Contacts of the helix formed by residues 384 - 395 (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 LEU 384 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343B LEU* 3.6 39.0 - - + +
346B LEU* 4.2 2.7 - - + -
347B ARG* 3.7 40.4 - - + +
350B LEU* 3.9 17.3 - - + -
365B ILE* 4.3 15.9 - - + -
379B VAL* 3.5 26.6 + - + +
382B ALA* 3.3 14.8 - - + +
383B ASN* 1.3 76.4 - - - +
385B ILE* 1.3 67.8 + - - +
386B PRO 3.4 0.2 - - - -
387B PRO* 3.3 5.5 - - - +
388B LEU* 3.2 29.6 + - + +
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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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369B THR* 5.9 1.1 - - + -
379B VAL* 4.3 18.4 - - + -
380B ILE* 3.9 19.5 - - + -
383B ASN* 4.4 0.6 - - - +
384B LEU* 1.3 76.8 - - - +
386B PRO* 1.3 73.3 - - + +
388B LEU* 2.9 24.8 + - + +
389B VAL* 2.9 30.7 + - + +
406B ALA 5.9 0.4 - - - +
407B ILE* 4.9 9.2 - - + -
410B ALA* 5.3 7.9 - - + -
423B TYR* 3.5 28.0 - - + -
424B LEU* 3.8 30.1 - - + -
427B GLN* 4.0 11.2 - - + -
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Residues in contact with PRO 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B ARG* 5.8 0.4 - - - +
383B ASN* 3.6 15.9 - - + +
384B LEU 3.6 2.7 - - - -
385B ILE* 1.3 97.4 - - + +
387B PRO* 1.3 67.1 - - + +
389B VAL* 3.3 6.7 + - + +
390B LYS* 3.0 22.4 + - - +
423B TYR* 3.7 12.3 - - - +
427B GLN* 3.4 26.0 - - + +
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Residues in contact with PRO 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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347B ARG* 3.8 39.3 - - - +
350B LEU* 3.9 23.8 - - + +
383B ASN 3.4 14.8 - - - +
384B LEU* 3.3 14.6 - - - +
386B PRO* 1.3 95.1 - - + +
388B LEU* 1.3 56.2 + - - -
390B LYS* 3.6 9.7 - - + +
391B LEU* 3.0 34.1 + - + +
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Residues in contact with LEU 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LEU* 3.4 26.0 - - + -
362B CYS* 3.8 27.1 - - + -
365B ILE* 3.8 30.3 - - + -
369B THR* 6.0 0.7 - - + -
379B VAL* 5.0 1.1 - - + -
384B LEU* 3.2 24.2 + - + +
385B ILE* 2.9 21.8 + - + +
387B PRO* 1.3 74.9 - - - +
389B VAL* 1.3 59.6 + - - +
391B LEU* 3.3 5.5 + - + +
392B LEU* 3.0 27.0 + - - +
403B ALA* 3.9 7.0 - - + +
406B ALA* 4.1 17.5 - - + -
407B ILE* 3.9 16.3 - - + +
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Residues in contact with VAL 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B ILE* 2.9 30.3 + - + +
386B PRO* 3.7 7.9 - - + +
388B LEU* 1.3 72.1 - - - +
390B LYS* 1.3 66.6 + - - +
392B LEU* 3.2 14.1 + - + +
393B GLU* 3.2 19.2 + - - +
407B ILE* 3.9 19.5 - - + -
427B GLN* 3.6 17.7 - - + +
428B GLY 3.6 23.8 - - - +
429B CYS* 4.0 15.7 - - + -
432B PRO* 4.2 8.8 - - + +
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Residues in contact with LYS 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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386B PRO 3.0 14.7 + - - +
387B PRO* 3.6 12.8 - - + +
388B LEU 3.3 0.2 - - - -
389B VAL* 1.3 76.7 - - - +
391B LEU* 1.3 58.4 - - + +
393B GLU* 3.0 40.5 + - - +
394B VAL* 3.2 24.6 + - + +
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Residues in contact with LEU 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B LEU* 3.8 25.4 - - + +
358B LYS* 4.1 30.3 - - + +
362B CYS* 3.7 27.6 - - - -
387B PRO* 3.0 22.5 + - + +
388B LEU* 3.7 7.2 - - + +
389B VAL 3.3 0.2 - - - -
390B LYS* 1.3 72.7 - - + +
392B LEU* 1.3 59.9 + - - +
393B GLU 3.0 5.2 - - - -
394B VAL* 4.7 4.3 - - + -
395B ALA* 3.0 50.5 + - + +
399B THR* 4.3 7.2 - - + -
400B LYS* 3.6 4.6 - - - +
403B ALA* 4.5 8.1 - - + -
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Residues in contact with LEU 392 (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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388B LEU 3.0 13.4 + - - +
389B VAL* 3.4 11.2 - - - +
391B LEU* 1.3 76.6 - - - +
393B GLU* 1.3 58.7 + - - +
400B LYS* 3.5 43.1 + - + +
403B ALA* 4.4 4.4 - - + +
404B CYS* 3.7 22.0 - - + +
407B ILE* 3.8 20.6 - - + -
429B CYS* 4.4 3.8 - - + +
432B PRO* 3.6 31.7 - - + +
433B LEU* 3.8 26.9 - - + +
436B LEU* 4.0 14.6 - - + +
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Residues in contact with GLU 393 (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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389B VAL* 3.2 17.4 + - - +
390B LYS* 3.0 32.5 + - - +
392B LEU* 1.3 81.0 - - - +
394B VAL* 1.3 68.4 + - + +
400B LYS* 3.5 16.6 + - - +
428B GLY 4.8 1.4 - - - +
432B PRO* 3.5 27.6 - - + +
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Residues in contact with VAL 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B LYS* 3.2 29.8 + - + +
391B LEU* 4.7 5.6 - - + -
393B GLU* 1.3 94.1 - - + +
395B ALA* 1.3 69.0 + - - +
400B LYS* 4.5 0.9 - - - +
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Residues in contact with ALA 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B GLU* 4.3 4.5 - - - +
358B LYS* 5.8 1.1 - - - +
391B LEU* 3.0 36.1 + - + +
393B GLU 3.9 0.4 - - - -
394B VAL* 1.3 85.1 - - - +
396B GLU* 1.3 66.6 + - - +
397B ASP* 3.7 0.9 + - - +
399B THR* 3.7 29.2 - - + -
400B LYS* 3.3 17.1 - - + +
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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