Contacts of the helix formed by residues 384 - 395 (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 LEU 384 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A LEU* 3.7 39.5 - - + +
346A LEU* 4.2 1.8 - - + -
347A ARG* 3.6 41.1 - - + +
350A LEU* 3.8 17.0 - - + -
365A ILE* 4.2 17.3 - - + -
379A VAL* 3.4 28.8 + - + +
382A ALA* 3.2 10.3 - - + +
383A ASN* 1.3 77.9 - - - +
385A ILE* 1.3 68.3 + - - +
386A PRO 3.4 0.2 - - - -
387A PRO* 3.3 5.6 - - - +
388A LEU* 3.2 29.9 + - + +
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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
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369A THR* 5.8 0.4 - - + -
379A VAL* 4.2 19.1 - - + -
380A ILE* 4.0 20.0 - - + -
383A ASN* 3.4 0.4 - - - +
384A LEU* 1.3 77.8 - - - +
386A PRO* 1.3 70.9 - - + +
388A LEU* 3.0 14.2 + - + +
389A VAL* 2.9 37.5 + - + +
406A ALA 5.6 1.1 - - - +
407A ILE* 4.8 9.9 - - + -
410A ALA* 5.1 8.5 - - + -
423A TYR* 3.6 29.2 - - + -
424A LEU* 3.8 28.3 - - + -
427A GLN* 4.1 9.0 - - + -
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Residues in contact with PRO 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ARG* 5.9 0.2 - - - +
383A ASN* 3.6 18.8 - - + +
385A ILE* 1.3 93.7 - - + +
387A PRO* 1.3 67.5 - - + +
389A VAL* 3.4 7.1 + - + +
390A LYS* 3.1 22.8 + - - +
423A TYR* 3.5 14.1 - - - +
427A GLN* 3.3 26.0 - - + +
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Residues in contact with PRO 387 (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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347A ARG* 3.8 35.2 - - - +
350A LEU* 3.8 26.0 - - + +
383A ASN 3.3 16.4 - - - +
384A LEU* 3.3 16.8 - - - +
386A PRO* 1.3 94.9 - - + +
388A LEU* 1.3 55.4 + - - +
390A LYS* 3.2 8.8 + - + +
391A LEU* 2.9 36.6 + - + +
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Residues in contact with LEU 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A LEU* 3.3 36.1 - - + -
362A CYS* 4.0 17.3 - - - -
365A ILE* 3.8 30.3 - - + -
369A THR* 6.1 0.2 - - + -
379A VAL* 5.1 0.2 - - + -
384A LEU* 3.2 25.6 + - + +
385A ILE* 3.0 22.1 + - + +
387A PRO* 1.3 77.5 - - - +
389A VAL* 1.3 57.0 + - - +
391A LEU* 3.4 5.1 + - + +
392A LEU* 3.0 26.2 + - - +
403A ALA* 3.8 10.3 - - + +
406A ALA* 4.2 17.3 - - + -
407A ILE* 4.0 13.0 - - + +
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Residues in contact with VAL 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ILE* 2.9 29.6 + - + +
386A PRO* 3.7 8.5 - - + +
388A LEU* 1.3 72.1 - - - +
390A LYS* 1.3 66.6 + - - +
392A LEU* 3.1 14.9 + - - +
393A GLU* 3.2 22.5 + - - +
407A ILE* 3.9 20.2 - - + -
427A GLN* 3.8 19.1 - - + +
428A GLY 3.7 22.7 - - - +
429A CYS* 3.9 18.8 - - + -
432A PRO* 4.4 3.6 - - + +
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Residues in contact with LYS 390 (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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386A PRO 3.1 13.7 + - - +
387A PRO* 3.4 12.6 - - + +
389A VAL* 1.3 78.0 - - - +
391A LEU* 1.3 62.3 + - + +
393A GLU* 3.1 32.8 - - - +
394A VAL* 3.2 25.1 + - + +
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Residues in contact with LEU 391 (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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350A LEU* 3.9 26.5 - - + +
358A LYS* 4.0 32.3 - - + +
362A CYS* 3.7 27.4 - - - -
387A PRO* 2.9 21.4 + - + +
388A LEU* 3.6 7.4 - - + +
390A LYS* 1.3 72.1 - - + +
392A LEU* 1.3 67.2 + - - +
393A GLU 3.1 1.8 - - - -
394A VAL* 4.6 4.3 - - + -
395A ALA* 3.0 48.3 + - + +
399A THR* 4.3 7.6 - - + -
400A LYS* 3.6 4.6 - - - +
403A ALA* 4.5 8.1 - - + -
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Residues in contact with LEU 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 LEU 3.0 14.0 + - - +
389A VAL* 3.1 13.7 + - - +
391A LEU* 1.3 76.4 - - - +
393A GLU* 1.3 55.8 + - - +
400A LYS* 3.4 48.0 + - + +
403A ALA* 4.3 3.5 - - + +
404A CYS* 3.7 23.1 - - + +
407A ILE* 3.9 17.9 - - + -
429A CYS* 4.4 4.3 - - + +
432A PRO* 3.5 32.6 - - + +
433A LEU* 3.8 29.2 - - + +
436A LEU* 4.2 13.0 - - + +
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Residues in contact with GLU 393 (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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389A VAL* 3.2 17.0 + - - +
390A LYS* 3.1 33.1 - - - +
391A LEU 3.1 0.2 - - - -
392A LEU* 1.3 80.5 - - - +
394A VAL* 1.3 66.3 + - + +
395A ALA 3.8 0.7 - - - -
400A LYS* 3.5 15.7 + - - -
428A GLY 4.6 2.4 - - - +
432A PRO* 3.7 27.5 - - + +
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Residues in contact with VAL 394 (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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390A LYS* 3.2 31.1 + - + +
391A LEU* 4.6 5.4 - - + -
393A GLU* 1.3 91.7 - - + +
395A ALA* 1.3 70.2 + - - +
400A LYS* 4.4 0.9 - - - +
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Residues in contact with ALA 395 (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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355A GLU* 4.1 4.5 - - - +
358A LYS* 6.0 0.2 - - - +
391A LEU* 3.0 35.4 + - + +
393A GLU 3.8 0.4 - - - -
394A VAL* 1.3 85.8 - - - +
396A GLU* 1.3 65.8 + - - +
397A ASP* 3.7 0.7 + - - +
399A THR* 3.7 30.3 - - + -
400A LYS* 3.2 18.5 - - + +
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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