Contacts of the helix formed by residues 337 - 350 (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 LYS 337 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335N PHE 4.2 1.3 - - - -
336N SER* 1.3 75.4 - - - +
338N SER* 1.3 61.7 + - - +
339N GLU* 3.1 5.7 + - + -
340N LEU* 3.3 19.5 + - + +
341N ALA* 3.3 10.6 + - - +
380N ALA 3.7 22.9 - - - +
381N LEU* 3.0 10.9 + - - +
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Residues in contact with SER 338 (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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335N PHE 4.2 7.6 - - - -
336N SER 2.9 10.5 + - - -
337N LYS* 1.3 72.2 - - - +
339N GLU* 1.3 66.6 + - - +
341N ALA* 3.6 10.0 - - - +
342N SER* 3.3 27.4 + - - -
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Residues in contact with GLU 339 (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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337N LYS* 3.1 2.4 + - + -
338N SER* 1.3 80.5 - - - +
340N LEU* 1.3 65.9 + - - +
341N ALA 3.4 0.3 + - - -
342N SER* 3.6 3.8 + - - -
343N ALA* 3.5 17.5 + - - +
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Residues in contact with LEU 340 (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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337N LYS* 3.3 14.1 + - + +
339N GLU* 1.3 80.1 - - - +
341N ALA* 1.3 57.7 + - - +
343N ALA* 3.1 9.0 + - + +
344N VAL* 2.9 35.3 + - + +
372N GLU 5.4 1.1 - - - +
380N ALA* 4.0 26.9 - - + +
381N LEU* 3.3 29.8 - - + -
392N ILE* 5.2 1.3 - - + -
394N LEU* 4.0 14.6 - - + -
401N TYR* 3.6 46.7 - - + +
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Residues in contact with ALA 341 (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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333N LEU* 3.8 24.5 - - - +
334N THR* 5.4 0.2 - - - -
335N PHE* 4.4 18.6 - - + +
337N LYS 3.3 10.9 + - - +
338N SER* 3.6 14.1 - - - +
339N GLU 3.2 0.6 - - - -
340N LEU* 1.3 75.1 - - - +
342N SER* 1.3 59.1 + - - +
343N ALA 3.0 4.5 - - - -
344N VAL* 2.9 23.9 + - - +
345N LEU* 3.0 15.2 + - - +
381N LEU* 4.3 4.6 - - - +
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Residues in contact with SER 342 (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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338N SER* 3.3 15.5 + - - -
339N GLU* 3.6 4.2 + - - -
340N LEU 3.5 0.2 - - - -
341N ALA* 1.3 76.8 - - - +
343N ALA* 1.3 60.0 - - - +
345N LEU* 4.1 10.3 - - - +
346N GLU* 3.5 21.7 + - - +
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Residues in contact with ALA 343 (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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339N GLU 3.5 11.2 + - - +
340N LEU* 3.1 17.5 - - + +
341N ALA 3.0 0.2 - - - -
342N SER* 1.3 80.5 - - - +
344N VAL* 1.3 55.4 + - - +
346N GLU* 3.3 15.0 - - - +
347N ALA* 3.0 24.6 + - - +
394N LEU* 3.7 20.1 - - + +
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Residues in contact with VAL 344 (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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333N LEU* 4.8 9.2 - - + -
335N PHE* 5.7 1.8 - - + -
340N LEU* 2.9 29.7 + - + +
341N ALA* 2.9 9.4 + - - +
343N ALA* 1.3 71.1 - - - +
345N LEU* 1.3 55.7 + - - +
346N GLU 3.0 1.8 - - - -
347N ALA* 2.9 2.6 + - - +
348N VAL* 2.8 47.8 + - + +
353N LEU* 4.2 10.8 - - + -
381N LEU* 4.5 8.1 - - + -
392N ILE* 3.8 23.6 - - + -
394N LEU* 4.0 14.6 - - + -
411N ILE* 4.2 19.3 - - + -
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Residues in contact with LEU 345 (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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325N TYR* 4.3 8.5 - - + -
329N ILE* 4.0 17.5 - - + -
330N PHE* 4.4 20.0 - - + -
333N LEU* 3.7 33.4 - - + +
341N ALA 3.0 13.8 + - - +
342N SER* 4.1 10.5 - - - +
344N VAL* 1.3 75.2 - - - +
346N GLU* 1.3 65.7 + - + +
348N VAL* 3.4 2.8 + - + +
349N GLU* 3.1 58.3 + - + +
418N PHE* 5.5 2.5 - - + -
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Residues in contact with GLU 346 (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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342N SER 3.5 13.7 + - - +
343N ALA* 3.3 15.7 + - - +
345N LEU* 1.3 81.7 - - + +
347N ALA* 1.3 61.3 + - - +
349N GLU* 3.5 14.7 + - - +
350N ASN* 3.1 38.9 + - - +
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Residues in contact with ALA 347 (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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343N ALA 3.0 8.8 + - - +
344N VAL 2.9 8.6 + - - +
346N GLU* 1.3 78.7 - - - +
348N VAL* 1.3 60.0 + - - +
350N ASN 3.2 1.6 + - - -
351N ASN 3.1 2.6 + - - -
352N THR* 3.0 50.3 + - + +
353N LEU* 3.3 12.1 + - + +
394N LEU* 3.6 33.0 - - + -
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Residues in contact with VAL 348 (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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333N LEU* 4.6 7.4 - - + -
344N VAL* 2.8 32.7 + - + +
345N LEU* 3.7 7.6 - - + +
347N ALA* 1.3 70.9 - - - +
349N GLU* 1.3 64.7 + - + +
351N ASN* 3.3 12.9 + - - +
353N LEU* 3.8 29.8 - - + -
411N ILE* 4.5 4.3 - - + +
414N VAL* 4.2 9.4 - - + -
415N CYS* 3.9 20.6 - - - -
418N PHE* 3.7 38.7 - - + +
422N ARG* 5.5 1.6 + - - -
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Residues in contact with GLU 349 (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* 5.4 4.0 - - - +
316N ARG* 5.1 5.5 - - - +
325N TYR* 2.9 33.8 + - - +
345N LEU* 3.1 40.4 + - + +
346N GLU* 3.8 12.3 - - - +
347N ALA 3.3 0.2 - - - -
348N VAL* 1.3 77.1 - - - +
350N ASN* 1.3 66.8 + - - +
351N ASN 3.7 0.2 + - - -
418N PHE* 4.4 19.8 - - + -
422N ARG* 5.1 9.9 + - - -
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Residues in contact with ASN 350 (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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346N GLU* 3.1 28.9 + - - +
347N ALA 3.2 7.4 + - - +
348N VAL 3.1 0.4 - - - -
349N GLU* 1.3 84.8 - - - +
351N ASN* 1.3 69.3 + - - +
352N THR* 2.9 20.3 + - - +
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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