Contacts of the helix formed by residues 384 - 394 (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 VAL 384 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383L HIS* 1.3 72.5 - - - +
385L TRP* 1.3 68.0 + - + +
387L MET* 3.1 26.7 + - - +
419L ALA* 4.1 10.8 - - + +
420L ASN* 3.3 25.2 - - - +
423L ALA* 4.3 4.9 - - + -
445L ILE* 4.0 11.5 - - + +
455L LEU* 3.8 24.9 - - + -
458L ALA* 4.1 25.1 - - + +
459L CYS* 4.1 28.0 - - - +
462L TRP* 4.5 8.9 - - + -
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Residues in contact with TRP 385 (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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383L HIS* 3.1 17.6 + - + -
384L VAL* 1.3 85.5 - - + +
386L HIS* 1.3 61.1 + - - +
387L MET 3.3 0.2 - - - -
388L PRO* 3.6 11.9 - - - +
389L ALA* 5.7 0.5 - - - +
442L ASN* 3.8 46.5 - - + +
445L ILE* 3.9 26.6 - - + +
446L ARG* 4.0 16.2 - - + -
449L THR* 5.8 0.9 - - + -
459L CYS* 3.0 43.7 + - + +
462L TRP 3.9 7.4 - - - -
463L LYS* 3.2 65.5 - - + +
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Residues in contact with HIS 386 (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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332L VAL* 3.7 39.6 + - + +
381L GLY 3.6 10.7 + - - -
382L ILE* 3.3 13.2 - - + -
383L HIS* 2.8 58.8 + + - +
385L TRP* 1.3 79.0 - - - +
387L MET* 1.3 64.0 + - - +
388L PRO* 3.4 1.1 - - - -
389L ALA* 3.1 10.3 + - - +
390L LEU* 3.0 36.3 + - + +
465L ILE 4.2 8.7 + - - -
466L LYS* 4.9 8.7 - - + -
467L PHE* 4.7 2.4 - - - -
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Residues in contact with MET 387 (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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170L LEU* 4.7 1.3 - - + -
383L HIS 3.7 2.6 + - - -
384L VAL* 3.1 19.2 + - - +
386L HIS* 1.3 77.0 - - - +
388L PRO* 1.3 66.7 - - + +
390L LEU* 3.3 4.6 + - - +
391L THR* 2.8 33.5 + - - +
400L LEU* 4.0 21.1 - - - -
402L PHE* 3.4 38.1 - - + -
420L ASN* 3.5 35.7 - - - +
423L ALA* 3.9 13.9 - - + +
424L LEU* 3.7 31.4 - - + +
427L CYS* 4.0 6.1 - - - -
445L ILE* 4.5 0.4 - - + -
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Residues in contact with PRO 388 (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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384L VAL 4.1 3.4 - - - +
385L TRP 3.6 13.2 - - - +
386L HIS 3.5 3.8 - - - -
387L MET* 1.3 94.4 - - + +
389L ALA* 1.3 56.5 + - - +
391L THR* 3.4 3.5 + - - -
392L GLU* 3.0 30.4 + - - +
427L CYS* 3.7 22.9 - - + -
437L LEU* 3.8 20.2 - - + +
441L GLY* 3.6 42.8 - - - +
442L ASN* 5.7 0.4 - - - +
444L ILE* 5.5 0.4 - - + -
445L ILE* 3.9 6.7 - - + -
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Residues in contact with ALA 389 (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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332L VAL* 4.5 21.5 - - + -
339L ARG* 6.1 1.1 - - - +
385L TRP 5.7 0.4 - - - +
386L HIS* 3.1 13.3 + - - +
388L PRO* 1.3 80.3 - - - +
390L LEU* 1.3 57.3 + - - +
392L GLU* 3.3 8.1 + - - +
393L ILE* 2.8 41.0 + - + +
437L LEU 6.3 0.2 - - - -
438L ALA* 6.5 0.7 - - - +
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Residues in contact with LEU 390 (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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330L THR* 3.8 22.4 - - - +
332L VAL* 4.2 9.4 - - + -
378L ALA* 4.3 11.9 - - + -
382L ILE* 3.8 29.4 - - + -
386L HIS* 3.0 37.6 + - + +
387L MET* 3.8 6.1 - - - +
389L ALA* 1.3 72.5 - - - +
391L THR* 1.3 61.3 + - - +
393L ILE* 4.7 1.6 - - + -
394L PHE* 2.9 52.6 + - + +
400L LEU* 4.2 20.1 - - + +
402L PHE* 4.1 15.3 - - + -
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Residues in contact with THR 391 (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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168L PRO* 4.8 13.5 - - + -
387L MET* 2.8 19.7 + - - +
388L PRO 3.7 3.6 - - - -
390L LEU* 1.3 74.8 - - - +
392L GLU* 1.3 58.4 + - - +
395L GLY* 2.8 31.7 + - - +
400L LEU* 4.7 2.4 - - - +
424L LEU* 3.8 19.6 - - - +
427L CYS* 4.0 14.9 - - + +
428L VAL* 4.7 12.1 - - + -
431L ARG* 4.0 22.4 + - - +
437L LEU* 3.7 20.0 - - + -
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Residues in contact with GLU 392 (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* 2.8 40.6 + - - -
388L PRO 3.0 18.0 + - - +
389L ALA* 3.6 7.2 - - - +
391L THR* 1.3 79.2 - - - +
393L ILE* 1.3 63.2 + - - +
395L GLY* 4.4 1.9 + - - -
436L ASP* 5.8 0.4 - - - +
437L LEU* 4.0 23.1 - - + +
438L ALA* 4.6 21.4 - - + +
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Residues in contact with ILE 393 (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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330L THR 4.5 5.4 - - - +
331L VAL* 4.1 34.8 - - + -
332L VAL* 4.7 9.6 - - + -
339L ARG* 3.5 37.9 - - + +
342L THR* 5.4 2.0 - - + -
343L LEU* 3.5 35.0 - - + +
346L VAL* 6.0 0.5 - - - +
350L ARG* 5.3 2.4 + - - -
389L ALA* 2.8 27.9 + - + +
390L LEU* 4.0 4.5 - - + +
392L GLU* 1.3 79.5 - - - +
394L PHE* 1.3 85.7 + - + +
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Residues in contact with PHE 394 (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* 3.8 17.0 - - - -
329L GLY 3.4 22.7 - - - -
330L THR* 4.2 9.0 - - - -
342L THR* 4.3 11.9 - - + -
343L LEU* 6.1 0.4 - - + -
346L VAL* 4.0 25.6 - - + -
350L ARG* 2.8 34.8 + - - +
376L PRO* 4.5 12.3 - - + -
378L ALA* 3.8 22.0 - - + -
390L LEU* 2.9 38.9 + - + +
393L ILE* 1.3 94.3 - - + +
395L GLY* 1.3 62.1 + - - +
398L SER* 3.6 24.5 - - - +
400L LEU* 4.5 3.1 - - + -
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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