Contacts of the helix formed by residues 372 - 382 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331A ASP* 3.8 25.3 + - - +
335A GLN* 5.2 1.0 + - - -
371A GLY* 1.3 76.8 - - - +
373A THR* 1.3 58.4 + - - +
374A GLU* 3.1 29.3 + - - +
375A GLN* 2.9 50.1 + - - +
376A ILE* 3.0 26.1 + - - +
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Residues in contact with THR 373 (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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372A ASN* 1.3 75.3 - - - +
374A GLU* 1.3 68.2 + - + +
376A ILE* 3.4 9.5 + - - +
377A GLN* 3.1 21.5 + - - +
413A GLY* 4.7 6.8 - - - +
416A GLN* 3.3 28.6 + - + +
417A ARG* 3.9 43.0 + - + +
420A ILE* 4.5 7.7 - - + +
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Residues in contact with GLU 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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335A GLN* 5.6 4.0 - - - +
372A ASN* 3.1 26.2 + - - +
373A THR* 1.3 80.5 + - + +
375A GLN* 1.3 60.2 + - + +
377A GLN* 3.1 9.1 + - - +
378A ALA* 2.8 25.7 + - - +
417A ARG* 5.2 7.4 - - - +
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Residues in contact with GLN 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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331A ASP* 3.1 29.0 + - - +
334A THR* 4.0 9.7 - - - +
335A GLN* 3.0 36.7 + - - +
338A ILE* 3.6 14.8 - - + -
368A ILE* 3.9 13.9 - - + +
371A GLY* 3.3 9.0 - - - -
372A ASN* 2.9 43.8 + - - +
374A GLU* 1.3 73.6 - - + +
376A ILE* 1.3 68.9 + - - +
377A GLN 3.1 1.1 - - - -
378A ALA* 3.2 9.5 + - - +
379A VAL* 3.1 25.8 + - - +
36C MET* 3.5 4.9 - - - +
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Residues in contact with ILE 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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369A THR* 3.5 36.6 - - + +
371A GLY 4.1 5.4 - - - +
372A ASN 3.0 19.1 + - - +
373A THR* 3.4 7.8 + - - +
374A GLU 3.3 0.4 - - - -
375A GLN* 1.3 77.3 - - - +
377A GLN* 1.3 61.9 + - - +
379A VAL* 3.4 7.3 + - + +
380A ILE* 3.2 23.7 + - + +
409A ASN 4.1 2.7 - - - +
410A ALA* 3.8 37.5 - - + +
412A SER* 5.0 1.3 - - - -
413A GLY* 4.1 21.5 - - - +
420A ILE* 4.0 22.7 - - + -
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Residues in contact with GLN 377 (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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373A THR 3.1 8.2 + - - +
374A GLU* 3.1 10.7 + - - +
375A GLN 3.1 0.4 - - - -
376A ILE* 1.3 75.3 - - - +
378A ALA* 1.3 54.5 + - - +
380A ILE* 3.2 20.5 + - - +
381A ASP* 2.8 70.3 + - - +
417A ARG* 2.7 46.1 + - - +
419A ASP* 5.5 2.3 - - - +
420A ILE* 4.2 8.8 - - + +
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Residues in contact with ALA 378 (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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338A ILE* 4.5 13.2 - - + -
343A LEU* 3.5 27.3 - - + +
374A GLU 2.8 13.5 + - - +
375A GLN* 3.2 12.5 + - - +
377A GLN* 1.3 76.6 - - - +
379A VAL* 1.3 56.0 + - - +
381A ASP* 3.4 9.2 + - - +
382A ALA* 3.0 24.4 + - - +
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Residues in contact with VAL 379 (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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343A LEU* 3.9 17.9 - - + -
365A ILE* 4.3 13.2 - - + -
368A ILE* 3.9 20.0 - - + -
369A THR* 3.8 31.0 - - + -
375A GLN 3.1 15.0 + - - +
376A ILE* 3.5 9.6 - - + +
378A ALA* 1.3 73.8 - - - +
380A ILE* 1.3 67.4 + - + +
382A ALA* 3.3 9.4 + - - +
384A LEU* 3.4 32.7 + - + +
385A ILE* 4.2 17.0 - - + -
388A LEU* 5.1 0.2 - - + -
410A ALA* 6.1 0.2 - - + -
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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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376A ILE* 3.2 15.4 + - + +
377A GLN* 3.2 25.0 + - - +
379A VAL* 1.3 78.1 - - + +
381A ASP* 1.3 58.9 + - - +
383A ASN* 3.0 23.7 + - - +
385A ILE* 4.0 26.0 - - + -
410A ALA* 6.0 0.7 - - + -
420A ILE* 3.7 45.5 - - + -
423A TYR* 3.9 38.9 + - + -
424A LEU* 5.2 2.7 - - + -
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Residues in contact with ASP 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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377A GLN* 2.8 57.8 + - - +
378A ALA* 3.7 8.4 - - - +
380A ILE* 1.3 72.4 - - - +
382A ALA* 1.3 56.1 + - - +
383A ASN* 3.1 14.7 + - - +
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Residues in contact with ALA 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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343A LEU* 3.7 32.3 - - + -
344A PRO* 4.8 6.2 - - + +
347A ARG* 4.0 11.8 - - - +
378A ALA 3.0 17.0 + - - +
379A VAL 3.8 5.6 - - - +
380A ILE 3.2 1.0 - - - -
381A ASP* 1.3 74.4 - - - +
383A ASN* 1.3 73.4 + - - +
384A LEU* 3.2 11.7 + - + +
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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