Contacts of the helix formed by residues 339 - 350 (chain L) in PDB entry 1RBO
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 ARG 339 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331L VAL* 3.9 25.2 - - + +
337L GLY 3.8 2.2 + - - -
338L GLU* 1.3 72.6 - - - +
340L ASP* 1.3 64.5 + - - +
342L THR* 3.6 1.6 - - - -
343L LEU* 2.9 56.9 + - + +
389L ALA* 6.1 1.2 - - - +
392L GLU* 2.8 44.1 + - - -
393L ILE* 3.5 33.0 - - + +
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Residues in contact with ASP 340 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338L GLU* 3.5 1.8 - - + +
339L ARG* 1.3 83.1 - - - +
341L ILE* 1.3 66.0 + - + +
343L LEU* 3.5 14.1 + - - +
344L GLY 3.0 16.8 + - - -
359L SER 4.3 18.3 - - - +
360L ARG* 3.6 25.1 - - + +
475L VAL* 5.7 1.1 - - + -
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Residues in contact with ILE 341 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310L HIS* 3.5 33.7 - - + +
312L ARG* 4.2 10.6 + - - +
338L GLU* 3.5 16.4 + - + +
339L ARG 3.4 0.6 - - - -
340L ASP* 1.3 76.0 - - + +
342L THR* 1.3 64.4 + - - +
344L GLY* 3.0 10.7 + - - -
345L PHE* 3.1 21.9 + - + -
360L ARG 4.0 8.7 - - - +
473L ASP* 3.6 35.7 - - - +
474L THR* 3.8 3.6 - - - -
475L VAL* 3.4 42.8 - - + +
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Residues in contact with THR 342 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328L SER 4.0 19.3 + - - +
329L GLY* 5.2 1.6 - - - +
331L VAL* 4.0 19.3 - - + +
337L GLY* 3.9 13.9 - - - -
338L GLU 2.7 23.8 + - - -
339L ARG 3.6 4.3 - - - -
341L ILE* 1.3 74.3 - - - +
343L LEU* 1.3 66.6 + - - +
344L GLY 3.1 0.3 + - - -
345L PHE* 3.2 19.0 + - + -
346L VAL* 2.9 39.4 + - + +
393L ILE* 5.4 3.1 - - + -
394L PHE* 4.3 12.6 - - + -
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Residues in contact with LEU 343 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339L ARG* 2.9 48.2 + - + +
340L ASP* 3.9 15.0 - - - +
342L THR* 1.3 75.9 - - + +
344L GLY* 1.3 62.9 + - - +
346L VAL* 3.4 10.6 + - + +
347L ASP* 3.1 21.2 + - - +
360L ARG* 3.4 23.1 + - - +
393L ILE* 3.5 40.4 - - + +
394L PHE* 6.1 0.4 - - + -
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Residues in contact with GLY 344 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312L ARG* 6.3 0.4 - - - -
340L ASP 3.0 15.0 + - - -
341L ILE 3.4 4.7 - - - -
342L THR 3.0 1.0 - - - -
343L LEU* 1.3 79.8 - - - +
345L PHE* 1.3 59.7 + - - +
347L ASP* 3.3 5.2 + - - +
348L LEU* 3.3 22.7 + - - +
360L ARG* 3.8 17.9 - - - +
362L ILE* 3.8 21.8 - - - +
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Residues in contact with PHE 345 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295L ARG* 4.7 2.7 - - - -
310L HIS* 4.3 12.8 - + - -
311L PHE* 3.6 38.8 - + + -
312L ARG* 3.9 27.0 - - + +
315L ALA* 4.8 3.8 - - + -
328L SER* 3.4 35.2 - - - -
341L ILE* 3.1 34.0 + - + -
342L THR* 3.2 28.7 + - + -
344L GLY* 1.3 72.7 - - - +
346L VAL* 1.3 69.9 + - + +
348L LEU* 3.2 11.5 + - + +
349L LEU* 3.0 32.0 + - + +
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Residues in contact with VAL 346 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328L SER* 4.5 4.3 - - - -
342L THR* 2.9 26.7 + - + +
343L LEU* 3.8 12.8 - - + +
345L PHE* 1.3 82.3 - - + +
347L ASP* 1.3 64.2 + - - +
349L LEU* 3.1 9.0 + - - +
350L ARG* 3.0 59.8 + - - +
376L PRO* 4.2 18.2 - - + -
393L ILE 6.0 0.4 - - - +
394L PHE* 4.0 29.2 - - + -
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Residues in contact with ASP 347 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343L LEU* 3.1 14.7 + - - +
344L GLY 3.5 9.0 - - - +
346L VAL* 1.3 80.1 - - - +
348L LEU* 1.3 56.9 + - - +
350L ARG* 4.6 12.4 + - - -
351L ASP* 3.0 54.9 + - - +
354L THR* 3.5 13.6 + - + +
360L ARG* 2.8 32.8 + - - +
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Residues in contact with LEU 348 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137L ASP* 5.1 0.7 - - - +
312L ARG* 4.1 27.1 - - + +
315L ALA* 6.0 2.2 - - + -
316L LYS* 3.9 37.9 - - + +
319L ARG* 2.8 19.9 + - - -
344L GLY 3.3 14.7 + - - +
345L PHE* 3.2 17.4 + - + +
347L ASP* 1.3 78.4 - - - +
349L LEU* 1.3 59.0 + - + +
354L THR* 3.8 29.4 - - + -
362L ILE* 4.5 17.3 - - + -
366L GLN* 4.2 14.6 - - + -
368L TRP* 3.4 16.7 + - - +
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Residues in contact with LEU 349 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311L PHE* 5.1 1.3 - - + -
315L ALA* 3.6 42.6 - - + +
318L LEU* 5.3 0.4 - - + -
319L ARG* 3.3 20.4 + - + +
326L ILE* 3.6 33.9 - - + -
328L SER* 4.8 9.9 - - - -
345L PHE* 3.0 27.6 + - + +
346L VAL* 3.1 11.6 + - - +
348L LEU* 1.3 82.5 - - - +
350L ARG* 1.3 59.9 + - + +
374L VAL* 2.9 46.3 + - + +
376L PRO* 4.9 6.3 - - + -
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Residues in contact with ARG 350 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155L ILE* 3.9 12.0 - - + +
319L ARG* 4.0 1.8 + - - -
346L VAL* 3.0 33.8 + - - +
347L ASP* 4.6 9.5 + - - -
349L LEU* 1.3 79.7 - - + +
351L ASP* 1.3 72.0 + - - +
373L GLY* 3.7 17.8 + - - -
374L VAL 3.4 17.7 - - - +
376L PRO* 3.6 17.4 - - + +
393L ILE 5.3 1.8 + - - -
394L PHE* 2.8 29.9 + - - +
397L ASP* 2.8 53.5 + - - +
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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