - - +
378B ALA* 3.0 25.5 + - - +
417B ARG* 5.4 7.0 - - - +
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Residues in contact with GLN 375 (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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331B ASP* 3.2 28.8 + - - +
334B THR* 3.9 10.7 - - - +
335B GLN* 3.0 37.5 + - - +
338B ILE* 3.7 12.1 - - + -
368B ILE* 3.8 15.2 - - - +
371B GLY* 3.4 8.8 - - - -
372B ASN* 2.9 43.6 + - - +
374B GLU* 1.3 76.0 - - + +
376B ILE* 1.3 65.0 + - - +
377B GLN 3.1 0.9 - - - -
378B ALA* 3.2 8.0 + - - +
379B VAL* 3.1 26.7 + - - +
36D MET* 3.8 3.5 - - - +
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Residues in contact with ILE 376 (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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368B ILE 4.7 0.2 - - - +
369B THR* 3.6 34.3 - - + +
371B GLY 4.2 6.5 - - - +
372B ASN 3.0 17.7 + - - +
373B THR* 3.3 7.8 + - - +
375B GLN* 1.3 76.1 - - - +
377B GLN* 1.3 63.1 + - - +
379B VAL* 3.4 7.0 + - - +
380B ILE* 3.2 24.9 + - + +
409B ASN 4.3 1.1 - - - +
410B ALA* 3.8 42.2 - - + +
412B SER* 5.2 2.0 - - - -
413B GLY* 4.0 21.1 - - - +
420B ILE* 4.1 21.3 - - + -
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Residues in contact with GLN 377 (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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373B THR 2.9 14.0 + - - +
374B GLU* 3.7 6.5 - - - +
376B ILE* 1.3 79.1 - - - +
378B ALA* 1.3 56.4 + - - +
380B ILE* 3.2 21.4 + - - +
381B ASP* 2.8 57.1 + - - +
417B ARG* 2.7 43.7 + - - +
419B ASP* 5.7 1.6 - - - +
420B ILE* 4.3 9.0 - - + +
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Residues in contact with ALA 378 (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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335B GLN* 6.1 0.7 - - - +
338B ILE* 4.4 14.4 - - + -
343B LEU* 3.4 26.4 - - + +
374B GLU 3.0 17.2 + - - +
375B GLN* 3.2 9.3 + - - +
377B GLN* 1.3 75.1 - - - +
379B VAL* 1.3 65.5 + - - +
381B ASP* 3.5 9.6 + - - +
382B ALA* 3.0 18.4 + - - +
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Residues in contact with VAL 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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343B LEU* 3.9 18.8 - - + -
365B ILE* 4.2 12.6 - - + -
368B ILE* 3.9 20.9 - - + -
369B THR* 3.8 30.1 - - + -
375B GLN 3.1 13.1 + - - +
376B ILE* 3.6 9.4 - - + +
378B ALA* 1.3 76.1 - - - +
380B ILE* 1.3 64.1 + - + +
382B ALA* 3.1 12.1 + - - +
384B LEU* 3.5 31.8 + - + +
385B ILE* 4.3 16.8 - - + -
388B LEU* 5.0 0.2 - - + -
410B ALA* 6.3 0.2 - - + -
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Residues in contact with ILE 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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376B ILE* 3.2 18.4 + - + +
377B GLN* 3.2 24.4 + - - +
379B VAL* 1.3 75.6 - - + +
381B ASP* 1.3 64.2 + - - +
383B ASN* 3.1 19.4 + - - +
384B LEU 4.4 0.4 + - - +
385B ILE* 3.9 26.0 - - + -
410B ALA* 6.1 0.4 - - + -
420B ILE* 3.9 41.3 - - + +
423B TYR* 3.8 42.9 + - + -
424B LEU* 5.2 2.2 - - + -
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Residues in contact with ASP 381 (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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377B GLN* 2.8 53.9 + - - +
378B ALA* 3.8 8.1 - - - +
379B VAL 3.4 0.2 - - - -
380B ILE* 1.3 72.3 - - - +
382B ALA* 1.3 57.7 + - - +
383B ASN* 3.2 12.2 + - - +
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Residues in contact with ALA 382 (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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343B LEU* 3.7 31.6 - - + -
344B PRO* 4.8 6.5 - - + +
347B ARG* 4.1 12.0 - - - +
378B ALA 3.0 16.2 + - - +
379B VAL 3.1 6.4 + - - +
381B ASP* 1.3 74.6 - - - +
383B ASN* 1.3 73.2 + - - +
384B LEU* 3.3 12.4 + - + +
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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
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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