Contacts of the helix formed by residues 318 - 328 (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 CYS 318 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308N TRP* 4.0 12.1 - - + -
313N THR* 3.9 26.2 - - + -
315N ASP* 3.3 24.5 + - - +
317N THR* 1.3 84.4 + - - +
319N PRO* 1.3 77.3 - - + +
320N PHE 4.1 1.6 - - - -
321N LEU* 3.6 27.4 - - - -
322N ASP* 2.9 22.7 + - - +
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Residues in contact with PRO 319 (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* 3.5 25.8 - - + +
317N THR 4.6 0.2 - - - +
318N CYS* 1.3 90.9 - - + +
320N PHE* 1.3 62.3 + - + +
322N ASP* 3.5 3.9 + - + +
323N LYS* 3.2 22.2 + - - +
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Residues in contact with PHE 320 (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 5.7 0.7 - - - -
304N GLU* 3.8 22.1 + - + +
305N PHE* 3.7 44.9 - + + -
308N TRP* 3.5 46.2 - + + -
318N CYS* 3.3 2.0 - - - -
319N PRO* 1.3 82.9 - - + +
321N LEU* 1.3 90.6 + - + +
323N LYS* 3.7 2.9 + - - +
324N ILE* 3.5 41.9 + - + +
417N PHE* 4.6 0.2 - + - -
421N ILE* 3.8 22.4 - - + -
441N VAL* 4.1 9.4 - - + -
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Residues in contact with LEU 321 (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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308N TRP* 4.8 0.4 - - - +
313N THR 3.8 9.2 - - - +
314N MET* 3.5 28.3 - - + +
315N ASP 3.2 26.9 - - - +
316N ARG* 4.1 3.8 - - - +
318N CYS* 3.6 12.4 + - - -
320N PHE* 1.3 106.9 - - + +
322N ASP* 1.3 55.8 + - - +
324N ILE* 3.4 1.9 + - - +
325N TYR* 2.7 57.6 + - + -
417N PHE* 4.1 23.3 - - + -
418N PHE* 6.0 3.6 - - + -
421N ILE* 4.7 11.7 - - + -
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Residues in contact with ASP 322 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316N ARG* 2.6 42.6 + - - +
317N THR* 4.6 5.2 - - - +
318N CYS 2.9 20.4 + - - +
319N PRO* 3.8 5.2 - - + +
321N LEU* 1.3 77.5 - - - +
323N LYS* 1.3 65.1 + - - +
325N TYR* 3.1 1.7 + - - +
326N GLN* 2.9 40.9 + - - +
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Residues in contact with LYS 323 (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* 3.6 31.0 - - + -
304N GLU* 3.2 30.7 + - - +
319N PRO 3.2 11.9 + - - +
320N PHE 4.0 4.0 - - - +
321N LEU 3.3 0.2 - - - -
322N ASP* 1.3 81.9 + - - +
324N ILE* 1.3 58.6 + - + +
326N GLN* 3.7 3.6 - - - +
327N GLU* 2.8 66.9 + - + +
445N ARG* 4.6 6.7 - - - +
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Residues in contact with ILE 324 (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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320N PHE* 3.5 37.1 + - + +
321N LEU* 3.4 4.6 + - - +
322N ASP 3.3 0.4 - - - -
323N LYS* 1.3 76.8 - - + +
325N TYR* 1.3 57.3 + - + +
328N ASP* 2.9 37.4 + - - +
329N ILE* 2.9 16.0 + - + -
417N PHE* 3.6 45.3 - - + -
441N VAL* 4.5 1.8 - - + -
445N ARG* 3.7 34.3 - - - +
448N MET* 4.0 14.8 - - + -
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Residues in contact with TYR 325 (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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314N MET 5.5 1.7 + - - -
316N ARG* 3.5 36.5 - - + +
321N LEU* 2.7 49.9 + - + +
322N ASP* 3.4 6.1 - - - +
324N ILE* 1.3 75.4 - - + +
326N GLN* 1.3 59.1 + - - +
329N ILE* 3.4 25.3 + - + -
330N PHE* 2.9 71.4 + + + -
345N LEU* 4.3 9.2 - - + -
349N GLU* 2.9 29.3 + - - +
417N PHE* 6.0 0.4 - + - -
418N PHE* 3.4 28.0 - + - -
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Residues in contact with GLN 326 (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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316N ARG* 3.2 29.3 - - - +
322N ASP* 2.9 32.4 + - - +
323N LYS* 3.8 4.3 - - - +
325N TYR* 1.3 77.7 - - - +
327N GLU* 1.3 65.2 + - + +
330N PHE* 3.7 16.6 - - - +
331N PRO* 3.3 16.1 - - - +
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Residues in contact with GLU 327 (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* 6.0 0.2 - - - +
323N LYS* 2.8 49.2 + - + +
326N GLN* 1.3 77.6 - - + +
328N ASP* 1.3 71.2 + - - +
331N PRO* 3.3 9.3 - - - +
445N ARG* 3.1 19.6 + - - +
452N LYS* 3.2 22.7 + - - +
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Residues in contact with ASP 328 (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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324N ILE* 2.9 15.4 + - - +
326N GLN 3.5 0.2 - - - -
327N GLU* 1.3 88.7 - - - +
329N ILE* 1.3 65.2 + - - +
330N PHE 3.5 1.1 - - - -
331N PRO* 3.3 4.3 - - - +
332N CYS* 3.1 29.0 + - - +
445N ARG* 2.5 53.2 + - - +
448N MET* 3.6 27.1 - - + +
449N SER* 3.5 21.4 + - - -
452N LYS* 4.5 3.8 + - - +
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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