Contacts of the helix formed by residues 298 - 311 (chain N) in PDB entry 4UJ3
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 ASP 298 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296N GLU 3.3 5.7 + - - +
297N ALA* 1.3 68.4 - - - +
299N LEU* 1.3 65.3 + - - +
300N SER* 3.1 13.2 + - - -
301N LEU* 2.6 56.2 + - + +
302N TYR* 2.9 24.0 + - - +
438N PHE* 4.3 4.5 - - - -
439N TRP* 5.4 0.4 - - - -
442N MET* 5.2 5.5 - - + +
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Residues in contact with LEU 299 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296N GLU* 6.1 0.9 - - - +
297N ALA* 3.3 13.6 + - + +
298N ASP* 1.3 72.5 - - - +
300N SER* 1.3 62.7 + - - +
302N TYR* 3.4 10.0 + - + +
303N ASN* 3.1 37.2 + - - +
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Residues in contact with SER 300 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298N ASP* 3.1 10.7 + - - -
299N LEU* 1.3 80.5 - - - +
301N LEU* 1.3 63.0 + - - +
303N ASN* 3.7 4.3 + - - +
304N GLU* 3.4 19.8 + - - +
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Residues in contact with LEU 301 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298N ASP* 2.6 32.9 + - + +
300N SER* 1.3 75.2 - - - +
302N TYR* 1.3 58.5 + - - +
304N GLU* 3.4 14.4 - - - +
305N PHE* 3.0 28.6 + - - +
320N PHE* 5.7 0.3 - - - -
323N LYS* 3.6 34.1 - - + -
438N PHE* 3.9 10.4 - - + -
442N MET* 3.6 26.9 - - + -
445N ARG* 3.8 19.5 - - - +
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Residues in contact with TYR 302 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297N ALA* 4.3 12.3 - - + -
298N ASP 2.9 19.3 + - - +
299N LEU* 3.6 11.9 - - + +
300N SER 3.2 0.2 - - - -
301N LEU* 1.3 76.1 - - - +
303N ASN* 1.3 72.0 + - - +
305N PHE* 3.2 3.9 + + - +
306N ARG* 2.9 61.3 + - - +
434N VAL* 4.6 8.8 - - + +
435N ASP* 2.5 31.1 + - - -
438N PHE* 3.4 47.1 - + + -
439N TRP* 6.2 0.9 - + - -
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Residues in contact with ASN 303 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299N LEU* 3.1 22.6 + - - +
300N SER* 4.3 3.7 - - - +
302N TYR* 1.3 81.3 - - - +
304N GLU* 1.3 66.5 + - - +
306N ARG* 2.9 32.5 + - - +
307N LEU* 3.0 25.5 + - - +
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Residues in contact with GLU 304 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300N SER 3.4 12.4 + - - +
301N LEU* 3.4 22.7 - - - +
303N ASN* 1.3 80.6 - - - +
305N PHE* 1.3 61.4 + - - +
307N LEU* 3.5 6.2 + - - +
308N TRP* 3.1 20.8 + - - +
319N PRO* 3.5 24.8 - - + +
320N PHE* 3.9 32.5 - - + +
323N LYS* 3.2 33.1 + - - +
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Residues in contact with PHE 305 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301N LEU 3.0 17.0 + - - +
302N TYR* 3.6 4.7 - + - +
303N ASN 3.2 0.4 - - - -
304N GLU* 1.3 72.7 - - - +
306N ARG* 1.3 58.2 + - - +
307N LEU 3.0 1.3 - - - -
308N TRP* 2.8 26.0 + + - +
309N LYS* 2.6 46.6 + - + +
320N PHE* 3.7 33.7 - + + -
424N ILE* 4.5 1.1 - - + -
434N VAL* 3.8 21.5 - - + -
437N MET* 3.9 27.6 - - + -
438N PHE* 3.6 45.5 - + + -
441N VAL* 3.8 21.5 - - + -
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Residues in contact with ARG 306 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302N TYR* 2.9 42.4 + - + +
303N ASN* 2.9 31.0 + - - +
305N PHE* 1.3 80.3 - - - +
307N LEU* 1.3 56.5 + - - +
309N LYS* 3.5 8.7 + - - +
310N ASP* 3.1 41.9 + - - +
434N VAL* 4.0 26.0 - - + -
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Residues in contact with LEU 307 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303N ASN 3.0 16.9 + - - +
304N GLU* 3.7 6.5 - - - +
305N PHE 3.0 0.8 - - - -
306N ARG* 1.3 75.6 - - - +
308N TRP* 1.3 68.2 + - - +
310N ASP* 3.1 20.8 + - + +
311N GLU* 3.3 16.3 + - + +
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Residues in contact with TRP 308 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304N GLU 3.1 13.0 + - - +
305N PHE* 2.8 17.8 + + - +
307N LEU* 1.3 79.5 - - - +
309N LYS* 1.3 66.0 + - - +
311N GLU 3.0 5.7 - - - -
312N PRO* 2.9 33.6 - - + +
313N THR* 2.9 49.5 + - + +
318N CYS* 4.0 14.3 - - + -
320N PHE* 3.5 45.6 - + + -
321N LEU* 4.5 1.0 - - + +
421N ILE* 3.8 44.4 - - + -
424N ILE* 3.4 42.0 - - + -
425N GLN* 4.5 2.9 - - + -
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Residues in contact with LYS 309 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305N PHE* 2.6 33.9 + - + +
306N ARG* 3.5 10.8 - - - +
307N LEU 3.2 0.2 - - - -
308N TRP* 1.3 84.6 - - + +
310N ASP* 1.3 75.6 + - - +
312N PRO* 3.4 15.1 - - - +
424N ILE* 4.7 4.0 - - + -
429N VAL 6.1 0.7 - - - -
432N GLN 5.7 0.2 - - - -
434N VAL* 3.4 37.4 - - + +
437N MET* 3.9 31.0 - - + -
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Residues in contact with ASP 310 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306N ARG* 3.1 29.2 + - - +
307N LEU* 3.1 14.4 + - + +
309N LYS* 1.3 94.2 + - - +
311N GLU* 1.3 69.3 + - + +
312N PRO* 3.5 3.9 - - - +
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Residues in contact with GLU 311 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307N LEU* 3.3 12.8 + - + +
308N TRP* 3.0 11.0 + - - +
310N ASP* 1.3 89.1 - - + +
312N PRO* 1.3 69.0 - - - +
313N THR* 3.6 8.5 + - - +
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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